title: Spleen, DKO, Day 4.5 post-MCMV-infection, mRNA-derived cDNA

description:
none
JVE006_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
The Cell Ranger pipeline (10x Genomics, v6.0.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1 and read 2 for the gene expression and cell surface protein libraries. Read 2 of the gene expression libraries was mapped to the reference genome (mouse mm10) using STAR. Subsequent barcode processing, unique molecular identifiers filtering and gene counting was performed using the Cell Ranger suite. CITE-seq reads were quantified using the feature-barcoding functionality.
Pre-processing of the RNA UMI matrix was done by the scater and scran R packages (v1.14.6) according to the workflow proposed by the Marioni lab. DoubletFinder (v2.0.2) was performed to predict any remaining doublets in the dataset.
Subsequent processing was done with Seurat v3.1.4 (gene filtering, SCTransform, clustering, dimensionality reduction, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: CellRanger output files for individual samples: barcodes_JVE001.tsv.gz, barcodes_JVE002.tsv.gz, barcodes_JVE003.tsv.gz, barcodes_JVE004.tsv.gz, barcodes_JVE005.tsv.gz, barcodes_JVE006.tsv.gz, features_JVE001.tsv.gz, features_JVE002.tsv.gz, features_JVE003.tsv.gz, features_JVE004.tsv.gz, features_JVE005.tsv.gz, features_JVE006.tsv.gz, matrix_JVE001.mtx.gz, matrix_JVE002.mtx.gz, matrix_JVE003.mtx.gz, matrix_JVE004.mtx.gz, matrix_JVE005.mtx.gz, matrix_JVE006.mtx.gz
Supplementary files format and content: ADT feature and HTO overview: feature_reference_JVE_NK_cells.csv
Supplementary files format and content: Seurat object of the NK subset of the three WT samples merged together: seuratObj_NK_cell_subset_WT.rds
Supplementary files format and content: Seurat object of the NK subset of the three WT and three DKO samples merged together: seuratObj_NK_cell_subset_WT_and_DKO.rds

extract_protocol:
Splenic single cell suspensions were enriched for NK cells by use of an NK cell-specific magnisort negative selection kit. The enriched fraction was stained in 50 µl containing FACS antibiodies, Fc block and the mouse cell surface protein antibody panel (TotalSeq-A, BioLegend). Cell hashing was performed by adding 1 µl of diluted hashtag oligos (HTO) to each biological replicate for identification purposes upon sequencing. Initially, biological replicates were sorted separately but pooled in the next step according to the total number of sorted cells.  On day 1,5 post-infection, a total of 190 000 and 65 000 cells were sorted from mock infected and MCMV infected samples, respectively. On day 4,5 post-infection, a total of 78 000 cells were sorted. Half of these numbers represented sorted NK cells (live,CD3-,CD19-,NK1.1+,CD49b+), the other half sorted non-NK cells (live,NK1.1+,CD49b+). Congenic markers (CD45.1 and CD45.2) were used to distinguish sorted WT (CD45.1.2+) and DKO (CD45.2+) cells.
Sorted single-cell suspensions were resuspended at an estimated final concentration of 1000 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library kit, version NextGEM 3.1 (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primer (3 nM, 5’CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos. Size selection with SPRIselect Reagent Kit (Beckman Coulter) was used to separate amplified cDNA molecules for 3’ gene expression and cell surface protein construction. TotalSeq-A protein library construction including sample index PCR using Illumina’s Truseq Small RNA primer sets and SPRIselect size selection was performed according to the manufacturer’s instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in a 70:20:10 ratio for the combined 3’ gene expression, cell surface protein samples and HashTag-Oligo (HTO) data, respectively.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

treatment_protocol: Mixed bone marrow chimeras were intraperitoneally (20 µl/g) infected with MCMV Smith Strain or vehicle alone (DMEM)

tag: treatment/timepoint

value: Day 4.5 post-MCMV-infection


title: MH615 flm 1-2

status: Public on Oct 27 2023

type: SRA

city: Richmond

first: Jonathan

middle: Michael

last: Plett

state: NSW

address: Bourke St. Entrance, Building L9

department: Hawkesbury Institute for the Environment

country: Australia

institute: Western Sydney University

description: Biological Replicate 2

library_source: transcriptomic

data_processing:
Raw reads were trimmed and mapped to either the P. microcarpus (Plett et al., 2023) or E. grandis (Myberg et al., 2014) genomes in CLC Workbench (v22).
Normalisation of raw count data and analysis of differential gene regulation was performed using the DESeq2 package in R (version 1.30.1; Love et al., 2014).
Genes having less than an average of 5 counts per sample for all conditions were considered to be unexpressed and removed prior to the analysis. Genes were considered to be significantly differentially expressed when the padj < 0.05 (calculated from DESeq2 based on a Benjamini-Hochberg method) and the log2(fold change) was above 1 (over-expressed) or below 1 (under-expressed) for fungal genes or above 2.23 (over-expressed) or below 2.23 (under-expressed) for plant genes (equivalent to 2x and 5x differentially expressed, respectively).
Assembly: https://phytozome-next.jgi.doe.gov/info/Egrandis_v2_0; https://mycocosm.jgi.doe.gov/Pismi2/Pismi2.home.html
Supplementary files format and content: Raw read counts of all genes across all samples for E. grandis
Supplementary files format and content: Raw read counts of all genes across all samples for Pisolithus microcarpus

molecule: total RNA

organism: Pisolithus microcarpus

source_name: Free living mycelium (axenic control)

growth_protocol: Plants and fungus were grown on half-strength MMN medium ((pH 5.5; 0.1 g l−1 glucose) at 22–30°C night/day temperature with a 16 h light cycle.

extract_protocol:
Spectrum Plant Total RNA (Sigma-Aldrich
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration

treatment_protocol: Once the E. grandis seedlings were two months old and the fungal cultures had grown for 2 weeks, the plants and fungi were separated into one of two treatment categories: (1) fungal-free controls whereby the seedlings were transferred onto new half-strength MMN medium; (2) ‘physical contact’ seedlings were transferred onto new half-strength MMN medium and then placed into direct contact with the active growing edge of a fungal colony and then samples were harvested at 2 week post-contact. These plates were then closed using micropore tape to allow for gas exchange with the external environment.

tag: tissue

value: Free living mycelium (axenic control)

tag: cell type

value: Fungal hyphae

tag: genotype

tag: treatment

value: Axenic Control


title: Spleen, DKO, Day 4.5 post-MCMV-infection, HTO-derived cDNA

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

description:
See Custom feature_type in feature_reference_JVE_NK_cells.csv (Anti CD45 + Anti MHC classI : 10 Replicates included Hashtag1 → Hashtag10)
JVE006_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen

value: Spleen

tag: library type

value: HTO

value: DKO


title: Spleen, DKO, Day 4.5 post-MCMV-infection, ADT-derived cDNA

description:
See Antibody Capture feature_type in feature_reference_JVE_NK_cells.csv
JVE006_ADT
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

value: ADT


title: Spleen, WT, Day 4.5 post-MCMV-infection, mRNA-derived cDNA

description:
none
JVE005_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA

value: WT


title: Spleen, WT, Day 4.5 post-MCMV-infection, HTO-derived cDNA

description:
See Custom feature_type in feature_reference_JVE_NK_cells.csv (Anti CD45 + Anti MHC classI : 10 Replicates included Hashtag1 → Hashtag10)
JVE005_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)


title: Spleen, DKO, Day 1.5 post-MCMV-infection, HTO-derived cDNA

description:
See Custom feature_type in feature_reference_JVE_NK_cells.csv (Anti CD45 + Anti MHC classI : Replicate 1 = Hashtag3 ; Replicate 2 = Hashtag4 ; Replicate 3 = Hashtag5 ; Replicate 4 = Hashtag6)
JVE004_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: Day 1.5 post-MCMV-infection


title: Spleen, DKO, Day 1.5 post-MCMV-infection, mRNA-derived cDNA

description:
none
JVE004_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA


title: Spleen, WT, Day 4.5 post-MCMV-infection, ADT-derived cDNA

description:
See Antibody Capture feature_type in feature_reference_JVE_NK_cells.csv
JVE005_ADT
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: Spleen, DKO, Day 1.5 post-MCMV-infection, ADT-derived cDNA

description:
See Antibody Capture feature_type in feature_reference_JVE_NK_cells.csv
JVE004_ADT
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: Spleen, WT, Day 1.5 post-MCMV-infection, HTO-derived cDNA

description:
See Custom feature_type in feature_reference_JVE_NK_cells.csv (Anti CD45 + Anti MHC classI : Replicate 1 = Hashtag3 ; Replicate 2 = Hashtag4 ; Replicate 3 = Hashtag5 ; Replicate 4 = Hashtag6)
JVE003_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)


title: Spleen, WT, Day 1.5 post-MCMV-infection, ADT-derived cDNA

description:
See Antibody Capture feature_type in feature_reference_JVE_NK_cells.csv
JVE003_ADT
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: Spleen, WT, Day 1.5 post-MCMV-infection, mRNA-derived cDNA

description:
none
JVE003_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA


title: Spleen, DKO, Day 0 uninfected, HTO-derived cDNA

description:
See Custom feature_type in feature_reference_JVE_NK_cells.csv (Anti CD45 + Anti MHC classI : Replicate 1 = Hashtag1 ; Replicate 2 = Hashtag2)
JVE002_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: Day 0 uninfected


title: Spleen, DKO, Day 0 uninfected, mRNA-derived cDNA

description:
none
JVE002_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA


title: library3_CM1_aPCA_output_bio_rep_2

city: Barcelona

first: cristina

last: Hidalgo-Carcedo

address: Dr. Aiguader 88

country: Spain

institute: CRG

library_source: genomic

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Supplementary files format and content: MS Excel format; contains Dimsum fitness estimates, inferred growth rates and their corresponding errors for all libraries; see README tab for a description of all columns

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: For each library and assay (abundancePCA and bindingPCA) each of the growth competitions was performed right after yeast transformation. After the first cycle of post-transformation plasmid selection, saturated cells were diluted again to OD600nm = 0.1 in SC -URA/MET/ADE media and allowed to grow 4 generations until OD600nm = 1.6 at 30ºC and 200rpm. A fraction of the culture was then used to inoculate 200mL of competition media containing methotrexate at a starting OD600nm = 0.05, and the rest was harvested and pellets frozen and stored as INPUT.  Cells in competition media were allowed to grow for 3-5 generations, collected and frozen and stored as OUTPUT.

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer, frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC at least for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (50 µL of QIAEX II beads, QIAGEN). The samples were washed twice with PE buffer and eluted twice by 125 µL of 10 mM Tris-HCI buffer, pH 8.5. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids.
The sequencing libraries were constructed in two consecutive PCR reactions. The first PCR (PCR1) was designed to amplify the mutated protein of interest and to increase the nucleotide complexity of the first sequenced bases by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) was necessary to add the remainder of the Illumina adapter and demultiplexing indexes. PCR2 reactions were run for each sample independently using Hot Start High-Fidelity DNA Polymerase. In this second PCR the remaining parts of the Illumina adapters were added to the library amplicon. The forward primer (5’ P5 Illumina adapter) was the same for all samples, while the reverse primer (3’ P7 Illumina adapter) differed by the barcode index  to be subsequently pooled together and demultiplex them after deep sequencing. All samples were pooled in an equimolar ratio and gel purified using the QIAEX II Gel Extraction Kit. The purified amplicon library pools were subjected to Illumina 150bp paired-end Nextseq500 sequencing at the CRG Genomics Core Facility.
DNA-seq of PCR amplicons

tag: strain

tag: molecule subtype

value: DNA amplicon


title: library2_CM2_aPCA_input_bio_rep_2


title: library1_CM6_aPCA_wt


title: library3_CM1_bPCA_output_bio_rep_1


title: library3_CM1_aPCA_input_bio_rep_1


title: library3_CM1_bPCA_input_bio_rep_1


title: library3_CM1_bPCA_input_bio_rep_3


title: library3_CM1_aPCA_output_bio_rep_3


title: library3_CM1_bPCA_output_bio_rep_3


title: library2_CM2_aPCA_input_bio_rep_3


title: library3_CM1_aPCA_output_bio_rep_1


title: library3_CM1_aPCA_input_bio_rep_3


title: library2_CM2_aPCA_input_bio_rep_1


title: library2_CM2_aPCA_output_bio_rep_1


title: library3_CM1_bPCA_output_bio_rep_2


title: library1_CM6_aPCA_output_bio_rep_1


title: library2_CM2_aPCA_output_bio_rep_2


title: library1_CM6_aPCA_input_bio_rep_2


title: library1_CM6_aPCA_output_bio_rep_2


title: library1_CM6_aPCA_input_bio_rep_1


title: library1_CM6_aPCA_input_bio_rep_3


title: library3_CM1_bPCA_input_bio_rep_2


title: library2_CM2_aPCA_output_bio_rep_3


title: library3_CM1_aPCA_input_bio_rep_2


title: Spleen, DKO, Day 0 uninfected, ADT-derived cDNA

description:
See Antibody Capture feature_type in feature_reference_JVE_NK_cells.csv
JVE002_ADT
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: library1_CM6_aPCA_output_bio_rep_3


title: Spleen, WT, Day 0 uninfected, HTO-derived cDNA

description:
See Custom feature_type in feature_reference_JVE_NK_cells.csv (Anti CD45 + Anti MHC classI : Replicate 1 = Hashtag1 ; Replicate 2 = Hashtag2)
JVE001_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)


title: EAC000 PDO, Matrigel [WES]

city: New York

first: Spyros

last: Karaiskos

state: NY

department: Herbert Irving Cancer Center

country: USA

institute: Columbia University

description: Whole Exome Sequencing

data_processing:
Gatk4 Broad Institute best practices pipeline.
Read alignment, sorting, marking duplicate reads.
Variant calling.
Assembly: hg38
Supplementary files format and content: VCF files

organism: Homo sapiens

source_name: EAC000 PDO

growth_protocol: EAC PDOs were maintained in organoid medium described in PMCID: PMC7350550, and in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Hydrogels were degraded with proteases, EAC PDOs were collected, and genomic DNA was harvested using QIAamp DNA Micro kit (Qiagen).
Twist Biosciences Whole Exome Kit.

treatment_protocol: EAC PDOs were embedded and cultured in hydrogels of different stiffnesses or Matrigel.

tag: cell line

value: EAC000 PDO

value: esophageal adenocarcinoma organoids

value: 3D culture in Matrigel of 100 Pa in storage modulus

tag: time

value: Day 14


title: Spleen, WT, Day 0 uninfected, mRNA-derived cDNA

description:
none
JVE001_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA


title: EAC000 PDO, 1000 Pa NorHA [WES]

description: Whole Exome Sequencing

value: 3D culture in NorHA hydrogel of 1000 Pa in storage modulus


title: Spleen, WT, Day 0 uninfected, ADT-derived cDNA

description:
See Antibody Capture feature_type in feature_reference_JVE_NK_cells.csv
JVE001_ADT
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: TSC1null_Rapamycin_rep3_Poly

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
BBmap (v. 36.59)(parameters: k = 13, ktrim=n, useshortkmers=t, mink = 5, qtrim=t, trimq = 10, minlength = 25) was used to trim reads for adapter sequences and low-quality base calls. The resulting reads were aligned to the human reference genome (build hg38) using HISAT2 (v.2.0.4). The aligned reads were summarized using the "featureCounts" function of the RSubread (v.2.6.4) R/Bioconductor package and the reads were assigned using the hg38 GTF annotation from the UCSC database {Karolchik, 2004 #1425}(parameters:ignoreDup=FALSE, useMetaFeatures=TRUE, countMultiMappingReads=FALSE).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: iPSC derived NPC

growth_protocol: TSC1 patient-derived neural progenitor cells (NPCs), including TSC1-null (-/-) and CRISPR-corrected TSC1-WT (+/+), along with culture conditions, have been previously described in Martin P, Wagh V, Reis SA, Erdin S, Beauchamp RL, Shaikh G, et al. TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling. Mol Autism. 2020;11:2.

extract_protocol:
Fractions corresponding to mRNA associated with more than two ribosomes were pooled and the RNA extracted using TRIzol (Thermo Fisher, Waltham, MA) according to the manufacturer’s protocol. Prior to loading samples on the sucrose gradient, RNA was extracted from 10% of the lysate using TRIzol, and the resulting RNA was denoted as total RNA.
Illumina v2.5 Kit

treatment_protocol: TSC1 NPC lines were treated for 2h with 50 nM rapamycin or DMSO as a vehicle control followed by cell lysis

tag: gender

value: female

value: iPSC derived NPC

value: Rapamycin

value: polysome associated mRNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-KO, IL-1ß, replicate 4

city: Portland

first: Anupriya

last: Agarwal

state: OR

address: 2730 S Moody Ave

department: OHSU Knight Cancer Institute/ CEDAR

institute: Oregon Health & Science Univ

description: Bisulfite converted DNA

data_processing:
Adapter trimming using Trim Galore (version 0.6.6) with the following command line options: "trim_galore --gzip --clip_r1 6 --clip_r2 6 --paired --fastqc"
Trimmed Reads were aligned to the mouse reference genome (mm10) using Bismark tool (v0.23.0) with the following command line options: "bismark --non_directional --gzip -N 1 --parallel 4 --unmapped --score_min L,-10,-0.2 --output_dir ../Aligned"
Deduplication step: "deduplicate_bismark --bam -s --multiple" (v0.23.0)
Methylation status inference using bismark methylation extractor (v0.23.0) : "bismark_methylation_extractor --gzip --cytosine_report --parallel 4 --bedGraph -s --ignore 5 --genome_folder /$PATH/Genomes/Mouse/GRCm38"
Assembly: GRCm38 (mm10)
Supplementary files format and content: CpG coverage (.cov) tab separated file containing six fields: "1) chromosome, 2) start position, 3) end position (=start position), 4) methylation percentage, 5) counts methylated, 6) counts unmethylated"

source_name: Bone Marrow

extract_protocol:
Bone marrow (BM) cells were isolated from each animal by flushing the bone 1x PBS 2% FBS. Red blood cells were lysed using ammonium chloride solution (Stemcell Tech). BM was FC blocked, then stained for lineage (CD3, CD4, CD8, B220, Gr-1, Ter-119, CD19, IgM, and CD127), Sca1, CD135, APC-conjugated lineage cocktail (described above), CD34, cKit, CD150, Fc Gamma (CD16/CD32), CD48, 7AAD and Annexin V. Live (7AAD-) cells were sorted for the following populations: LSK (Lin-Sca1+cKit+), CMP (Lin- Sca1- ckit+ CD34+ Fc Gamma-), and GMP (Lin- Sca1- ckit+ CD34+ Fc Gamma+).
Approximately 500 cells per cell type/conditon were resuspended in RLT Plus buffer (Qiagen) and directly bisulfite converted using Zymo EZ Methylation Direct kit. Libraries were constructed using post-bisulfite adapter tagging method optimized for low input material (Clark et. al., Nature Protocols, 2017; doi:10.1038/nprot.2016.187). Libraries were sequenced on NovaSeq6000 instrument PE 100 bp.

treatment_protocol: Tet2-KO and WT animals were treated intraperitoneally with either 500 ng/mouse/day of recombinant IL-1ß (Peprotech, Cranbury, NJ) or vehicle for 5 weeks prior to bone marrow extraction

value: Bone Marrow

value: Granulocyte-Macrophage Progenitor

tag: age

value: 6-12 weeks


title: EAC000 PDO, 100 Pa NorHA [WES]

description: Whole Exome Sequencing

value: 3D culture in NorHA hydrogel of 100 Pa in storage modulus


title: WT_Rapamycin_rep3_Poly

value: TSC1-Corrected WT


title: TSC1null_Rapamycin_rep2_Poly


title: WT_Rapamycin_rep2_Poly


title: WT_Rapamycin_rep2_Total

value: total mRNA


title: TSC1null_DMSO_rep1_Total

value: DMSO


title: TSC1null_Rapamycin_rep3_Total


title: TSC1null_DMSO_rep2_Total


title: TSC1null_Rapamycin_rep1_Poly


title: WT_Rapamycin_rep3_Total


title: TSC1null_DMSO_rep3_Poly


title: TSC1null_DMSO_rep3_Total


title: TSC1null_DMSO_rep1_Poly


title: TSC1null_Rapamycin_rep1_Total


title: TSC1null_DMSO_rep2_Poly


title: TSC1null_Rapamycin_rep2_Total


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-KO, vehicle, replicate 3

description: Bisulfite converted DNA

value: vehicle


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-WT, vehicle, replicate 2

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-WT, IL-1ß, replicate 4

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-WT, vehicle, replicate 4

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-KO, IL-1ß, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-WT, vehicle, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-KO, vehicle, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-WT, IL-1ß, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-KO, IL-1ß, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-KO, vehicle, replicate 4

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-WT, vehicle, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-WT, IL-1ß, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-KO, IL-1ß, replicate 2

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-WT, IL-1ß, replicate 2

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1-, ckit+, CD34+, Fc Gamma+), Tet2-KO, vehicle, replicate 2

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-KO, IL-1ß, replicate 4

description: Bisulfite converted DNA

value: Common Myeloid Progenitor


title: WT_Rapamycin_rep1_Total


title: WT_DMSO_rep3_Total


title: WT_DMSO_rep3_Poly


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-KO, IL-1ß, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-KO, IL-1ß, replicate 2

description: Bisulfite converted DNA


title: WT_DMSO_rep2_Total


title: WT_DMSO_rep1_Poly


title: WT_DMSO_rep1_Total


title: WT_Rapamycin_rep1_Poly


title: Control_4898 (C4_4898_Poly)

data_processing:
BBmap (v. 36.59)(parameters: k = 13, ktrim=n, useshortkmers=t, mink = 5, qtrim=t, trimq = 10, minlength = 25) was used to trim reads for adapter sequences and low-quality base calls. The resulting reads were aligned to the human reference genome (build hg38) using HISAT2 (v.2.0.4). The aligned reads were summarized using the "featureCounts" function of the RSubread (v.2.6.4) R/Bioconductor package and the reads were assigned using the hg38 GTF annotation from the UCSC database {Karolchik, 2004 #1425}(parameters:ignoreDup=FALSE, useMetaFeatures=TRUE, countMultiMappingReads=FALSE).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw gene counts for every gene and every sample

source_name: post-mortem brain, Broadmann Area 19

extract_protocol:
Polysome fractionation was performed using an optimized sucrose gradient.
RNA sequencing libraries were generated using the Smart-seq2 protocol.
RNA-seq of polysomal and total RNA samples

value: post-mortem brain, Broadmann Area 19

tag: condition

value: Control

tag: fraction

value: polysomal RNA


title: Control_1674 (C2_1674_Total)

value: total RNA


title: Control_1674 (C2_1674_Poly)


title: Control_4670 (C3_4670_Poly)


title: Control_4898 (C4_4898_Total)


title: Control_4670 (C3_4670_Total)


title: Control_4337 (C1_4337_Total)


title: Control_4337 (C1_4337_Poly)


title: ASD_5308 (A6_5308_Total)

value: ASD


title: WT_DMSO_rep2_Poly

value: female

value: iPSC derived NPC


title: ASD_4849 (A5_4849_Total)


title: ASD_5308 (A6_5308_Poly)


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-WT, IL-1ß, replicate 4

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-KO, vehicle, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-KO, IL-1ß, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-KO, vehicle, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-KO, vehicle, replicate 4

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-KO, vehicle, replicate 2

description: Bisulfite converted DNA


title: ASD_4849 (A5_4849_Poly)


title: ASD_4721 (A4_4721_Poly)


title: ASD_4721 (A4_4721_Total)


title: ASD_4231 (A3_4231_Total)


title: ASD_4231 (A3_4231_Poly)


title: ASD_797 (A2_797_Total)


title: Bone marrow derived dentritic cells, RT-MPs, 24 h, rep3

city: Wuhan

first: Yu

last: Tian

address: NO.156,Wujiadun,Jianghan District

country: China

institute: Cancer center,Union hospital, Tongji medical colloge,Huazhong university of science and technology

data_processing:
The number of reads of each gene was calculated by using featureCountsv1.5.0 software through the SAM comparison file generated by Hisat comparison and the GTF annotation file of the genome, and then the gene expression was expressed by calculating the FPKM value of the gene according to the exon length.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM value of each sample

source_name: Bone marrow derived dentritic cells

growth_protocol: Bone marrow derived dentritic cells(BMDCs) were maintained in RMPI 1640 supplemented with 2% fetal bovine serum (FBS), GM-CSF (20 ng/mL) and antibiotics in humidified atmosphere with 5% CO2 at 37 C

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen)
RNA sequencing libraries were generated using the KAPA Stranded mRNA-Seq Kit for illumina with multiplexing primers, according to the manufacturer’s protocol.

treatment_protocol: BMDCs were untreated or treated with RT-MPs for 24 h.

value: Bone marrow derived dentritic cells

value: WT

value: RT-MPs


title: ASD_797 (A2_797_Poly)


title: ASD_1349 (A1_1349_Total)


title: ASD_1349 (A1_1349_Poly)


title: Bone marrow derived dentritic cells, RT-MPs, 24 h, rep1


title: Bone marrow derived dentritic cells, RT-MPs, 24 h, rep2


title: Bone marrow derived dentritic cells, Control, 24 h, rep3


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-KO, IL-1ß, replicate 1

description: Bisulfite converted DNA

value: Bone Marrow

value: LSK progenitor cell

value: 6-12 weeks


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-KO, vehicle, replicate 2

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-KO, IL-1ß, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-KO, vehicle, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-WT, IL-1ß, replicate 2

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-WT, IL-1ß, replicate 4

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-KO, vehicle, replicate 4

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-KO, IL-1ß, replicate 2

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-KO, vehicle, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-WT, IL-1ß, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-WT, IL-1ß, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-WT, IL-1ß, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-WT, IL-1ß, replicate 2

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-WT, vehicle, replicate 1

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-WT, vehicle, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-KO, IL-1ß, replicate 4

description: Bisulfite converted DNA


title: Bone marrow derived dentritic cells, Control, 24 h, rep2


title: EAC PDO, 100 Pa NorHA, rep3 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-11

data_processing:
https://github.com/nf-core/rnaseq
Sequence reads were trimmed for adaptor sequence/low-quality sequence using https://github.com/nf-core/rnaseq
Trimmed sequence reads were mapped to GRCm39/mm10 STAR 2.7.10
Read count extraction and normalization were performed using Htseq count
Picard CollectRNAMetrics was used for sample Quality Control
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw reads for each Sample

growth_protocol: EAC PDOs were maintained in organoid medium described in PMCID: PMC7350550, and in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Hydrogels were degraded with proteases, EAC PDOs were collected, and RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared after rRNA depletion

treatment_protocol: EAC PDOs were embedded ad cultured in hydrogels of different stiffnesses.

value: EAC000 PDO

value: esophageal adenocarcinoma organoids

value: 3D culture in NorHA hydrogel of 100 Pa in storage modulus

value: Day 14


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-WT, vehicle, replicate 4

description: Bisulfite converted DNA

value: vehicle


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-WT, vehicle, replicate 4

description: Bisulfite converted DNA

value: Common Myeloid Progenitor


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-WT, IL-1ß, replicate 3

description: Bisulfite converted DNA


title: Bone Marrow, (Lin- Sca1- ckit+ CD34+ Fc Gamma-), Tet2-WT, vehicle, replicate 2

description: Bisulfite converted DNA


title: Pdx1-Mut-RNA-2

city: Chicago

first: Benjamin

middle: J

last: Weidemann

state: IL

address: 303 E. Superior St.

department: Medicine

institute: NORTHWESTERN UNIVERSITY

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Assembly: mm10
Supplementary files format and content: Comma-delimited raw counts file: RNA_raw_counts.csv

source_name: Pancreatic Islet

growth_protocol: DMEM + 15% FBS (cells), RPMI + 10% FBS or human AB serum (islets)

extract_protocol:
DirectZol MicroPrep (Zymo)
NEBNext Ultra II Low-input/single-cell for RNA,

value: Pancreatic Islet

tag: Sex

value: male


title: Pdx1-Mut-RNA-3


title: Pdx1-Mut-RNA-5


title: Pdx1-Mut-RNA-4


title: Bone marrow derived dentritic cells, Control, 24 h, rep1

value: Control


title: EAC PDO, 100 Pa Matrigel, rep3 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-12

value: 3D culture in Matrigel of 100 Pa in storage modulus


title: EAC PDO, 350 Pa NorHA, rep3 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-10

value: 3D culture in NorHA hydrogel of 350 Pa in storage modulus


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-WT, vehicle, replicate 3

description: Bisulfite converted DNA


title: Pdx1-Mut-RNA-1


title: EAC PDO, 1000 Pa NorHA, rep3 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-9

value: 3D culture in NorHA hydrogel of 1000 Pa in storage modulus


title: Pdx1-Con-RNA-3


title: Pdx1-Con-RNA-4


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-WT, vehicle, replicate 1

description: Bisulfite converted DNA


title: Pdx1-Con-RNA-2


title: EAC PDO, 100 Pa NorHA, rep2 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-7

value: WT


title: Bone Marrow (Lin-, Sca1+, cKit+), Tet2-WT, vehicle, replicate 2

description: Bisulfite converted DNA


title: hBEC, Control

city: Boston

first: Kalki

last: Kukreja

state: MA

address: 200 Longwood Avenue

institute: Harvard University

description: Untreated ALI hBEC organotypic cultures

data_processing:
Libraries were demultiplexed and counts data were generated using cell ranger (version: 7.1.0 ). We excluded intronic reads to get counts data.
The three pooled donors were demultiplexed using vireo (https://github.com/single-cell-genetics/vireo)
To obtain the final counts matrix used for data analysis, total count and mitochondrial count filters were applied using parameters described in McCauley,Kukreja et. al. 2022, bioRxiv
Assembly: GRCh38/91
Supplementary files format and content: Raw counts (tsv.gz): library identity, barcode, gene names, and raw counts for all cells
Supplementary files format and content: Library barcodes and metadata (metadata.csv): library identity, barcode, and associated metadata for all cells across samples

source_name: Airway epithelium

growth_protocol: Primary human bronchial epithelial cells (HBECs) from normal donors were obtained from Lonza (Cat. # CC-2540) and were expanded for two passages with Growth Medium (BEGM supplemented with one SingleQuots kit, Lonza Cat. # CC-3171) in uncoated T75 flasks (Corning Cat. # 430641U). After expansion, cells were seeded on uncoated 12-well TransWell (Corning Cat. # 3460) plates at a density of 1e6 cells per plate and expanded for 7 days in Differentiation Medium (50:50 BEGM (Lonza Cat. # CC-3171)/high-glucose DMEM (ThermoFisher Cat. # 11965175) supplemented with one SingleQuots kit with no T3 and final retinoic acid concentration of 50 nM, Lonza # CC-4175. After 7 days, media was removed from the apical surface and cells were differentiated at air-liquid interface for an additional 30-45 days with media replaced every 48-72 hours.

extract_protocol:
HBECs were collected 14 days post-injury by treating with 0.05% Trypsin-EDTA (prepared by dilution of 0.25% Trypsin- EDTA (ThermoFisher Cat. # 25200056) with calcium/magnesium-free PBS), for 20 minutes at 37 °C. Trypsin dissociation was halted with Trypsin Neutralizer Solution (ThermoFisher Cat. # R002100) at 1:1 dilution and cells were filtered through a 40 μm strainer and pelleted by centrifugation at 300x g for 5 minutes. Cells were resuspended in phosphate buffered saline (ThermoFisher Cat. # 10010072) with 0.1% bovine serum albumin (ThermoFisher Cat. # B14) and counted on a Countess Cell Counter (ThermoFisher) to determine cell number and viability. For cell counting, 10 μL of cell suspension was mixed with 10 μL of Trypan Blue Solution (ThermoFisher Cat. # 15250061) and 10 μL of that 1:1 mix was loaded into Countess chip and read with default program. Viable cell numbers were used to determine cell concentration. Optiprep Density Gradient Medium (Sigma Cat. # D1556) was added to achieve a final concentration of 15% Optiprep and 120-150,000 cells/ml. Cells were captuerd by 10X Chromium as per manufacturer's protocol.
Library construction for 10X Chromium as per manufacturer's protocol

treatment_protocol: After differentiation at air-liquid interface, cells were washed 3X with warm 1XS PBS and treated with MEM (ThermoFisher Cat. # 10370088, 500 μL apical, 1 mL basal) for 1 hour at 37°C to remove differentiated luminal cells. Following incubation, luminal cells were removed by pipetting gently up and down 3-5X before removing apical media and washing with 500 μL MEM in apical chamber. Cytokines were diluted in Differentiation Medium at concentrations indicated. Cells were cultured for an additional 14 days, replacing media every 48-72 hours.

value: Airway epithelium

tag: donor ids


title: Pdx1-Con-RNA-1


title: EAC PDO, 350 Pa NorHA, rep2 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-6


title: EAC PDO, 1000 Pa NorHA, rep2 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-5


title: EAC PDO, 100 Pa Matrigel, rep1 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-4


title: hBEC, OSM

description: OSM treated ALI hBEC organotypic cultures

value: OSM, 10 ng/mL


title: hBEC, IFNG

description: IFNG treated ALI hBEC organotypic cultures

value: IFNG, 10 ng/mL


title: EAC PDO, 100 Pa Matrigel, rep2 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-8


title: k30-PlkoB

city: Jinan

first: Tian

middle: Bao

last: Qing

address: Jiyan ROAD

institute: Shandong Cancer Hospital and Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole transcriptome using tophat2 with default parameters.
Reads count of three samples were calculated by HT-Seq based on the gtf file of ensembl human.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample

source_name: KYSE30-stable cell line

growth_protocol: Human KYSE30 cells were cultured in RPMI-1640 media supplied with 10% fetal bovine serum (Hyclone) at 37°C with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Two specific shRNAs targeting the RNA sequences of SNORD12B were were cloned into pLKO.1-blast vector system and confirmed by seqencing. A non-targeting scrambled shRNA which had no known homology with any mammalian gene was designed and used as the  nonspecific control. The vectors with shRNAs along with viral packaging plasmids were transfected into human embryonic kiney 293T cells. Virus supernatant was harvested after 48 hours and incubated on KYSE30 cells for 24 hours. Cells were selected with 5ug/mL blasticidin for 2 weeks.

value: esophageal squamous cell carcinoma

value: vector


title: EAC PDO, 100 Pa NorHA, rep1 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-3

value: EAC000 PDO

value: esophageal adenocarcinoma organoids


title: CS16_4

city: Newcastle upon Tyne

first: Deborah

last: Henderson

state: Tyne and Wear

address: International Centre for Life

department: Biosciences

country: United Kingdom

institute: Newcastle University

description:
CS16_counts.csv
CS16_md.csv

data_processing:
The paired FASTQ files were de-multiplexed a perl script using the spatial barcodes encoded in read 1. Read 2 from successfully de-multiplexed pairs were trimmed for quality using Trimmomatic version 0.36 . A reference was created using Ensembl human reference genome (GRCh38.p12). The trimmed reads were aligned to this reference using STAR version 2.5.3a in single read alignment mode.  The number of reads were quantified using HTSEQ version 0.6.1  and a count matrix was created.
Demuliplex script: https://github.com/tallulandrews/scRNASeqPipeline/blob/master/0_custom_undo_demultiplexing.pl
The Spot detector software was used to align the fluorescent image with the brightfield image to determine the pixel co-ordinates for the spots.
We used Spaniel R package which provides a framework for quality control, visualization and pre-processing to process the data. Clusters were generated using Seurat with a resolution of 0.8.
Assembly: GRCh38
Supplementary files format and content: .jpg (H & E image)
Supplementary files format and content: counts.csv (filtered count matrix for each spot)
Supplementary files format and content: md.csv (metadata for each spot)
Library strategy: Spatial transcriptomics

source_name: embryonic heart

extract_protocol:
The regions containing the aortic valves were sectioned to an ST Library Preparation slide (10X Genomics, cat # 1000132), H&E stained, and the tissue sections and underlying spots (covering a 100um region ) captured using a Nikon A1R Confocal microscope at 20x Magnification.
Following enzymatic cleavage of the barcoded probes and associated captured RNA transcripts from the slide, sequencing libraries were generated and sequenced at 50,000 reads per sampling region (spot) using an Illumina NovaSeq 6000.

value: embryonic heart

tag: developmental stage


title: Bone Marrow, Tet2-KO, IL-1ß, replicate 1 & 2, HTO cDNA

description: Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

data_processing:
Aligning and gene counting with CellRanger version 3.1.0
Filtering quality cells with Seurat (v 3.2.3)
Demultiplexing cell identity with Seurat (v 3.2.3)
Clustering and Differential Expression with Seurat (v 3.2.3)
Assembly: mm10-1.2.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Whole Bone Marrow

extract_protocol:
Bone marrow cells (BM) were isolated from each animal by flushing the bones with 1x PBS 2% FBS. Red blood cells were lysed using aqueous solution of ammonium chloride solution (Stemcell Tech.). Lineage -negative fraction of BM was isolated using lineage cell depletion kit (Myltenyl Biotec). 20, 000 cells from each mouse were stained in 50ul volume using Totalseq A Hashtag antibodies following company protocols (BioLegend). Equal volumes of two samples from each group were pooled, cell pool was assessed for cell concentration and viability, and approximately 20,000 cells of pooled sample resuspended in PBS + 0.04% BSA was used for single cell analysis.
Single-cell cDNA and HTO libraries were generated using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, PN 1000121 (10x genomics and Biolegend) per manufacturer’s protocols.
Single-end sequencing of libraries was performed per manufacturer’s protocol on a Novaseq 6000 (Illumina) sequencer with HTO libraries constituting 5% of the sample.

value: Lin- BM

value: Whole Bone Marrow

value: 6-12 weeks old

value: HTO


title: Bone Marrow, Tet2-KO, IL-1ß, replicate 1 & 2, scRNAseq

description: 10 x Genomiocs 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic single cell

value: mRNA


title: Bone Marrow, Tet2-KO, IL-1ß, replicate 3 & 4, HTO cDNA


title: Bone Marrow, Tet2-KO, IL-1ß, replicate 3 & 4, scRNAseq


title: EAC PDO, 350 Pa NorHA, rep1 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-2

value: Day 14


title: CS16_2

description:
CS16_counts.csv
CS16_md.csv


title: k30-shSNORD12B-2

value: SNORD12B knockdown


title: EAC PDO, 1000 Pa NorHA, rep1 [RNA-seq]

description:
total RNA sequenced
RCA-EAC-NorHA-1

value: 3D culture in NorHA hydrogel of 1000 Pa in storage modulus


title: k30-shSNORD12B-1


title: Bone Marrow, Tet2-KO, vehicle, replicate 3 & 4, scRNAseq


title: Bone Marrow, Tet2-KO, vehicle, replicate 1 & 2, scRNAseq


title: CS16_1

description:
CS16_counts.csv
CS16_md.csv


title: CS19_5

description:
CS19_counts.csv
CS19_md.csv


title: Bone Marrow, Tet2-KO, vehicle, replicate 3 & 4, HTO cDNA


title: patient43

city: Herlev

first: Jaslin

middle: P

last: James

address: Borgmester Ib Juuls vej 1

department: Department of Pathology

country: Denmark

institute: Herlev hospital

data_processing:
ampliSeqRNA plugin (V5.12)
LIMMA/EDGER packages in R
Assembly: hg19 Ampliseq transcriptome V1.1
Supplementary files format and content: Processed data files are in csv format
Supplementary files format and content: Processed data file include normalized reads of the gene expression using Trimmed mean method

source_name: colon

extract_protocol:
MagMAX™ FFPE DNA/RNA Ultra Kit
Ion AmpliSeq™ Transcriptome Human Gene Expression Panel
sequenced on Ion GeneStudio™ S5 System

value: colon

tag: disease

value: CD

value: NAP


title: patient42

tag: tissue


title: CS16_3

description:
CS16_counts.csv
CS16_md.csv


title: Bone Marrow, Tet2-WT, IL-1ß, replicate 3 & 4, HTO cDNA

tag: cell type


title: patient41


title: patient40


title: Bone Marrow, Tet2-WT, IL-1ß, replicate 3 & 4, scRNAseq

tag: genotype


title: patient39


title: CS19_2

description:
CS19_counts.csv
CS19_md.csv


title: CS19_4

description:
CS19_counts.csv
CS19_md.csv


title: patient38


title: Bone Marrow, Tet2-WT, IL-1ß, replicate 1 & 2, HTO cDNA


title: Bone Marrow, Tet2-WT, IL-1ß, replicate 1 & 2, scRNAseq


title: CS19_3

description:
CS19_counts.csv
CS19_md.csv


title: patient37


title: Bone Marrow, Tet2-WT, vehicle, replicate 3 & 4, HTO cDNA


title: Tonsil, donor#2, scRNAseq

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

description: 10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done with the Cell Ranger software.
Assembly: hg38
Supplementary files format and content: Tab seperated value files and count matrix files

source_name: Tonsil ILC

growth_protocol: Purified CD34+ progenitors were cultured for 2 weeks with OP9 stroma, FLT3-ligand, KIT-ligand, and IL3.

extract_protocol:
Peripheral blood NK cells were purified using the RosetteSep Human NK Cell Enrichment Cocktail (STEMCELL Technologies). CD34+ hematopoietic progenitor cells were enriched using the Indirect Human CD34 MicroBead Kit (Miltenyi Biotec). Following cell sorting, cells were stained for flow cytometry and CD34+ cells were further purified via sorting to >99.9% purity on an FACSAria II cell sorter (BD Biosciences). Human innate lymphoid cells were enriched from fresh tonsil tissue and blood samples  using a custom human NK cell enrichment RosetteSep reagent containing a mixture of bivalent antibodies against glycophorin A and CD3, CD4, CD19, CD20, CD36, CD66b, and CD123.
Approximately, 10,000 cells were loaded on the 10X Genomics Chromium platform and libraries were constructed with a Chromium Next GEM Single Cell 5´ reagent kit v2 dual index according to the manufacturer instructions

value: Tonsil ILC


title: Bone Marrow, Tet2-WT, vehicle, replicate 3 & 4, scRNAseq


title: patient36


title: CWR22Rv1 cells, 2FF treated, biol rep 3

first: Jennifer

last: Munkley

state: Tyne & Wear

data_processing:
Analysis was conducted in Galaxy version 22.01
Quality control was performed with FastQC
Reads were quantified using featureCounts
Differential gene expression analysis was performed with limma-voom
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of raw read counts for each sample

source_name: Prostate cancer

extract_protocol:
RNEasy Kit following manufacturer's protocol (Qiagen)
TruSeq Stranded mRNA Sequencing Library Prep Kit following manufacturer's protocols.

value: Prostate cancer

tag: treatment


title: CWR22Rv1 cells, 2FF treated, biol rep 2


title: CWR22Rv1 cells, 2FF treated, biol rep 1


title: Bone Marrow, Tet2-WT, vehicle, replicate 1 & 2, HTO cDNA

tag: library type


title: Tonsil, donor#1, scRNAseq

description: 10X Genomics


title: NK, donor #4, scRNAseq

description: 10X Genomics

source_name: Blood NK cells

value: Blood NK cells


title: patient35

value: HC


title: patient34


title: patient33


title: NK, donor #2, scRNAseq

description: 10X Genomics


title: CS19_1

description:
CS19_counts.csv
CS19_md.csv


title: NK, donor #3, scRNAseq

description: 10X Genomics


title: Bone Marrow, Tet2-WT, vehicle, replicate 1 & 2, scRNAseq

tag: strain


title: patient32


title: CD34, donor #2, scRNAseq

description: 10X Genomics

source_name: Blood CD34 cells

value: Blood CD34 cells


title: NK, donor #1, scRNAseq

description: 10X Genomics


title: CD34, donor #1, scRNAseq

description: 10X Genomics


title: patient29


title: patient31


title: human primary CD4+ T cells, Donor 4, Inf NMN

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

data_processing:
Quality control of raw fastq data was carried out by FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and fastp.
Then clean reads were aligned to the UCSC GRCh38 reference using Hisat2 v2.2.1.
HTSeq v0.6.1 was used to generate raw read count for each gene. Differential expression analysis was performed using DESeq2.
Genes with log2|fold change| > 1 and adjusted p-value < 0.05 (FDR) were considered significantly different.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw count for each Sample

source_name: Primary cells

growth_protocol: Primary CD4+ T cells were purified from peripheral blood of healthy donors using RosetteSep™ Human CD4+ T Cell Enrichment Cocktail (Stemcell™ Technologies) by negative selection, and maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS; Gibco), 2 mM L-glutamine (Gibco) and 100 U/ml penicillin /100 μg/ml streptomycin (Gibco) in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using AllPrep DNA/RNA Mini Kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KR1352-v3.16) following manufacturer's protocols.

treatment_protocol: Purified primary human CD4+ T cells were treated without or with NMN for 24 hours and then infected without or with HIV-1JRFL for another 24 hours.

value: Primary cells

value: Purified peripheral CD4+ T cells

value: WT

value: NMN-treated, infected

value: 49 hours


title: PGP1_S3_2

city: BErgen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

data_processing:
CLC Genomics workbench v 23.0.4
Trimming was performed using the CLC workbench tool. Quality limit set at 0.05. Maximum number of ambiguities = 2, Automated read through adapter trimming on.
Sequences were aligned to the  Qiagen hg38 reference sequence using CLC workbench. Mismatch cost = 2, Insertion cost = 3, deletion cost = 3, length fraction= 0.8, similarity fraction = 0.8
Total counts were extracted from aligned sequences using CLC workbench
Assembly: hg38
Supplementary files format and content: txt file containing raw total counts per file

source_name: Posterior foregut

growth_protocol: iPSC were differentiaterd toward pancreatic endocine fate using protocol by Rezania et al 2014

extract_protocol:
Cells were harvested at different stages and RNA were extracted using Rneasy mini kit (qiagen)
Library was constructed by Qiagen

treatment_protocol: Differentiation chemicals

value: Posterior foregut

value: iPSC

value: wt

value: Pancreatic endocrine differentiation


title: PGP1_S4_2

source_name: Pancreatic endoderm

value: Pancreatic endoderm


title: PGP1_S7_3

source_name: Islet like cells

value: Islet like cells


title: PGP1_S4_3


title: PGP1_S6_1

source_name: Immature endocrine cell

value: Immature endocrine cell


title: PGP1_S3_3


title: PGP1_S7_1


title: PGP1_S6_3


title: PGP1_S4_1


title: PGP1_S5_1

source_name: Pancreatic endocrine precursor

value: Pancreatic endocrine precursor


title: PGP1_S6_2


title: PGP1_S5_2


title: PGP1_S5_3


title: PGP1_S3_1


title: human primary CD4+ T cells, Donor 4, Inf

value: Untreated, infected

value: 48 hours


title: Donor 2, CD57+

city: Oslo

first: Karl-Johan

last: Malmberg

address: Ullernchausseen 70

institute: Oslo University Hospital

description: 3' mRNA library: count matrices of gene expression

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression) was performed using the 10x Genomics Cell Ranger pipeline with default settings (v3.0.2) and aligning to the hg19 genome build and Ensembl 93 annotations.
Assembly: hg19
Supplementary files format and content: Cellranger output files, count matrices: barcode.tsv, genes.tsv, matrix.mtx

source_name: Peripheral blood

extract_protocol:
Cells were harvested and surface stained with the following antibodies: CD57-FITC (HNK-1) from BioLegend; KIR3DL1S1-APC (Z27.3.7), CD56-ECD (N901), CD158b1/b2,j-PE-Cy5.5 (GL183), from Beckman Coulter; KIR2DL1-APC-Cy7 (REA284), NKG2C-PE (REA205), NKG2A-PE Vio770 (REA110) from Miltenyi Biotec. 12,000 cells were directly sorted into Eppendorf tubes at 4°C for each sample using a FACSAriaII (Beckton Dickinson).
Standard 10X Genomics library preparation

tag: individual

value: Donor 2

value: Peripheral blood

value: NK cells

tag: sorted nk subsets


title: Donor 2, Non-educated

value: Non-educated


title: patient30

value: colon

value: HC

value: NAP


title: Donor 2, Educated

value: Educated


title: patient28


title: human primary CD4+ T cells, Donor 4, Control

tag: cell line

value: Primary cells

value: Purified peripheral CD4+ T cells

value: WT

value: Untreated, mock

tag: time


title: A549 CTRL replicate #2

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

data_processing:
The analysis were performed on the OneStopRNASeq platform.
Specifically, paired-end RNASeq reads were aligned to human genome hg38 with STAR
Gene expression were quantified with featureCounts
Genome annotation file used was Gencode(v34)
Differential analysis processed with DESeq2
Assembly: hg38
Supplementary files format and content: excel: count and TPM

source_name: lung

growth_protocol: A549 Cells were grown adhered to tissue culture plates at 37°C, under 5% CO2 and atmospheric oxygen. Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100units/ml penicillin-streptomycin, and 2mM L-glutamine.

extract_protocol: Total RNA was extracted from each sample using the RNeasy Kit for total RNA isolation (Qiagen #74104).

treatment_protocol: Cells were transduced with lentivirus containing lentiCRISPR v2 containing either a control non-targeting guide (CTRL) or a guide targeting UXS1 (UXS1 g1). Cells were selected with puromycin for 5 days and collected for RNA extraction at day 7 after lentiviral infection.

value: lung

value: lung adenocarcinoma

value: CRISPR non-targeting guide


title: A549 CTRL replicate #1


title: A549 UXS1 KO replicate#1

value: CRISPR gene KO of UXS1


title: patient25

value: CD


title: A549 UXS1 KO replicate#2


title: A549 UXS1 KO replicate#3


title: A549 CTRL replicate #3


title: patient26


title: patient27


title: patient24


title: SC2010RRLJ06

city: Shanghai

first: Yi

last: Shi

address: Fenglin 180

institute: FUDAN University, China

data_processing:
Sequencing library was generated from cDNA following Illumina Nextera XT protocol and the final library was sequenced on Illumina Hiseq x10.
On average about 15 million 150bp paired end reads were generated per sample.
Assembly: mm10
Supplementary files format and content: NO files include raw counts for each sample

source_name: mesangial cell

extract_protocol:
RNA was harvested using Trizol (TAKARA). 1 ug of total RNA was used for the construction of sequencing libraries.
cDNA library was prepared from cells using the SMART-Seq v4 Ultra Low RNA Kit (Clonetech) following manufacturers instructions.

value: mesangial cell


title: SC2010RRLJ03


title: SC2009RRLJ13


title: SC2009RRLJ16


title: SC2008RRLJ03


title: Donor 2, Bulk

value: Donor 2

value: Peripheral blood

value: Bulk


title: Donor 2, NKG2A+

value: NK cells


title: human primary CD4+ T cells, Donor 3, NMN

value: NMN-treated, mock

value: 48 hours


title: human primary CD4+ T cells, Donor 3, Inf

value: Untreated, infected


title: human primary CD4+ T cells, Donor 3, Control

value: Primary cells


title: Donor 1, Non-educated

value: Donor 1

value: Non-educated


title: Donor 1, Adaptive

value: Adaptive


title: human primary CD4+ T cells, Donor 3, Inf NMN

value: Purified peripheral CD4+ T cells

value: WT

value: NMN-treated, infected


title: Donor 2, CD56brights


title: human primary CD4+ T cells, Donor 2, NMN


title: patient22

value: colon

value: UC

value: NAP


title: SC2008RRLJ06

value: mesangial cell


title: patient20


title: Donor 1, NKG2A+

value: Peripheral blood


title: patient23

value: CD


title: Donor 1, Educated

value: NK cells

value: Educated


title: human primary CD4+ T cells, Donor 2, Inf

value: 48 hours


title: SC2009RRLJ10


title: human primary CD4+ T cells, Donor 2, Inf NMN


title: SC2010RRLJ12

value: control


title: SC2010RRLJ15


title: Donor 1, CD56brights


title: patient21

source_name: Rectum

value: Rectum


title: patient19


title: patient18


title: SC2010RRLJ09


title: Donor 1, Bulk

value: Donor 1

value: Bulk


title: human primary CD4+ T cells, Donor 1, NMN

value: Primary cells

value: NMN-treated, mock


title: SC2010RRLJ05

source_name: podocyte

value: podocyte


title: human primary CD4+ T cells, Donor 2, Control

value: Purified peripheral CD4+ T cells

value: WT

value: Untreated, mock


title: patient17

value: colon

value: UC

value: NAP


title: human primary CD4+ T cells, Donor 1, Inf NMN

value: NMN-treated, infected


title: SC2010RRLJ02


title: patient16


title: human primary CD4+ T cells, Donor 1, Inf

value: Untreated, infected


title: SC2008RRLJ05


title: human primary CD4+ T cells, Donor 1, Control


title: patient14

value: HC


title: CWR22Rv1 cells, Fucotrim II treated, biol rep 2

value: Prostate cancer

value: Fucotrim II


title: SC2009RRLJ15


title: SC2008RRLJ02


title: patient13


title: CWR22Rv1 cells, Fucotrim I treated, biol rep 3

value: Fucotrim I


title: SC2009RRLJ09


title: CWR22Rv1 cells, Fucotrim I treated, biol rep 2


title: patient11

value: Rectum


title: TUMOR Pool 4

city: Helsinki

first: Topi

last: Tervonen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
3' RNA-Seq (Drop-seq-like)
Twelve samples are pooled into a single sequencing library. Samples are separated with 12nt long barcodes that are listed in the EGFR_sample_information.xlsx file.

data_processing:
Sequencing with 75 cycles produced 20 bp Read 1 (bases 1-12 sample barcode, bases 13-20 UMI) and 55 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was filtered to remove reads shorter than 20 bp.
The original pipeline suggested in (Macosko EZ et al. Cell 2015; https://github.com/broadinstitute/Drop-seq) for processing of Drop-seq data was used. Briefly, reads were additionally filtered to remove poly-A tails of length 6 or greater, then aligned to the mouse (GRCm39) genome using STAR aligner, with default settings. Uniquely mapped reads were grouped according to the 1-12 barcode, and gene transcripts were counted by their Unique Molecular Identifiers (UMIs) to reduce bias emerging from the PCR amplification. Digital expression matrices (DGE) reported the number of transcripts per gene in a given sample (according to the distinct UMI sequences counted).
Differentially expressed genes were identified using DESeq2.
Assembly: GRCm39
Supplementary files format and content: Gene_expression_counts.xlsx: Digital Gene Expression (DGE): Excel file containing UMI read counts for each sample.

source_name: Human breast cancer

extract_protocol: Whole tumor tissue RNA was extracted using Precellys hard-tissue beads and TRIzol. RNA was then DNase treated and purified using RNeasy Mini Kit from Qiagen.

value: Breast tumor explant

tag: tumor type

value: mixed sample (non-demultiplexed)

tag: receptor positivity


title: PGP1_S7_2

value: Islet like cells

value: iPSC

value: wt

value: Pancreatic endocrine differentiation


title: CWR22Rv1 cells, Fucotrim II treated, biol rep 1


title: SC2010RRLJ14

value: podocyte

value: WT

value: control


title: SC2009RRLJ12


title: Bone Marrow, Tet2-KO, vehicle, replicate 1 & 2, HTO cDNA

source_name: Whole Bone Marrow

value: Lin- BM

value: Whole Bone Marrow

tag: age

value: 6-12 weeks old

value: HTO


title: CWR22Rv1 cells, Fucotrim I treated, biol rep 1

value: Prostate cancer


title: patient10

value: UC

value: NAP


title: SC2010RRLJ08


title: patient15

source_name: colon

value: colon

value: CD


title: patient9


title: D_42

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Bos Taurus reference genome (ARS-UCD1.2) using Bowtie2 (2.2.2)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as transcripts per million (TPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: ARS-UCD1.2
Supplementary files format and content: xlsx file include TPM values for each sample

organism: Bos taurus

source_name: Oviduct

extract_protocol:
Total RNA was isolated from organoid cells using an RNeasy Plus Micro Kit, according to the manufacturer’s protocol. To remove genomic DNA contaminants, on-column DNA digestion was performed using RNase-free Dnase.
RNA libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

value: Oviduct

value: Oviductal organoid

tag: culture temperature_(°c)


title: E_42


title: CWR22Rv1 cells, P-SiaFNEtoc treated, biol rep 3

source_name: Prostate cancer

value: P-SiaFNEtoc


title: patient12

value: Rectum


title: PC3 cells, OEControl, biol rep 2

value: Lenti-ORF control


title: PC3 cells, GCNT1 OE, biol rep 3

value: GCNT1 overexpression


title: PC3 cells, GCNT1 OE, biol rep 1


title: PC3 cells, OEControl, biol rep 3


title: PC3 cells, GCNT1 OE, biol rep 2


title: C_42


title: PC3 cells, OEControl, biol rep 1


title: patient8


title: SC2010RRLJ01

source_name: glomerular endothelial cell

value: glomerular endothelial cell


title: CWR22Rv1 cells, P-SiaFNEtoc treated, biol rep 1


title: patient6


title: CWR22Rv1 cells, DMSO Control, biol rep 3

value: DMSO


title: patient5


title: CWR22Rv1 cells, DMSO Control, biol rep 2


title: patient7


title: E_37


title: B_42


title: SC2009RRLJ14


title: D_37


title: SC2008RRLJ04


title: CWR22Rv1 cells, DMSO Control, biol rep 1


title: patient4


title: C_37


title: SC2010RRLJ04


title: patient3


title: SC2009RRLJ08


title: CWR22Rv1 cells, P-SiaFNEtoc treated, biol rep 2


title: ETO_3

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

data_processing:
Sequenced were mapped to GRCh38 whole genome using STAR 2.7.0d with parameters --readFilesCommand zcat --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
feature counted with htseq-count version 0.11.2
Genome_build: GRCh38 release 96
Supplementary_files_format_and_content: raw table of counts for each sample

source_name: Human Retinal Microvascular Endothelial Cells

growth_protocol: Human retinal microvascular endothelial cells (HRMECs) were grown on fibronectin-coated flasks in Endothelial Cell Medium (ECM)

extract_protocol:
Total RNA was isolated from cells using a Maxwell RSC instrument (Promega) following manufacturer’s instructions
Libraries were prepared using a TruSeq stranded mRNA-seq library from total RNA

treatment_protocol: HRMECs were cultured and passaged until replicative senesence was reached. HRMECs were treated with 1 µM Etoposide for 4 days. After removal of etoposide HRMECs were split 1:1 and kept for 4 days, until senescence was established.

value: Etoposide Treatment

value: Endothelial Cells

tag: passage

value: P6 to P8


title: patient1


title: A_42


title: patient2


title: SC2010RRLJ07

value: WT

value: control


title: SC2008RRLJ01


title: EP_CT_3

value: Early Passage

value: P3 to P8


title: B_37


title: 6-week diabetes biol replicate 2, seRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: renal cortex

extract_protocol:
Renal cortex was freshely collected and digested in Hanks buffer with 10 mg/ml collagenase IV (Sigma-Aldrich) and 200 U/ml DNase I (Invitrogen, Carlsbad, MO, USA) at 37°C for twenty minutes. Renal cortex samples were dissociated using a gentle MACS Dissociation (Miltenyi Biotec, Bergisch Gladbach, Germany). Cells were washed and re-suspended in PBS and stained with a Viability Dye. Single-cell suspensions were prepared with PBS containing 0.04% bovine serum albumin. Cell viability and counts were verified with a hemocytometer.
Chromium Single Cell 3' Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell 3' Chip kit v2 (PN-120236), and Chromium i7 Multiplex Kit (PN-120262) were used for 10× Genomics examination. Approximately 14000 cells were subjected to the 10× Genomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation. MessageRNA was prepared using 10× Genomics Chromium Single Cell 3′reagent kit (V2 chemistry), while cells were partitioned into the GEMs with cell-specific and transcript-specific barcodes (16 bp 10× Barcode and 10 bp Unique Molecular Identifier (UMI), respectively). After RT-PCR, cDNA was recovered, purified, and amplified for library preparation.

value: renal cortex

value: 6-w db

value: 6 weeks old


title: LP_CT_3

value: Late Passage

value: P15 to P20


title: Bone marrow derived macrophages, RT-MPs@S, 24 h, rep3

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Mus_musculus.GRCm38.97.fa  from NCBI using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM value for each sample

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow derived macrophages (BMDMs) were maintained in RPMI 1640 supplemented with M-CSF (20 ng/mL), 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen)
RNA sequencing libraries were generated using the KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Lewis-S cells were estabiested by overexpress Spike protein on Lewis lung carcinoma cells.RT-MPs and RT-MPs@S were separated from medium of irradiated Lewis and Lewis-S,respectively. BMDMs were treated with RT-MPs or RT-MPs@S for 48 h.

value: Bone marrow derived macrophages


title: EV_C_42

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Bos Taurus reference genome (ARS-UCD1.2) using Bowtie2 (2.2.2)
Mapped reads were used for annotation against bovine mature and precursor miRNAs listed in the mirBase database (release 22)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as TMM-adjusted Counts Per Million (CPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: ARS-UCD1.2
Supplementary files format and content: xlsx file include CPM values for each sample

source_name: Oviductal organoid

extract_protocol:
For EV isolation, oviductal organoid conditioned media samples were subjected to a series of centrifugations starting at 500 xg for 10 minutes to remove cells, followed by 3000 xg for 10 minutes to remove the cellular debris, and at 12,000 xg for 30 min to remove protein aggregates and large particles. All centrifugation steps were performed at 4 °C. The supernatant of the samples was filtered through a 0.22 µM sterile filter to remove particles larger than 200 nm. For the EV isolation, 2 ml of pre-centrifuged follicular samples were subjected to an ultracentrifugation procedure at 120,000 xg for 70 min at 4 °C using the Beckman SWTi55 rotor. The EVs pellet was washed with sterile PBS and then centrifuged again at 120,000 xg for 70 min. EVs were resuspended in 500 µL of PBS and further standardized by elution in 180 µL of sterile DPBS (1X) (ThermoFisher Scientific 14190-144) using the Exo-spin mini columns (CELL guidance systems EX03-50) according to the manufacturer's protocol. Isolated EVs were stored at -80°C for further analysis. Total RNA including miRNAs was isolated from EVs using a Norgen Exosomal RNA Isolation kit (Norgen, Canada), according to the manufacturer’s instructions. On-column DNA digestion was performed to remove genomic DNA contaminants.
Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: fluid source

value: Culture media

value: Oviductal organoid

value: Extracellular Vesicles

tag: culture temprature_(°c)


title: 6-week diabetes biol replicate 1, seRNAseq

description: 10x Genomics

tag: tissue


title: LP_CT_2


title: ETO_2


title: control biol replicate 2, scRNAseq

description: 10x Genomics

tag: cell type

value: m/m

value: 9-10 weeks old


title: EV_A_42


title: EP_CT_2

value: Endothelial Cells


title: Bone marrow derived macrophages, RT-MPs, 24 h, rep3

tag: genotype

value: RT-MPs


title: ETO_1

tag: treatment

value: Etoposide Treatment

value: P6 to P8


title: 10-week diabetes biol replicate 2, seRNAseq

description: 10x Genomics

value: 10-w db

value: 10 weeks old


title: EV_C_37


title: EV_B_37


title: A_37

value: Oviduct


title: SC2010RRLJ10

value: glomerular endothelial cell

value: WT

value: control


title: 10-week diabetes biol replicate 1, seRNAseq

description: 10x Genomics

value: renal cortex


title: LP_CT_1

value: Late Passage

value: P15 to P20


title: EV_A_37

value: Culture media

value: Oviductal organoid


title: Bone marrow derived macrophages, RT-MPs, 24 h, rep1

value: Bone marrow derived macrophages


title: EV_B_42

value: Extracellular Vesicles


title: EP_CT_1

value: Early Passage

value: Endothelial Cells

value: P3 to P8


title: control biol replicate 1, scRNAseq

description: 10x Genomics

value: m/m

value: 9-10 weeks old


title: Bone marrow derived macrophages, RT-MPs@S, 24 h, rep2


title: D8, control, 3

status: Public on Oct 26 2023

city: College Station

first: Ling

last: Yu

state: Texas

address: Raymond Stotzer Pkwy

department: VTPP

institute: TAMU

description:
Adult_digit cells_monolayer culture
D8_control.3

data_processing:
The raw data was aligned to genome by HISAT2
The alignned reads were assembled with transcripts by htseq-count
Differential expression analysis was done by DESeq2
Assembly: mm10
Supplementary files format and content: Processed data files include normalized counts with all cell types of interest and DE analysis of  P3D8_Chondrogenesis and P3E3_Chondrogenesis groups

source_name: Single cell-derived clone from P3 fibroblasts

growth_protocol: Cells were cultured on fibronectin coated culture dishes in DMEM supplemented with 10 ng/ml EGF, 10 ng/ml PDGF, 0.5 ng/ml LIF and 2% fetal bovine serum in 10 cm culture dishes. Cells were incubated at 37°C under 5% carbon dioxide and collected at 80% confluency.

extract_protocol:
Total RNA was extracted from cultures using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s recommended protocol. The aggregation cultured samples were homogenized before RNA extraction. The quantity and quality of total RNAs were checked by Nanodrop ratios of 260/280 and 260/310 and further checked with concentration, RIN, and 28S/18S ratio by Agilent 2100 at BGI Genomics.
The 100-bp length paired-end reads from cultures were generated using BGISEQ-500 at BGI Genomics.

treatment_protocol: Cells were cultured on none-coated petri dishes in DMEM supplemented with 2% fetal bovine serum and 50 ng/ml BMP2 for cell aggregatation. After 4 days, cells were switched to 50 ng/ml BMP9 treatment for chondrogenic induction. Cells were incubated at 37°C under 5% carbon dioxide.

value: Digit fibroblast cells

tag: culture conditions

value: monolayer culture

tag: confluence


title: Bone marrow derived macrophages, RT-MPs@S, 24 h, rep1

first: Yu

last: Tian

tag: strain


title: D8, control, 2

description:
Adult_digit cells_monolayer culture
D8_control.2


title: D8, control, 1

description:
Adult_digit cells_monolayer culture
D8_control.1


title: Bone marrow derived macrophages, RT-MPs, 24 h, rep2

value: RT-MPs


title: D8, B2-B9, 1

description:
Adult_digit cells_chondrogenic 3D culture
D8_B2-B9.1

value: chondrogenic 3D culture


title: BLA_NoRecall_nr5_N9

city: Stanford

first: Wenfei

last: Sun

address: 318 Campus Dr.

institute: Stanford University

description: Smartseq

data_processing:
Fastq reads were mapped with STAR(2.7.9a)
Assembly: mm10
Supplementary files format and content: Cell by gene matrix format

extract_protocol:
OligodT primers were used to enrich mRNA
Brain tissues were dissociated with Worthington Papain Digestion Kit RNA libraries were prepared using smart seq 3
Novaseq 6000 was used for sequencing with standard Illumina protocols

treatment_protocol: Fear conditioning paradigm

value: TRAP2 Ai14

value: No recall


title: E3, B2-B9, 1

description:
Adult_digit cells_chondrogenic 3D culture
E3_B2-B9.1


title: BLA_NoRecall_nr5_K8

description: Smartseq


title: D8, B2-B9, 2

description:
Adult_digit cells_chondrogenic 3D culture
D8_B2-B9.2


title: BLA_NoRecall_nr5_M21

description: Smartseq


title: BLA_NoRecall_nr5_N17

description: Smartseq


title: BLA_NoRecall_nr5_L3

description: Smartseq


title: E3, control, 3

description:
Adult_digit cells_monolayer culture
E3_control.3


title: E3, control, 1

description:
Adult_digit cells_monolayer culture
E3_control.1


title: E3, B2-B9, 3

description:
Adult_digit cells_chondrogenic 3D culture
E3_B2-B9.3


title: E3, control, 2

description:
Adult_digit cells_monolayer culture
E3_control.2


title: E3, B2-B9, 2

description:
Adult_digit cells_chondrogenic 3D culture
E3_B2-B9.2


title: D8, B2-B9, 3

description:
Adult_digit cells_chondrogenic 3D culture
D8_B2-B9.3


title: BLA_NoRecall_nr5_N13

description: Smartseq


title: BLA_NoRecall_nr5_N7

description: Smartseq


title: BLA_NoRecall_nr5_K4

description: Smartseq


title: BLA_NoRecall_nr5_M22

description: Smartseq


title: BLA_NoRecall_nr5_N2

description: Smartseq


title: BLA_NoRecall_nr5_J23

description: Smartseq


title: BLA_NoRecall_nr5_M11

description: Smartseq


title: BLA_NoRecall_nr5_J4

description: Smartseq


title: BLA_NoRecall_nr5_N21

description: Smartseq


title: BLA_NoRecall_nr5_L12

description: Smartseq


title: BLA_NoRecall_nr5_J5

description: Smartseq


title: BLA_NoRecall_nr5_K13

description: Smartseq


title: BLA_NoRecall_nr5_K15

description: Smartseq


title: BLA_NoRecall_nr5_N11

description: Smartseq


title: BLA_NoRecall_nr5_M20

description: Smartseq


title: BLA_NoRecall_nr5_N5

description: Smartseq


title: BLA_NoRecall_nr5_J10

description: Smartseq


title: BLA_NoRecall_nr5_K3

description: Smartseq


title: BLA_NoRecall_nr5_G16

description: Smartseq


title: BLA_NoRecall_nr5_G20

description: Smartseq


title: BLA_NoRecall_nr5_H6

description: Smartseq


title: BLA_NoRecall_nr5_I8

description: Smartseq


title: BLA_NoRecall_nr5_I4

description: Smartseq


title: BLA_NoRecall_nr5_G14

description: Smartseq


title: BLA_NoRecall_nr5_G11

description: Smartseq


title: BLA_NoRecall_nr5_H12

description: Smartseq


title: BLA_NoRecall_nr5_H16

description: Smartseq


title: BLA_NoRecall_nr5_I14

description: Smartseq


title: BLA_NoRecall_nr5_G10

description: Smartseq


title: BLA_NoRecall_nr5_H7

description: Smartseq


title: BLA_NoRecall_nr5_I22

description: Smartseq


title: BLA_NoRecall_nr5_G8

description: Smartseq


title: BLA_NoRecall_nr5_G3

description: Smartseq


title: BLA_NoRecall_nr5_I11

description: Smartseq


title: BLA_NoRecall_nr5_I18

description: Smartseq


title: BLA_NoRecall_nr5_G21

description: Smartseq


title: BLA_NoRecall_nr5_G23

description: Smartseq


title: BLA_NoRecall_nr5_I10

description: Smartseq


title: BLA_NoRecall_nr5_B9

description: Smartseq


title: BLA_NoRecall_nr5_E6

description: Smartseq


title: BLA_NoRecall_nr5_F12

description: Smartseq


title: BLA_NoRecall_nr5_F1

description: Smartseq


title: BLA_NoRecall_nr5_D19

description: Smartseq


title: BLA_NoRecall_nr5_D9

description: Smartseq


title: BLA_NoRecall_nr5_D11

description: Smartseq


title: BLA_NoRecall_nr5_E1

description: Smartseq


title: BLA_NoRecall_nr5_F4

description: Smartseq


title: BLA_NoRecall_nr5_D10

description: Smartseq


title: BLA_NoRecall_nr5_B7

description: Smartseq


title: BLA_NoRecall_nr4_P11

description: Smartseq


title: BLA_NoRecall_nr5_A4

description: Smartseq


title: BLA_NoRecall_nr5_B16

description: Smartseq


title: BLA_NoRecall_nr5_B18

description: Smartseq


title: BLA_NoRecall_nr5_A1

description: Smartseq


title: BLA_NoRecall_nr5_A22

description: Smartseq


title: BLA_NoRecall_nr4_L23

description: Smartseq


title: BLA_NoRecall_nr4_O10

description: Smartseq


title: BLA_NoRecall_nr5_B23

description: Smartseq


title: BLA_NoRecall_nr4_O2

description: Smartseq


title: BLA_NoRecall_nr5_C6

description: Smartseq


title: BLA_NoRecall_nr4_M19

description: Smartseq


title: BLA_NoRecall_nr5_C10

description: Smartseq


title: BLA_NoRecall_nr5_B19

description: Smartseq


title: BLA_NoRecall_nr5_F16

description: Smartseq


title: BLA_NoRecall_nr4_N5

description: Smartseq


title: BLA_NoRecall_nr4_P3

description: Smartseq


title: BLA_NoRecall_nr5_F11

description: Smartseq


title: BLA_NoRecall_nr5_F2

description: Smartseq


title: BLA_NoRecall_nr5_B10

description: Smartseq


title: BLA_NoRecall_nr4_O17

description: Smartseq


title: BLA_NoRecall_nr4_N14

description: Smartseq


title: BLA_NoRecall_nr4_O21

description: Smartseq


title: BLA_NoRecall_nr4_J6

description: Smartseq


title: BLA_NoRecall_nr4_J4

description: Smartseq


title: BLA_NoRecall_nr4_K7

description: Smartseq


title: BLA_NoRecall_nr4_J3

description: Smartseq


title: BLA_NoRecall_nr4_L10

description: Smartseq


title: BLA_NoRecall_nr4_K21

description: Smartseq


title: BLA_NoRecall_nr4_K17

description: Smartseq


title: BLA_NoRecall_nr4_K23

description: Smartseq


title: BLA_NoRecall_nr4_J12

description: Smartseq


title: BLA_NoRecall_nr4_N9

description: Smartseq


title: BLA_NoRecall_nr4_O16

description: Smartseq


title: BLA_NoRecall_nr4_I18

description: Smartseq


title: BLA_NoRecall_nr4_I12

description: Smartseq


title: BLA_NoRecall_nr4_H21

description: Smartseq


title: BLA_NoRecall_nr4_H9

description: Smartseq


title: BLA_NoRecall_nr5_C18

description: Smartseq


title: BLA_NoRecall_nr5_E23

description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr4_I17

description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr5_A21

description: Smartseq


title: BLA_NoRecall_nr4_G20

description: Smartseq


title: BLA_NoRecall_nr5_B13

description: Smartseq


title: BLA_NoRecall_nr4_I13

description: Smartseq


title: BLA_NoRecall_nr4_G13

description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr4_G12

description: Smartseq


title: BLA_NoRecall_nr4_F5

description: Smartseq


title: BLA_NoRecall_nr4_F21

description: Smartseq


title: BLA_NoRecall_nr4_F16

description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr4_E4

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr4_B5

description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr4_E22

description: Smartseq


title: BLA_NoRecall_nr3_O8_S253

description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr4_A14

description: Smartseq


title: BLA_NoRecall_nr4_C18

description: Smartseq


title: BLA_NoRecall_nr3_O19_S264

description: Smartseq


title: BLA_NoRecall_nr3_O6_S251

description: Smartseq


title: BLA_NoRecall_nr3_O5_S250

description: Smartseq


title: BLA_NoRecall_nr4_B20

description: Smartseq


title: BLA_NoRecall_nr3_O7_S252

description: Smartseq


title: BLA_NoRecall_nr4_B21

description: Smartseq


title: BLA_NoRecall_nr4_A8

description: Smartseq


title: BLA_NoRecall_nr4_B6

description: Smartseq


title: BLA_NoRecall_nr4_D23

description: Smartseq


title: BLA_NoRecall_nr4_E13

description: Smartseq


title: BLA_NoRecall_nr4_D14

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_N21_S243

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_L20_S207

description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_L19_S206

description: Smartseq


title: BLA_NoRecall_nr3_N13_S235

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_N20_S242

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_J21_S162

description: Smartseq


title: BLA_NoRecall_nr3_I6_S124

description: Smartseq


title: BLA_NoRecall_nr3_J23_S164

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_J5_S146

description: Smartseq


title: BLA_NoRecall_nr3_J22_S163

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_H14_S109

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_E7_S33

description: Smartseq


title: BLA_NoRecall_nr3_G1_S73

description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_F18_S67

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_E5_S31

description: Smartseq


title: BLA_NoRecall_nr3_F15_S64

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_D22_S25

description: Smartseq


title: BLA_NoRecall_nr3_E15_S41

description: Smartseq


title: BLA_NoRecall_nr3_C6_S286

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_D12_S15

description: Smartseq


title: BLA_NoRecall_nr3_D17_S20

description: Smartseq


title: BLA_NoRecall_nr3_E20_S46

description: Smartseq


title: BLA_NoRecall_nr3_D5_S8

description: Smartseq


title: BLA_NoRecall_nr3_D11_S14

description: Smartseq


title: BLA_NoRecall_nr3_C20_S300

description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_C4_S284

description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_C5_S285

description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_A8_S242

description: Smartseq


title: BLA_NoRecall_nr3_B8_S265

description: Smartseq


title: BLA_NoRecall_nr3_B4_S261

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr3_A15_S249

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr2_M7_S251

description: Smartseq


title: BLA_NoRecall_nr2_L7_S228

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr2_N2_S269

description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr2_M1_S245

description: Smartseq


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description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr2_M9_S253

description: Smartseq


title: BLA_NoRecall_nr2_M8_S252

description: Smartseq


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description: Smartseq


title: BLA_NoRecall_nr2_M11_S255

description: Smartseq


title: BLA_NoRecall_nr2_L3_S224

description: Smartseq


title: BLA_NoRecall_nr2_N18_S285

description: Smartseq


title: BLA_NoRecall_nr2_N10_S277

description: Smartseq


title: BLA_NoRecall_nr2_M15_S259

description: Smartseq


title: BLA_NoRecall_nr2_M17_S261

description: Smartseq