title: PBMCs, Caucasian, B002_L001, LONZA3038016

city: Singapore

first: Boxiang

last: Liu

address: 12 Science Drive 2, MD1 - Tahir Foundation Building, Level 5

country: Singapore

institute: National University of Singapore

data_processing:
The DRAGEN Single-Cell RNA pipeline in the Illumina DRAGEN v3.8.4 software (version 07.021.602.3.8.4-20-g74395e76) was used for pre-processing of paired-end FASTQ files from each individual scRNA-seq gene expression library. Reads from each pool were mapped to GENCODE Release 32 (GRCh38, Ensembl 98, date 2019-09-05).  The count data was processed and analyzed in R. Within each pool, every cell (barcode) and read was assigned to an individual within that pool using Genotype Data (provided) in DRAGEN v3.8.4.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw data were processed from fatsq files, which contain cDNA sequences. Single-cell expression data were processed using *rds file containing single cell expression and metadata matrix.

extract_protocol:
Eight ml of blood was drawn from each donor using CPT tubes with sodium heparin (BD Vacutainer CPT, cat. no. 362753). PBMC isolation followed a standardized protocol across sites, using FBS (Sigma-Aldrich cat. no. F2442, lot 19G014 and 20A363) for cell isolation, pooling, and washing. Blood samples were processed within 2 hours at room temperature via density-gradient centrifugation (1,500 x g, 30 min, 20°C, with soft acceleration/deceleration). Plasma was aspirated, and PBMCs were pelleted at 300 x g for 15 min, then resuspended in ACK lysing buffer (Thermo Fisher, cat. no. A10492). Cells were washed twice (PBS pH 7.4, 1% FBS, 1 mM EDTA) and cryopreserved in CryoStor CS10 (STEMCELL Technologies, cat. no. 079555). Cryovials were stored at -80°C before transfer to liquid nitrogen. The full protocol is available on Protocols.io: https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-b8r9rv96.
Both AIDA and LONZA individuals were sequenced in pools of 16 individuals, including 15 AIDA samples and 1 LONZA control sample (chosen from 5 LONZA PBMC samples). Chromium Next GEM Single Cell 5’ Kit v2 was used for library construction

value: blood

value: PBMCs


title: day1_4F2

status: Public on Dec 05 2024

type: SRA

city: Cambridge

first: Jianfeng

last: Ge

state: Cambridgeshire

address: 37, ST THOMAS'S SQUARE

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing: deseq output data for both L1475 and A549 on condition of OSKM vs TA control

molecule: total RNA

organism: Mus musculus

source_name: lung

growth_protocol: L1475 and A549 were cultured in DMEM+10% FBS medium

extract_protocol: RNA was havested using Rnaset mini plus kit (Qiagen). 1 ug of total RNA was used for the library prep

treatment_protocol: Both L1475 and A549 was expressed OSKM fators, TA was plasmid control

tag: tissue

value: lung

tag: cell line

tag: cell type

value: cell line

tag: treatment

value: OSKM expressing


title: day1_4F1


title: ATAC_P2_nonIR_rep2

city: New York

first: Richard

last: Koche

state: New York

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to mouse assembly mm10 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001 and then filtered for blacklisted regions.
The BEDTools suite was used to create normalized bigwig files scaled by the size factors from DESeq2 normalization of the raw counts matrix.
Assembly: mm10
Supplementary files format and content: normalized bigwigs

molecule: genomic DNA

source_name: cerebellum

growth_protocol: Nestin-expressing progenitors were FACS isolated from fresh cerebellum (2-3 cerebella pooled/sample) at P2 from nonIR and IR Nestin-Cfp/+ pups. Briefly, tissue was dissociated with Accutase and CFP+ cells were FACS isolated. ~30,000-50,000 cells were immediately processed using the Omni-ATAC protocol.

extract_protocol:
OMNI-ATAC protocol and ATAC-seq library preparation was performed as described in (Corces et al, 2017) without any modification.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Injury was performed using a single dose of 4Gy gamma-irradiation targeted to the hindbrain of postnatal day 1 old pups.

value: cerebellum

tag: Sex

value: male

value: FACS-isolated nestin-expressing progenitors (NEPs) directly from cerebellum

tag: time

value: Postnatal day (P)2

value: nonIR (control)


title: PBMCs, Korean cohort, B002_L001, H014

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

source_name: blood


title: PBMCs, Korean cohort, B002_L001, H015


title: ATAC_P2_nonIR_rep1


title: PBMCs, Korean cohort, B002_L001, H013


title: LH143

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
Image analysis was performed  in real time by the NovaSeq Control Software (NCS) v.1.7.0 and Real Time Analysis (RTA) v.3.4.4
The Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data
Read libraries were mapped to the mouse genome (GRCm38) using HISAT
Gene-level quantification (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Genome_build: GRCm38
Supplementary_files_format_and_content: genecounts.txt contain a matrix of raw gene counts (unfiltered and un-normalised data)

extract_protocol:
Lung tissue was placed in RNAlater (Ambion, Life Technologies, Mulgrave, VIC, Australia), and frozen at -80C. Total RNA was extracted with TRIzol (Ambion, Life Technologies, Mulgrave, VIC, Australia) followed by RNAeasy (QIAGEN) as per manufacturer's instructions. Library preparation and sequencing were performed by the Australian Genome Research Facility (AGRF).
RNA libraries were prepared by AGRF for sequencing using TruSeq Stranded mRNA (single end, 100bp).

tag: strain

value: BALB/c

tag: experimental group

tag: timepoint

value: Female

tag: rna integrity number


title: day3_4F2


title: PBMCs, Korean cohort, B002_L001, H012


title: LH142

value: Male


title: ATAC_P2_IR_rep2

value: IR (irradiated at postnatal day 1)


title: ATAC_P2_IR_rep1


title: PBMCs, Korean cohort, B002_L001, H011


title: LH141


title: PBMCs, Korean cohort, B002_L001, H010


title: LH140

value: PBS


title: Organoid_PBS_rep2

city: Urbana

first: Ruicheng

last: Shi

state: IL

address: 2001 South Lincoln Avenue, room 36122

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Fastq files were aligned mouse reference genome GRCm39 using STAR STAR2.7.10b
The count matrix were generated using Rsubread featurecount and the differentially expressed genes were analyzed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited txt file (normalized read count table), normalized by median of ratios

source_name: small intestine crypt derived organoids

extract_protocol:
Total RNA was isolated from organoids using TRIzol per manufacturer's instruction
Ribosomal RNA was removed with the Ribozero kit (Illumina). The RNAseq libraries were prepared with TruSeq Stranded mRNAseq Sample Prep kit (Illumina).

value: small intestine crypt derived organoids

tag: genotype

value: WT


title: day1_TA1

value: control


title: PBMCs, Korean cohort, B002_L001, H009

value: blood

value: PBMCs


title: Organoid_LDL_rep3

value: LDL-treated


title: LH139

value: lung


title: PBMCs, Korean cohort, B002_L001, H007


title: Organoid_LDL_rep2


title: LH144


title: LH138


title: PBMCs, Korean cohort, B002_L001, H006


title: LH137


title: Organoid_PBS_rep1


title: LH136


title: Organoid_LDL_rep1


title: SEG, SOX17 mAb, rep2

city: Chapel Hill

first: Li

last: Qian

state: North Carolina

address: 111 Mason Farm Road, MBRB

department: Department of Pathology

institute: UNC

data_processing:
read alignment by BWA
Peak detection by Picard and MACS
Different peak expression using DiffBind
Assembly: mm10
Supplementary files format and content: bigWig

source_name: heart

growth_protocol: Lonza EGM2 media

extract_protocol:
ChIP-IT High Sensitivity (Active Motif #53040)
Novogene ChIPseq library prep

treatment_protocol: retroviral infection of select samples

value: heart

value: iEC

tag: chip antibody

value: Abcam #ab224637


title: Organoid_PBS_rep3


title: LH135


title: LH134


title: SEG, SOX17 mAb, rep1


title: PBMCs, Korean cohort, B002_L001, H003


title: LH133


title: Sox17 only, input, rep2


title: LH132


title: MEFs treated with doxycycline, Day 1, ATAC-seq

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

data_processing:
Reads were trimmed to 50 bp using the Trimmomatic tool (Bolger et al., 2014) in The Galaxy suite (Galaxy Community, 2022).
Sequencing reads were mapped to the mm10 version of the mouse genome using the Bowtie2 algorithm (Langmead & Salzberg, 2012) with the ‘very sensitive end to end option’.
The Samtools Fixmate command was used (Li et al, 2009) prior to duplicate removal with the MarkDuplicates command from Picard tools using the option ‘do not write duplicates to the output file’.
Reads from all samples were downsampled to the same sequencing depth using the Downsample BAM option from Picard tools.
Peaks were called using the MACS2 algorithm (Zhang et al, 2008) with the options ‘no model’, ‘extension-200’, ‘shift-100’ and a q-value cutoff of 0.05.
Bigwig files were constructed using the bamCoverage command from the Deeptools suite (Ramírez et al, 2014).
Assembly: mm10
Supplementary files format and content: The "ATAC-seq_peaks_XXX".bed files are bed-format files containing the ATAC-seq peaks, produced by the MACS2 algorithm, as described above.
Supplementary files format and content: The "ATAC-seq_XXX.bigwig" files are bigwig files, produced by bamCoverage command from the Deeptools suite, as described above.

source_name: Mouse Embryonic Fibroblasts (MEFs)

growth_protocol: MEFs (Mouse Embryonic Fibroblasts) were cultured at 37ο C and 5% CO2 concentration, in high-glucose DMEM (Sigma-Aldrich, D6429) supplemented with heat-inactivated FBS at 10% final concentration (Pan Biotech, P30-1985), 1x GlutaMAX™ Supplement (Gibco™, 35050-061), 1x MEM Non-Essential Amino Acids Solution (Gibco™, 11140-050) and Penicillin-Streptomycin mix (Gibco™, 15140-122) diluted at 1/100. For cellular reprogramming MEF medium was used, as described above, but supplemented with 15% FBS. The medium was refreshed every two days. Bruce-4 Embryonic Stem Cells (ESCs) were cultured in complete ESC medium [Knock Out DMEM (Gibco, Cat. No. 10829018), 20% ES-tested FBS (Pansera, Cat. No. P30-2602), Penicillin/Streptomycin 1X (Thermo Fischer Scientific, Cat. No. 15140122), GlutaMAX 1X (Gibco, Cat. No. 35-050-061). Non-Essential Amino Acids 1X (Gibco, Cat. No. 11140050) and mLIF 20ng/mL (Santa Cruz Biotechnology, sc-4378).

extract_protocol:
ATAC-seq libraries from different timepoints were prepared starting from 50,000 cells, following previously published protocols (Buenrostro et al, 2013, 2015; Ackermann et al, 2016; Corces et al, 2017). Briefly, cell pellets were lysed in Lysis Buffer [10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin (Promega, G9441)] for 3 min on ice, washed with Wash Buffer [10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20] and centrifuged at 500g for 10 min at 4o C.
Each pellet (nuclei) was resuspended in 50ul Transposition reaction mix [1x Tagment DNA Buffer (Illumina, 15027866), 16.5ul 1x PBS, 0.1% Tween-20, 0.01% Digitonin (Promega, G9441), 2.5ul Tn5 Transposase (Tagment DNA Enzyme 1, Illumina, 15027865)] and incubated at 37o C for 30 min on a thermomixer at 1000rpm. DNA purification was performed using the Qiagen MinElute Reaction Cleanup Kit (Qiagen, 28204). Library purification was performed with the AMPure XP beads (Beckman Coulter, A63880). The quality of libraries was assessed using an Agilent 2100 Bioanalyzer and libraries were quantified with the Qubit™ High Sensitivity (HS) spectrophotometric method (Invitrogen). Libraries were sequenced paired-end using a NovaSeq 6000 sequencer at the Greek Genome Center at BRFAA.

treatment_protocol: MEFs were plated in 10cm plates and reprogramming was initiated after 24 hours (day 0) with the addition of doxycycline (DOX) at 2ug/ml (Sigma-Aldrich, D9891) for OKSM transgene expression induction. The Day 0 and ESCs sample were not treated with doxycycline.

value: Mouse Embryonic Fibroblasts (MEFs)

value: MEFs treated with doxycycline at 2ug/ml for 1 day


title: PBMCs, Korean cohort, B002_L001, H008


title: Sox17 only, SOX17 mAb, rep2


title: PBMCs, Korean cohort, B002_L001, H001


title: PBMCs, Korean cohort, B002_L001, H002


title: Sox17 only, input, rep1


title: LH131

value: BALB/c


title: LH130


title: PBMCs, Caucasian, B001_L001, LONZA3038016

data_processing:
The DRAGEN Single-Cell RNA pipeline in the Illumina DRAGEN v3.8.4 software (version 07.021.602.3.8.4-20-g74395e76) was used for pre-processing of paired-end FASTQ files from each individual scRNA-seq gene expression library. Reads from each pool were mapped to GENCODE Release 32 (GRCh38, Ensembl 98, date 2019-09-05).  The count data was processed and analyzed in R. Within each pool, every cell (barcode) and read was assigned to an individual within that pool using Genotype Data (provided) in DRAGEN v3.8.4.
Assembly: GRCh38/hg38
Supplementary files format and content: Single-cell expression data were processed using *rds file containing single cell expression and metadata matrix.


title: Sox17 only, SOX17 mAb, rep1


title: LH129

value: Female


title: PBMCs, Japanese cohort, B001_L001, H015


title: SEG, input rep1


title: SEG, input rep2


title: PBMCs, Japanese cohort, B001_L001, H013


title: LH127


title: PBMCs, Japanese cohort, B001_L001, H014


title: PBMCs, Korean cohort, B002_L001, H005


title: LH128

value: Male


title: PBMCs, Korean cohort, B002_L001, H004


title: PBMCs, Japanese cohort, B001_L001, H012


title: PBMCs, Japanese cohort, B001_L001, H011


title: SEG, ERG mAb, rep1

value: Abcam #ab133264


title: LH125


title: Erg only, input, rep2


title: SEG, ERG mAb, rep2


title: LH124


title: LH126


title: PBMCs, Japanese cohort, B001_L001, H010


title: Erg only, ERG mAB, rep2


title: LH123


title: PBMCs, Japanese cohort, B001_L001, H009


title: Erg only, input, rep1


title: LH122

value: PBS


title: PBMCs, Japanese cohort, B001_L001, H008


title: Erg only, ERG mAB, rep1


title: PBMCs, Japanese cohort, B001_L001, H007


title: SEG, d7, rep3

data_processing:
Transcript expression was quantified using Salmon
DESeq2 was used to compare gene expression between conditions at each timepoint
Assembly: mm10
Supplementary files format and content: csv file of DESeq2 counts of all samples

growth_protocol: EGM2 media

extract_protocol:
Rneasy mini ket
Novogene mRNA

value: Day 7


title: LH120


title: PBMCs, Japanese cohort, B001_L001, H006


title: PBMCs, Japanese cohort, B001_L001, H005


title: PBMCs, Japanese cohort, B001_L001, H004


title: SEG, d7, rep2


title: LH119


title: SEG, d3, rep3

value: Day 3


title: PBMCs, Japanese cohort, B001_L001, H003


title: LH116


title: PBMCs, Japanese cohort, B001_L001, H001


title: PBMCs, Japanese cohort, B001_L001, H002


title: LH118


title: SEG, d3, rep2


title: LH115


title: Sox17, d7, rep3


title: LH114


title: Sox17, d7, rep2


title: TMEM88 KD time course, GEX

city: St Lucia

first: Sophie

last: Shen

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Bioscience

institute: The University of Queensland

data_processing:
Raw BCL files generated by Illumina sequencers were demultiplexed into FASTQ files using cellranger mkfastq, which wraps Illumina's bcl2fastq software (cellranger version 3.0.2 and bcl2fastq v2.19.0.316). The cellranger count pipeline was used to align, filter and count barcodes and UMIs from the fastq files to generate feature-barcode (raw count) matrices.
For barcoded samples, barcode sequences were both appended to the GrCh38 reference genome with "BC01-18" identifiers to allow their expression to be recognised as custom "gene" expression, as well as sequenced as independent libraries with exclusively the barcode sequences as the reference. For HTO libraries, CITE-seq-Count was used to generate a count matrix for the hashing reads from the fastq files.
Cellranger aggr was used in the analysis for comparing the three time course datasets.
For sample demultiplexing, 'HTODemux' from the Seurat package in R was used for both HTO and barcode (BC) demultiplexing. Doublets identified from 'HTODemux' and the scds doublet detection package were removed. The Seurat package was also used for cell filtering and count normalisation. Where relevant, the R package RISC was used for dataset integration. See methods for further details and downstream analysis.
Assembly: GrCh38, BC reference file
Supplementary files format and content: All files containing 'raw_count' and 'raw_barcode' in the name are direct output from cellranger count, which provides three files: cell barcodes (*barcodes.tsv.gz), gene names (*features.tsv.gz) and the count matrix (*matrix.mtx.gz).
Supplementary files format and content: Files containing "raw_hto" in the name are direct output from CITE-seq-count, which provides three files: cell barcodes (*barcodes.tsv.gz), HTO barcode sequence (*features.tsv.gz) and the HTO count matrix (*matrix.mtz.gz)
Supplementary files format and content: Supplemental files containing "integrated_sig_time" are from RISC integration of raw counts from the three signalling dataset libraries and the control time course dataset after cell filtering as detailed in the methods. The .mtx file contains batch-corrected (integrated) and normalised values. The metadata file additionally contains cell type annotations with reference to three in vivo datasets (columns "PijuanSala_LabelTransfer", "Hutchins_CTDomains" and "Tyser_GastrulaLT". See methods for more details), as well as final clusters, annotations, and anchor genes presented in the accompanying manuscript.
Supplementary files format and content: Supplemental files containing "integrated_tm88" are from RISC integration of raw counts from cellranger aggr processing of the three time course datasets and cell quality filtering as detailed in the methods. The .mtx file contains batch-corrected (integrated) and normalised values. The metadata additionally contains label transfer results against one in vivo dataset (column: "LT_PijuanSala2019"), initial cell clusters, filtered cell clusters, as well as final cell type annotations, marker genes, and anchor genes presented in the accompanying manuscript.
Supplementary files format and content: Supplemental files "barcode.fa" and "barcode.gtf" are the fasta and gtf files added to the GrCh38 genome reference for the samples utilising the barcoded iPSC lines for sample multiplexing. The barcode.fa file contains more sequence flanking each of the unique 15bp barcodes in each cell line for better mapping.

source_name: WTC CRISPRi TMEM88-g2.3 hiPSCs (WTC CRISPRi GCaMP background/RRID: CVCL_VM38)

growth_protocol: Mesendoderm directed iPSC differentiation protocol (used as the control in this study) was adapted from a small molecule-directed cardiomyoycte differentiation protocol (https://doi.org/10.1038/nmeth.2999). In brief, undifferentiated cells are cultured in mTeSR+ pluripotency media and seeded onto vitronectin-coated plates the day prior to differentiation (day -1) with ROCK inhibitor to promote survival. The following day, once cells have formed an ~80% confluent monolayer, differentiation is induced (day 0) by changing culture media to RPMI containing 3uM CHIR99021 (small molecule Wnt agonist), 500mg/mL bovine serum albumin (BSA), and 213mg/mL ascorbic acid (AA). Media is changed every second day, maintaining the RPMI, BSA and AA backbone until day 7 and onwards where the BSA and AA are replaced with 1x B27 supplement plus insulin.

extract_protocol:
Cells were dissociated with EDTA/Trypsin. For hashtagged samples, 1e6 cells were stained with their corresponding TotalSeq-A anti-human Hashtag antibody (see HTO antibody details above). Cells were sorted for viability using propidium iodide before being pooled for 10X Genomics Chromium Single Cell 3' V3 capture, targeting 2e4 cells.
mRNA libraries were constructed according to manufacturer's instructions (Chromium Single Cell 3' V3). The barcoding (BC) libraries were generated from a portion of the cleaned up full length amplified cDNA from each mRNA sample pool. In brief, the cDNA regions containing the barcode cassette were amplified and partial P5 and P7 sequencing adaptors were appended in one round of PCR. After clean-up to remove primers, additional PCR was performed as per the SI-PCR protocol in the Chromium gene expression library construction workflow  with a unique i7 indexed R primer from Chromium i7 Multiplex Kit for a total of 14 cycles. For more details, see methods. The HTO libraries were generated following additional methods from Stoeckius et al., (2018) to capture the fraction of droplets containg HTO-derived cDNA and generate the hashing libraries.

treatment_protocol: Treatments in the signalling dataset were each added to the differentiation media on day 3 and removed on day 5 of differentiation. Likewise, the XAV treatment for the XAV-treated time course dataset was also added to the differentiation backbone media on day 3 and removed on day 5. For the TMEM88 knockdown sample, doxycycline was added from day 0 of differentiation for the entire duration to induce the tetracycline-inducible CRISPRi-mediated TMEM88 knockdown of expression.

value: WTC CRISPRi TMEM88-g2.3 hiPSCs (WTC CRISPRi GCaMP background/RRID:CVCL_VM38)

value: mesendoderm derivatives

value: TMEM88 knockdown

tag: library type

value: mRNA


title: SEG, d3, rep1


title: LH121

value: lung


title: Sox17, d7, rep1

value: heart


title: Control time course, GEX

value: Control


title: Sox17, d3, rep3

value: iEC


title: LH112


title: XAV-treated time course, GEX

value: 5uM XAV-939 treatment


title: LH111


title: SEG, d7, rep1


title: Sox17, d3, rep2


title: Sox17, d3, rep1


title: LH109


title: LH110


title: Signalling perturbations library 2, GEX

source_name: barcoded hiPSCs (WTC WT background/RRID: CVCL_Y803)

value: barcoded hiPSCs (WTC WT background/RRID:CVCL_Y803)

value: See barcoding details above


title: Signalling perturbations library 3, BC

value: BC


title: Erg, d7, rep3


title: LH108

value: BALB/c

value: Male


title: Signalling perturbations library 2, BC


title: Signalling perturbations library 1, GEX


title: Erg, d7, rep1


title: LH107

value: Female


title: LH106


title: Signalling perturbations library 1, BC


title: LH113


title: Signalling perturbations library 3, GEX


title: Erg, d3, rep3


title: Erg, d3, rep2


title: LH105


title: hc35_RNA

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

description: 10x Genomics v3.1 snRNA-seq

data_processing:
Raw sequencing was processed using cellranger-arc (10x Genomics), generating snRNA-seq UMI count matrices for intronic and exonic reads mapping in the sense direction of a gene for hg38 GRCh38 human genome assembly and Gencode v32 gene annotations.
We performed unsupervised clustering with RNA UMI counts using Seurat v5 integrative analysis pipeline. First, cell barcodes were filtered for low quality nuclei by requiring ≥ 500 ATAC fragments, > 5 TSS enrichment (GRCh38 GENCODE v46) using SnapATAC2, ≥ 200 genes detected per nuclei.
Assembly: hg38 GRCh38
Supplementary files format and content: The raw_feature_bc_matrix.h5 is a Cell Ranger output that includes feature-barcode matrices containing cellular, non-cellular, and background barcodes.
The atac_fragments.tsv.gz is a Cell Ranger output that contains one line per unique fragment. And the atac_fragments.tsv.gz.tbi is the Tabix index for the fragment file.
hippocampus_RNA_seurat_object_filtered_cells.h5: Seurat object after quality control
hippocampus_RNA_seurat_object_filtered_cells_metadata.tsv: cell metadata for the Seurat object

source_name: hippocampus

extract_protocol:
Frozen brain tissue was pulverized using a mortar and pestle on dry ice and pre-chilled with liquid nitrogen. Pulverized brain tissue was resuspended in 1mL of chilled NIM-DP-L buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1X Protease Inhibitor (Pierce), 1U/μL Recombinant RNase inhibitor (Promega, PAN2515), and 0.1% Triton X-100). Tissue was Dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until solution was uniform. Nuclei were filtered using a 30μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021) and pelleted (1000 rcf, 10 min at 4˚C) (Eppendorf, 5920 R). Pellet was resuspended in 1 mL NIM-DP buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1x Protease Inhibitor, 1U/μL Recombinant RNase inhibitor) and pelleted (1000 rcf, 10 min at 4˚C). Pelleted nuclei were resuspended in 400uL 2μM 7-AAD (Invitrogen, A1310) in Sort Buffer (1mM EDTA, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor, 1% fatty acid-free BSA in PBS). 120,000 nuclei were sorted (Sony, SH800S) into a LoBind tube containing Collection Buffer (5U/uL Recombinant RNase inhibitor, 1X Protease Inhibitor, 5% fatty acid-free BSA in PBS). 5X Permeabilization Buffer (50mM Tris-HCl pH 7.4, 50mM NaCl, 15mM MgCl2, 0.05% Tween-20, 0.05% IGEPAL, 0.005% Digitonin, 5% fatty acid-free BSA in PBS, 5mM DTT, 1U/μL Recombinant RNase inhibitor, 5X Protease Inhibitor) was added for a final concentration of 1X. Nuclei were incubated on ice for 1 minute, then centrifuged (500 rcf, 5min at 4C). Supernatant was discarded and 650uL of Wash Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1%.Tween-20, 1% fatty acid-free BSA in PBS, 1mM DTT, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor) was added without disturbing the pellet followed by centrifuging (500 rcf, 5 min at 4˚C). Supernatant was removed, and the pellet was resuspended in 7uL of 1X Nuclei Buffer (Nuclei Buffer (10x Genomics), 1mM DTT, 1 U/μL Recombinant RNase inhibitor). 1 μL of nuclei was diluted in 1X Nuclei Buffer, stained with Trypan Blue (Invitrogen, T10282) and counted. 16-20k nuclei were used for tagmentation reaction and controller loading.
Libraries were generated following manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression). 10x multiome ATAC-seq and RNA-seq libraries were paired-end sequenced on NextSeq 500 and NovaSeq 6000 to a depth of ~50,000 reads per cell for each modality.
snATAC-seq
snRNA-seq

value: hippocampus

tag: donor id


title: LH104

value: PBS


title: hc9_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc212191_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH103


title: control, d7, rep3

value: fibroblast

value: Day 7


title: hc40_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH102


title: LH101


title: hc19_RNA

description: 10x Genomics v3.1 snRNA-seq


title: control, d7, rep2


title: LH100


title: hc26_RNA

description: 10x Genomics v3.1 snRNA-seq


title: Erg, d7, rep2


title: LH117


title: control, d3, rep3

value: Day 3


title: LH099


title: hc73_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH098


title: control, d3, rep2


title: control, d3, rep1


title: hc12_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH097


title: hc11_RNA

description: 10x Genomics v3.1 snRNA-seq


title: Erg, d3, rep1


title: Lung

city: Kumamoto

first: Ken

last: Takashima

state: Kumamoto

address: 1-1-1, Honjo, Chuo-ku

department: Department of Immunology

country: Japan

institute: Kumamoto University

data_processing:
Raw sequencing data were processed and the reads were aligned to the mouse genome (mouse mm10; refdata-gex-mm10-2020-A), and then gene expression were quantificatted by Cell Ranger (ver7.1.0) software.
Assembly: mouse mm10
Supplementary files format and content: .tsv, .mtx

source_name: Lung

extract_protocol:
Lung tissue was fixed with formaldehyde and dissociated with gentleMACS Octo Dissociator (Miltenyi Biotec). After hybridizing the detection probe of the Chromium Fixed RNA Kit for mouse transcriptome (10x Genomix) to intracellular RNA, a ligation reaction was performed to join the hybridized probes. After mixing each sample so that the number of cells is equal, the barcoded primer beads and cells are encapsulated using Chromium Next GEM Chip Q Single Cell Kit on Chromium X (10x Genomix). The probe and primer are annealed, and an extension reaction is performed to create a detection probe.
The library was prepared by PCR amplification and purification using indexed primers included in Dual Index Kit TS Set A (10x Genomix).

treatment_protocol: DMSO and Pitavastatin：WT mice were intraperitoneally injected with 8 uL DMSO or pitavastatin calcium solution in 200 ul of PBS (pitavastatin final: 10 mg/kg/day) in for three days.  Lung tissue were harvested, snap frozen in a liquid nitrogen and stored at -80 deg. WT and Ob：From 13 weeks female WT and Ob/OB mice, lung tissue were harvested, snap frozen in a liquid nitrogen and stored at -80 deg.

value: Lung

value: multiplexed/mixed


title: LH096

value: lung


title: m_VC_3

city: Changsha

first: Lihua

last: Xie

address: No.138, Tongzipo Road

country: China

institute: The Third Xiangya Hospital of Central South University

data_processing:
RNA-Seq: Sequencing quality was examined by FastQC; Sequence reads were trimmed for 5' and 3' junction sequences and filtered for too short fragments (≤20bp) using cutadapt; Trimmed sequence reads was mapped to CrCM38/mm10 using StringTie software; Transcript abundance calculations were performed by Ballgown and expression was expressed as FPKM.
tsRNA-Seq: Sequencing quality are examined by FastQC ; After Illumina quality control, the sequencing reads were 5' , 3' -adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt; Trimmed reads are aligned allowing for 1 mismatch only to the  mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software; The abundance of tRF & tiRNA is evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes tsRNA raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes tsRNA CPM for each Sample
Supplementary files format and content: tab-delimited text file includes gene FPKM for each Sample

extract_protocol:
Total RNA was extracted by Trizol. Total amount of 1.5 ug RNA per sample was used as input material for the RNA sample preparations.For tsRNA：total RNA samples are pretreated to remove some RNA modifications that  interfere with small RNA-seq library construction.
For RNA-Seq: Total RNA samples were processed by oligo dT enrichment (rRNA removal) and then KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used to construct the library, and Agilent 2100 was used for quality control. For tsRNA-Seq, the extracted total RNA was subjected to pretreatment using the rtStar™ TRF&tiRNA pretreatment kit (Arraystar, USA) and then sequencing libraries was  prepared utilized the rtStar™ FirstStrand cDNA synthesis kit (3ʹ and 5ʹ adapters) (Arraystar, USA) .

treatment_protocol: Treatment groups: Control, COPD, tail vein injection of BMSCs (VC) . Intervention: Combined cigarette smoke (CS) exposure and intraperitoneal injection of cigarette smoke extract (CSE) for COPD induction, tail vein injection of BMSCs Dosage: 4×10^6 BMSCs + 100 μl PBS. Control and COPD group received corresponding amount of PBS

value: MSCs treatment


title: LH095


title: hc98_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH094


title: m_VC_1


title: hc69984_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc1216_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc1203_RNA

description: 10x Genomics v3.1 snRNA-seq


title: m_VC_2


title: control, d7, rep1

value: heart


title: LH093


title: m_COPD_3

value: COPD model


title: hc1153_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc1271_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH092


title: m_COPD_2


title: LH091


title: m_COPD_1


title: hc8_RNA

description: 10x Genomics v3.1 snRNA-seq


title: m_Con_3

value: Control


title: hc1265_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH090


title: m_Con_1


title: hc46426_RNA

description: 10x Genomics v3.1 snRNA-seq


title: m_Con_2


title: LH088


title: LH089


title: CD8 enriched, sgTmed10, biol rep4

city: Amsterdam

first: Daniel

last: Peeper

state: Outside the US or Canada

address: Plesmalaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Raw read counts were aligned to mouse reference genome GRCm38 Ensembl version 69 using STAR (v2.7.1a) using two-pass mode and default settings. Differentially expressed genes were identified by DESeq2 (v1.24). Gene ontology term enrichment of biological process gene sets was performed on significantly differentially expressed genes (FDR < 0.05) using Panther (v16.0)10999. This list was then used as input for REVIGO 8176. Representative GO terms were then analyzed for directionality by gene set enrichment analysis using GSEA software (v4.1.0). For RNA sequencing analyses for the ACT experiment, analyses were performed for each isolation condition separately (input, tumor digest and CD8-enriched fractions). Genes with summed counts lower than 10 within one isolation condition were excluded from analysis.
Assembly: Raw read counts were aligned to mouse reference genome GRCm38 Ensembl version 69
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Tumor digest, CD8+ T cell enriched

growth_protocol: 0.5 x 106 B16F10-OVA cells were injected in both flanks of C57BL/6 mice and allowed to establish for four days. After four days, mice were randomized and administered PBS (mock), or two million sgCtrl or sgTmed10 CD8 T cells (which were generated as per above) by intravenous tail injection. Mice received 1E5 units of human IL-2 (Clinigen) twice-daily for three days after ACT by intraperitoneal injection. Tumor growth was followed by measuring tumor volume three times weekly by calipers, where tumor volume is calculated with the formula: "length " ("mm" )" × width (mm)" /"2" . Seven days after ACT, sentinel tumors were harvested. The rest of the mice were followed until the total tumor volume exceeded 1500mm3. Mice were given ad libitum access to drinking water, chow and a nutritionally fortified water gel (DietGel). Tumors were harvested and cut into ±0.5mm2 pieces and incubated in 5mL dissociation medium (RPMI with 10U/mL DNAse I and 200U/mL collagenase type IV) at 37°C for one hour while shaking. After dissociation, tumor preparations were then mashed subsequently through 100μm and 70μm cell strainers (Corning) and washed (addition of buffer, followed by centrifugation at 1000 x g for five minutes) in PBS (Gibco) containing 0.1% bovine serum albumin (BSA, Sigma; isolation buffer) before being resuspended and incubated in red blood cell lysis buffer (155mM NH4Cl, 10mM NaHCO3, 0.1mM EDTA in distilled water; all Sigma) for five minutes. Tumor samples were then washed twice in isolation buffer, before being used in downstream experiments as described above. CD8 cells were isolated from these tumor samples using the Dynabeads™ FlowComp™ Mouse CD8 Kit (Thermo Fisher Scientific) following manufacturer’s instructions.

extract_protocol:
RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were not otherwise treated.

value: Tumor digest, CD8+ T cell enriched

value: CD8T cells OT-I/Cas9


title: hc6021_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc73787_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH085

value: BALB/c


title: hc5551_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH087


title: CD8 enriched, sgTmed10, biol rep2


title: LH086

value: Male


title: LH084


title: CD8 enriched, sgTmed10, biol rep1


title: LH083

value: Female


title: hc5610_RNA

description: 10x Genomics v3.1 snRNA-seq

value: hippocampus


title: CD8 enriched, sgCtrl, biol rep4

value: sgCtrl


title: CD8 enriched, sgCtrl, biol rep3


title: LH082


title: LH081


title: hc1745_RNA

description: 10x Genomics v3.1 snRNA-seq


title: CD8 enriched, sgCtrl, biol rep2


title: LH080

value: PBS


title: CD8 enriched, sgCtrl, biol rep1


title: hc5087_RNA

description: 10x Genomics v3.1 snRNA-seq


title: Tumor digest, sgTmed10, biol rep 4

source_name: Tumor digest

value: Tumor digest

value: B16F10-OVA tumor digest

value: sgTmed10 (CD8 Tcells)


title: LH078


title: Tumor digest, sgTmed10, biol rep 3


title: LH079


title: CD8 enriched, sgTmed10, biol rep3


title: hc5021_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc1134_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH077


title: LH075


title: Tumor digest, sgTmed10, biol rep 1


title: Tumor digest, sgTmed10, biol rep 2


title: LH074


title: Tumor digest, sgCtrl, biol rep 3

value: sgCtrl (CD8 Tcells)


title: hc13344_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc81_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH073

value: lung


title: hc935_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc13394_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc5614_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH072


title: Pre-inject, sgTmed10, biol rep 3

source_name: CD8+ T cells

value: CD8+ T cells


title: hc6052_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH076


title: LH070


title: LH071


title: Pre-inject, sgTmed10, biol rep 2


title: hc13414_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH069


title: Pre-inject, sgTmed10, biol rep 1


title: hc76_RNA

description: 10x Genomics v3.1 snRNA-seq


title: Tumor digest, sgCtrl, biol rep 1


title: hc5579_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc78_RNA

description: 10x Genomics v3.1 snRNA-seq


title: LH067


title: Pre-inject, sgCtrl, biol rep 2


title: Tumor digest, sgCtrl, biol rep 2


title: hc77_RNA

description: 10x Genomics v3.1 snRNA-seq


title: Pre-inject, sgCtrl, biol rep 1


title: LH066


title: LH065


title: hc4781_RNA

description: 10x Genomics v3.1 snRNA-seq


title: High Five cells, CCI3 72hpi, replicate 3

city: Shanghai

first: Rui

last: Min

state: Shanghai

address: meilong road 130,Shanghai,China

institute: East China University of Science and Technology

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Assembly: 7111
Supplementary files format and content: txt

organism: Trichoplusia ni

source_name: Ovarian

extract_protocol:
RNA concentration was measured using NanoDrop 2000(Thermo). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligoattached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Ovarian

value: High Five

value: Ovarian epithelial cells

value: WT

value: Infected under CCI3, 72 hpi


title: LH064

value: BALB/c


title: hc35_ATAC

description: 10x Genomics snATAC-seq

library_source: genomic single cell


title: hc29_RNA

description: 10x Genomics v3.1 snRNA-seq


title: High Five cells, CCI3 72hpi, replicate 2


title: LH063


title: hc212191_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, CCI3 72hpi, replicate 1


title: hc40_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, CCI1 72hpi, replicate 3

value: Infected under CCI1, 72 hpi


title: LH062

value: Male


title: hc26_ATAC

description: 10x Genomics snATAC-seq

value: hippocampus


title: High Five cells, CCI1 72hpi, replicate 2


title: hc19_ATAC

description: 10x Genomics snATAC-seq


title: Pre-inject, sgCtrl, biol rep 3

value: CD8T cells OT-I/Cas9

value: sgCtrl


title: LH068

value: PBS


title: LH061

value: Female


title: LH060


title: hc9_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, CCI1 72hpi, replicate 1


title: hc73_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, CCI3 24hpi, replicate 3

value: Infected under CCI3, 24 hpi


title: LH059


title: hc12_ATAC

description: 10x Genomics snATAC-seq


title: hc11_ATAC

description: 10x Genomics snATAC-seq


title: LH058


title: High Five cells, CCI3 24hpi, replicate 1


title: High Five cells, CCI3 24hpi, replicate 2


title: Tumor digest, sgCtrl, biol rep 4

value: Tumor digest

value: B16F10-OVA tumor digest

value: sgCtrl (CD8 Tcells)


title: LH056

value: lung


title: High Five cells, CCI3 12hpi, replicate 3

value: Ovarian

value: High Five

value: Infected under CCI3, 12 hpi


title: hc98_ATAC

description: 10x Genomics snATAC-seq


title: LH055


title: High Five cells, CCI3 12hpi, replicate 1

value: Ovarian epithelial cells

value: WT


title: LH053

value: BALB/c


title: hc1203_ATAC

description: 10x Genomics snATAC-seq


title: hc69984_ATAC

description: 10x Genomics snATAC-seq


title: LH052

value: Male


title: hc1153_ATAC

description: 10x Genomics snATAC-seq

value: hippocampus


title: High Five cells, CCI3 6hpi, replicate 2

value: Infected under CCI3, 6 hpi


title: LH051


title: hc8_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, CCI3 6hpi, replicate 1


title: LH057


title: LH050


title: High Five cells, CCI1 24hpi, replicate 3

value: Infected under CCI1, 24 hpi


title: High Five cells, CCI1 24hpi, replicate 2


title: hc46426_ATAC

description: 10x Genomics snATAC-seq


title: hc1265_ATAC

description: 10x Genomics snATAC-seq


title: LH048


title: High Five cells, CCI1 24hpi, replicate 1


title: High Five cells, CCI1 12hpi, replicate 3

value: Infected under CCI1, 12 hpi


title: hc73787_ATAC

description: 10x Genomics snATAC-seq


title: hc1216_ATAC

description: 10x Genomics snATAC-seq


title: LH054


title: hc13394_ATAC

description: 10x Genomics snATAC-seq


title: LH047

value: Female


title: High Five cells, CCI3 6hpi, replicate 3


title: hc1271_ATAC

description: 10x Genomics snATAC-seq


title: LH046


title: High Five cells, CCI1 12hpi, replicate 1


title: hc6021_ATAC

description: 10x Genomics snATAC-seq


title: LH044

value: PBS


title: High Five cells, CCI1 12hpi, replicate 2


title: hc5551_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, CCI1 6hpi, replicate 3

value: Infected under CCI1, 6 hpi


title: LH049


title: hc81_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, CCI1 6hpi, replicate 1


title: LH042


title: hc5610_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, 84h, replicate 3

value: culture 84 h


title: High Five cells, CCI1 6hpi, replicate 2


title: hc937_RNA

description: 10x Genomics v3.1 snRNA-seq


title: hc1745_ATAC

description: 10x Genomics snATAC-seq


title: LH041


title: LH043


title: hc4781_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, 84h, replicate 2


title: High Five cells, 84h, replicate 1


title: hc5087_ATAC

description: 10x Genomics snATAC-seq


title: LH038


title: High Five cells, 60h, replicate 3

value: culture 60 h


title: hc5021_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, 60h, replicate 2


title: LH037

value: lung


title: hc13414_ATAC

description: 10x Genomics snATAC-seq


title: LH039


title: High Five cells, 60h, replicate 1

value: Ovarian


title: LH036


title: hc937_ATAC

description: 10x Genomics snATAC-seq


title: LH035


title: High Five cells, 36h, replicate 3

value: High Five

value: culture 36 h


title: hc935_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, 36h, replicate 2

value: Ovarian epithelial cells


title: LH040


title: LH034


title: LH033


title: High Five cells, 36h, replicate 1

value: WT


title: LH032

value: BALB/c


title: hc5614_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, 12h, replicate 3

value: culture 12 h


title: LH031


title: High Five cells, 12h, replicate 2


title: hc6052_ATAC

description: 10x Genomics snATAC-seq

value: hippocampus


title: hc29_ATAC

description: 10x Genomics snATAC-seq


title: High Five cells, 12h, replicate 1


title: High Five cells, CCI3 12hpi, replicate 2

value: Infected under CCI3, 12 hpi


title: hc5579_ATAC

description: 10x Genomics snATAC-seq


title: hc76_ATAC

description: 10x Genomics snATAC-seq


title: LH028

value: Male


title: LH027


title: hc78_ATAC

description: 10x Genomics snATAC-seq


title: 42 SAM24413632

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

data_processing:
Reads were aligned to the genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package.
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: Each sample has a TSV data file with counts, gene exonic size (width) and RPKM as provided by HTSeqGenie

organism: Macaca fascicularis

source_name: Brain Cerebral Cortex

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
NGS Lab

value: Brain Cerebral Cortex

tag: agent

tag: time point

tag: animal id


title: hc13344_ATAC

description: 10x Genomics snATAC-seq

tag: tissue


title: 48 SAM24413638


title: 35 SAM24413625


title: LH026


title: hc77_ATAC

description: 10x Genomics snATAC-seq


title: LH025

value: Female


title: 10 SAM24413600


title: THP-1 macrophages treated with Escherichia coli rpt3

city: Sydney

last: Zhang

state: NSW

address: Botany Street

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

data_processing:
FastQC v0.12.0
Assembly: Reference human genome GRCh38.p14
Supplementary files format and content: Tab-delimited text files of raw counts

extract_protocol:
Total RNA was extracted using the Isolate II RNA minikit (Bioline)
libraries were created using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) and then subjected to sequencing on the Illumina NovaSeq6000 platform.

tag: cell line

value: Monocytic

value: Escherichia coli


title: THP-1 macrophages treated with Escherichia coli rpt2

tag: cell type


title: 20 SAM24413610


title: LH030


title: LH024


title: THP-1 macrophages treated with Escherichia coli rpt1

tag: treatment


title: 46 SAM24413636


title: THP-1 macrophages treated with Aeromonas veronii rpt3

value: Aeromonas veronii


title: LH022

tag: Sex


title: LH029


title: LH023


title: 45 SAM24413635


title: THP-1 macrophages treated with Aeromonas veronii rpt2


title: LH021


title: LH045


title: 44 SAM24413634


title: THP-1 macrophages treated with Aeromonas veronii rpt1


title: LH020

value: PBS


title: 43 SAM24413633


title: ts_VC_3

description:
tRF_counts.txt
tRF_CPM.txt

value: Lung

value: MSCs treatment


title: LH019

value: lung


title: 41 SAM24413631


title: THP-1 macrophages without treatment rpt3

value: Media control


title: THP-1 macrophages without treatment rpt2


title: 47 SAM24413637


title: THP-1 macrophages without treatment rpt1


title: 40 SAM24413630


title: LH018


title: ts_COPD_3

description:
tRF_counts.txt
tRF_CPM.txt

value: COPD model


title: 39 SAM24413629


title: ts_VC_2

description:
tRF_counts.txt
tRF_CPM.txt


title: ts_VC_1

description:
tRF_counts.txt
tRF_CPM.txt


title: iMGL, WT, Replicate 2

city: Vienna

first: Sebastian

last: Eder

address: Zimmermannplatz 10

country: Austria

institute: Children's Cancer Research Institute

description:
10x Genomics
iMGL_WT_2

data_processing:
The raw sequencing data were processed with Cell Ranger v7.1.0 software (10x Genomics) for demultiplexing, barcode processing, gene counting and alignment to the GRCh38 human reference transcriptome.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC

extract_protocol:
For iMono differentiation at day 11 or 14 and iMGL cell suspension were gently harvested from the wells, passed through a strainer to remove clumps and debris and then stained with DAPI. Single living cells (Gated based on DAPI staining for living/dead cells and SSC-A/FSC-W for removing duplets) were then sorted using a BD FACS Aria II in 1.5mL Eppendorf tubes with 1X PBS +0.1% BSA (final concentration 0,04% BSA). iMonos treated with DMSO, belvarafenib or dabrafenib were stained with antibodies against CD14 and CD1c. iLCH cells were stained with antibodies against CD1a and CD207. For treated iMonos single living cells expressing either CD14 or CD1c and for iLCH single living CD1a+/CD207+ and CD1a+/CD207- cells were sorted using a BD FACS Aria II in 1.5mL Eppendorf tubes with 1X PBS +0.1% BSA (final concentration 0,04% BSA).
scRNA-seq libraries were generated using the Chromium iX Controller (10x Genomics) and the Chromium Next GEM Single Cell 3' Kit v3.1 (Dual Index; 10x Genomics), according to manufacturer’s instructions.

value: iPSC

value: WT

tag: time

value: Day 41


title: LH016

tag: strain

value: BALB/c


title: ts_COPD_2

description:
tRF_counts.txt
tRF_CPM.txt


title: iMGL, V600E, Replicate 3

description:
10x Genomics
iMGL_V600E_3


title: LH015

tag: experimental group


title: ts_COPD_1

description:
tRF_counts.txt
tRF_CPM.txt


title: iMGL, WT, Replicate 1

description:
10x Genomics
iMGL_WT_1


title: 37 SAM24413627


title: 38 SAM24413628


title: LH014

tag: timepoint


title: iMGL, V600E, Replicate 2

description:
10x Genomics
iMGL_V600E_2


title: 36 SAM24413626


title: LH013

tag: rna integrity number


title: ts_Con_2

description:
tRF_counts.txt
tRF_CPM.txt

value: Control


title: iMGL, V600E, Replicate 1

description:
10x Genomics
iMGL_V600E_1

tag: genotype


title: 33 SAM24413623


title: LH017


title: LH011


title: iLCH, V600E, Replicate 2

description:
10x Genomics
iLCH_V600E_2

value: Day 17


title: 32 SAM24413622

value: Brain Cerebral Cortex


title: LH010

value: Male


title: ts_Con_1

description:
tRF_counts.txt
tRF_CPM.txt


title: 31 SAM24413621


title: Meki,_treated, 7d, scRNAseq

city: Verona

first: Davide

last: Pasini

state: VR

address: Piazzale Ludovico Antonio Scuro 10

country: Italy

institute: University of Verona

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation, were made using Cell Ranger v4.0.0
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files, matrix values files

source_name: pancreas

extract_protocol:
tumour samples were collected in Splitting Medium (AdDMEM/F12 medium supplemented with HEPES (10 mM), Glutamax, and Pen/Strep) supplemented with 0.1% BSA and RhoKi (10.5 uM). After washing with PBS, specimens were cut in small pieces (1mm3) and incubated for 20 minutes in a tube rotator at 37°C in warm Digestion Medium (PBS 1X, 2mg/mL Dispase I, 1.25mg/mL Collagenase Type II, 100ug/mL DNAse I, and 0,05% FBS) supplemented with RhoKi. The cell suspension was pipetted and incubated on ice to let the larger tissue clumps settle to the bottom of the tube. The surnatant was collected, spun down and the pellet was resuspended in Splitting Medium supplemented with 0.1% BSA and 10 mg/ml Soybean trypsin inhibitor and stored on ice (Fraction 1). Then, the larger undigested clumps were digested again for 10 minutes, and every step previously described was repeated twice until the collection of Fraction 2 and 3. After digestion, Fractions 1, 2, and 3 were combined, filtered (40um nylon cell strainer) and centrifuged. The pellet was then resuspended in ACK lysing buffer supplemented with DNAse I to remove red blood cells from the sample and spun down. Cells were washed with PBS supplemented with 10% FBS and 1x104 cells (concentration 1.000 cells/ul) were submitted for sequencing
libraries were generated with GemCode Single Cell 3’ Gel Bead and Library Kit v3 (10x Genomics)

value: pancreas

value: Meki


title: vehichle,_treated, 7d, scRNAseq


title: iLCH, V600E, Replicate 1

description:
10x Genomics
iLCH_V600E_1

value: Day 16


title: iMonocyte, V600E, treatment, DMSO

description:
10x Genomics
iMono_V600E_DMSO

value: Day 12


title: iMonocyte, V600E, treatment, Dabrafenib

description:
10x Genomics
iMono_V600E_DABR


title: 30 SAM24413620


title: vehichle,_treated, 2d, scRNAseq


title: LH008

value: PBS


title: LH007

value: Female


title: ts_Con_3

description:
tRF_counts.txt
tRF_CPM.txt

value: Lung


title: 34 SAM24413624


title: iMonocyte, V600E, treatment, Belvarafenib

description:
10x Genomics
iMono_V600E_BELV


title: PSC_NT_B_rep2

data_processing:
Reads were aligned to the GRCm38 genome and quantified using salmon v1.4.0
GRCm38
tab-delimited file containing raw counts for each sample

source_name: mouse psc

extract_protocol:
RNA were isolated using the TRIzol® Reagent (Life Technologies), followed by the column based PureLink RNA Mini Kit (Thermo Fisher Scientific). Purified RNA quality was evaluated using RNA 6000 Nano kit on a Bioanalyzer 2100 (Agilent) and only RNA with an RNA Integrity Number (RIN) greater than 7.5 were used.
RNA-seq library were obtained using poly(A) enrichment with TrueSeq Stranded mRNA Library Prep kit (Illumina).

value: mouse psc

tag: condition

value: untreated


title: iMonocyte differentiation, WT, Day 14, Replicate 3

description:
10x Genomics
iMono_diff_D14_WT_3

value: iPSC

value: Day 14


title: 28 SAM24413618


title: LH012

data_processing:
Image analysis was performed  in real time by the NovaSeq Control Software (NCS) v.1.7.0 and Real Time Analysis (RTA) v.3.4.4
The Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data
Read libraries were mapped to the mouse genome (GRCm38) using HISAT
Gene-level quantification (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Genome_build: GRCm38
Supplementary_files_format_and_content: genecounts.txt contain a matrix of raw gene counts (unfiltered and un-normalised data)

value: lung


title: LH006

value: BALB/c


title: PSC_NT_B_rep1


title: iMonocyte differentiation, WT, Day 14, Replicate 2

description:
10x Genomics
iMono_diff_D14_WT_2

value: WT


title: hc1134_ATAC

description: 10x Genomics snATAC-seq

value: hippocampus


title: 26 SAM24413616

value: Brain Cerebral Cortex


title: 27 SAM24413617


title: PSC_TGFB_A_rep4


title: LH009


title: LH004

value: Male


title: PSC_TGFB_A_rep3


title: iMonocyte differentiation, V600E, Day 14, Replicate 3

description:
10x Genomics
iMono_diff_D14_V600E_3


title: iMonocyte differentiation, WT, Day 14, Replicate 1

description:
10x Genomics
iMono_diff_D14_WT_1


title: Meki,_treated, 2d, scRNAseq

value: pancreas


title: 25 SAM24413615


title: LH003


title: 24 SAM24413614


title: iMonocyte differentiation, V600E, Day 14, Replicate 2

description:
10x Genomics
iMono_diff_D14_V600E_2


title: PSC_TGFB_A_rep2


title: 29 SAM24413619


title: iMonocyte differentiation, V600E, Day 14, Replicate 1

description:
10x Genomics
iMono_diff_D14_V600E_1


title: 23 SAM24413613


title: LH002


title: LH001


title: PSC_TGFB_A_rep1


title: PSC_NT_A_rep2


title: WS3，brain organoid，day56 - RNA-seq

city: hangzhou

first: zhao

last: xingsen

address: kaixuan road268

institute: zhejiang university

description:
Library name: WS3
RNAseq

data_processing:
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Genome_build: GRCh38
Supplementary files format and content: csv files include counts for each Sample

source_name: brain organoids

extract_protocol:
Human organoids were homogenized in TRIzol reagent (Thermo Fisher Scientific) to extract total RNA and was purified with chloroform following the manufacturer’s protocol. The concentration of RNA was quantified using a NanoDrop spectrophotometer 2000 (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain organoids


title: iMonocyte differentiation, WT, Day 11

description:
10x Genomics
iMono_diff_D11_WT

value: Day 11


title: PSC_NT_A_rep1


title: 21 SAM24413611


title: iMonocyte differentiation, V600E, Day 11

description:
10x Genomics
iMono_diff_D11_V600E


title: LH005

extract_protocol:
Lung tissue was placed in RNAlater (Ambion, Life Technologies, Mulgrave, VIC, Australia), and frozen at -80C. Total RNA was extracted with TRIzol (Ambion, Life Technologies, Mulgrave, VIC, Australia) followed by RNAeasy (QIAGEN) as per manufacturer's instructions. Library preparation and sequencing were performed by the Australian Genome Research Facility (AGRF).
RNA libraries were prepared by AGRF for sequencing using TruSeq Stranded mRNA (single end, 100bp).


title: WS2，brain organoid，day56 - RNA-seq

description:
Library name: WS2
RNAseq


title: 19 SAM24413609


title: EFF+TETshRNA-Treated HADF_D5

city: Pittsburgh

first: CHANDAN K

last: SEN

state: PA

address: 221 Republic Street

institute: University of Pittsburgh

data_processing:
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger with default paramaters (cellranger)
Gene-barcode matrices were determined using 10X Genomics Cellranger  with default parameters (cellranger run)
Aligned reads were examined for read quality metrics and stored as Seurat objects using Seurat v4.0 package in R.
Assembly: hg:38
Supplementary files format and content: barcode files
Supplementary files format and content: gene names file
Supplementary files format and content: count matrix file

source_name: cultured cells

growth_protocol: Primary human adult dermal fibroblasts (HADF, cat. no. PCS-201-012, ATCC) were grown in fibroblast basal medium (cat. no. PCS-201-030, ATCC) supplemented with fibroblast growth kit-serum-free (cat. no. PCS-201-040, ATCC) containing penicillin-streptomycin (10,000 U/mL) (cat. no. 15140122, Thermo Fisher Scientific) at 37°C in a humidified chamber with 95% air and 5% CO21. The transfected cells were cultured in Endothelial Cell Growth Basal Medium-2 (EBM-2) (cat. no. CC-4147, ATCC) media.

extract_protocol:
Single cells were isolated from cultured cells. Single cells were encapsulated for NEXT GEMs preparation using barcoded beads and cDNA synthesis using the Chromium Single Cell 3′ Reagent Kit v3 (10X Genomics).
library construction was done according to the manufacturer’s recommendations  (10X Genomics)

treatment_protocol: Cells were seeded in a 12-well plate at density 0.1x106 cells/well in an antibiotic-free medium for 24 h before transfection. When the confluency was approximately 70%, transfection was achieved by lipofectamine-mediated delivery of EFF (1:1:1 ratio) and siRNA smart pool for human TET1 (100nM), TET2 (100nM) and TET3 (100nM) using DharmaFECTTM transfection reagent (cat. no T-2001-03, GE Dharmacon) and OptiMEM serum-free medium (cat. no. 31985062, ThermoFisher Scientific) was used for this experiment. Samples were collected at d5 after transfection for single cell RNA seq experiments.

value: cultured cells

value: HADF

value: Primary Dermal Fibroblast


title: ChEC cells, R788

city: Hamburg

first: Andreas

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode09

data_processing:
Basecalling and demultiplexing was performed using the Guppy basecalling software v6.1.3 with the SUP profile (dna_r9.4.1_450bps_sup.cfg) into fastq files.
Assembly: mouse.GRCm39.primary_assembly, gencode.vM29 gene annotation
Supplementary files format and content: bambu_counts_gene.txt: tab-delimited, raw counts
Supplementary files format and content: sequencing_summary.txt.gz: nanopore sequencing summary

source_name: choroidal endothelial cells

extract_protocol:
Cells were washed once with PBS and total RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. RNA quality was determined using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). All samples had a RIN ≥ 9.5.
10 µg total RNA for each sample were used for library preparation with the Nanopore Direct cDNA sequencing kit (#SQK-DCS109, Oxford Nanopore Technologies) with native barcode expansions (#EXP-NBD104, ONT) according to manufacturer's protocol (version: DCB_9091_v109_revL_14Aug2019). First, cDNA was synthesized. The ONT primer VNP was incubated for 5 minutes together with the RNA and dNTPs at 65°C and then snap cooled on a pre-chilled block. Afterwards the SSP primer, 5x RT Buffer (supplied with reverse transcriptase) and RNaseOUT™ (#10777019, Thermo Fisher) were added, the samples were mixed by flicking and incubated for 2 minutes at 42°C. Maxima H Minus RT (#EP0753, Thermo Fisher Scientific) was added, samples were mixed and incubated for 90 minutes at 42°C, 5 minutes at 85°C and were then cooled to 4°C. RNA was digested for 10 minutes with RNAse Cocktail Enzyme Mix (#AM2286, Thermo Fisher Scientific) at 37°C followed by cleanup of the samples using AMPure XP beads (#A63881, Beckman Coulter) according to ONT protocol. The eluted cDNA was used for 2nd strand synthesis. To this end, PR2 primer and 2X LongAmp Taq Master Mix (#M0287L, NEB) were mixed with the cDNA samples and incubated for 1 minute at 98°C, 1 minute at 50°C and 15 minutes at 65°C. The double stranded DNA was cleaned up with AMPure XP beads and taken forward to end preparation with the NEBNext® Ultra II End Repair/dA-Tailing Module (#E7546L, NEB). After bead cleanup, native barcode ligation was performed. Each sample was labelled with a single assigned barcode by incubation of the sample together with the barcode and Blunt/TA Ligase Master Mix (#M0367L, NEB) for 10 minutes at 21 °C. After another cleanup step, samples were eluted in 21.7 µl nuclease-free water and pooled. 65 µl of the pooled sample were directly used for adapter ligation, the remaining sample was stored at -20°C. The adapter mix II was ligated to the sample using the NEBNext® Quick Ligation Module (#E6056L, NEB) for 10 minutes at 21°C. During the following bead cleanup, the library was washed with short fragment buffer and eluted in 12 µl elution buffer.

value: choroidal endothelial cells


title: BEC cells, R786

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode08

source_name: brain endothelial cells

value: brain endothelial cells


title: WS1，brain organoid，day56 - RNA-seq

description:
Library name: WS1
RNAseq


title: 18 SAM24413608


title: EFF-Treated_HADF_D5


title: CTRL3，brain organoid，day56 - RNA-seq

description:
Library name: CTRL3
RNAseq


title: BEC cells, R785

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode07


title: 17 SAM24413607


title: CTRL2，brain organoid，day56 - RNA-seq

description:
Library name: CTRL2
RNAseq


title: Pancreatic Islet, D4_H_LY

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
Sequenced FASTQ files were aligned, filtered, barcoded, demultiplexed and UMI counted (excluding introns) using Cell Ranger Chromium Single Cell RNA-seq multi version 7.0.0 by 10X Genomics with Cell Ranger.  Empty droplets and ambient RNA remove from count matrices with remove-background function from cellbender (version 0.2.2)
Each dataset was filtered to retain cells with ≥ 1000 UMIs, ≥400 genes expressed, and <20% of the reads mapping to the mitochondrial genome.
UMI counts were then normalized so that each cell had a total of 10,000 UMIs across all genes and log-transformed with a pseudocount of 1 using the “LogNormalize” function in the Seurat package (version 4.0.3)
The top 2000 most highly variable genes were identified using the “vst” selection method of “FindVariableFeatures” function and counts were scaled using the “ScaleData” function.
Datasets for each donor from DMSO, Harmine, Harmine + GLP and Harmine + LY treatments were integrated by using the “RunHarmony” function in the harmony package (version 0.1.0)
Assembly: GRCh38 human genome reference
Supplementary files format and content: Tab separated values files and matrix files (features.tsv, barcodes.tsv and matrix.mtx per sample)

source_name: Pancreatic Islet

growth_protocol: Cadaveric human islets were cultured in RPMI islet culture medium that contained 20% fetal bovine serum and antibiotics.

extract_protocol:
Single cell suspension was obtained by gently dispersing human cadaveric islets in 1X PBS with 0.5% BSA.
Cells were processed according to Chromium 3’ Gene Expression V3 Kit (10X Genomics) using the manufacturer’s guidelines followed by sequencing on an S1 Novaseq chip (Illumina Inc.).

treatment_protocol: DMSO (control), Harmine (10μM), GLP1RA (5nM), LY364947 (10μM), Harmine + GLP1RA (GLP), and Harmine + LY364947 (LY) treatments were performed in the same culture media for 96 hours.

value: Pancreatic Islet

tag: donor

value: wild-type


title: 16 SAM24413606


title: CTRL1，brain organoid，day56 - RNA-seq

description:
Library name: CTRL1
RNAseq


title: REC cells, R783

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode06

source_name: retinal endothelial cells

value: retinal endothelial cells


title: Pancreatic Islet, D4_H_GLP

description: 10x Genomics


title: 15 SAM24413605


title: REC cells, R784

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode05


title: 22 SAM24413612


title: Pancreatic Islet, D4_H

description: 10x Genomics

value: H


title: ChEC cells, R790

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode04


title: 13 SAM24413603


title: Pancreatic Islet, D4_D

description: 10x Genomics

value: D


title: Pancreatic Islet, D3_H_LY

description: 10x Genomics


title: ChEC cells, R789

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode03


title: 14 SAM24413604


title: BEC cells, R787

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode02


title: 12 SAM24413602


title: Pancreatic Islet, D3_H_GLP

description: 10x Genomics


title: MCp after the treatment patient 2011

type: RNA

city: UPPSALA

first: PERLA

middle: ABIGAIL

last: ALVARADO VAZQUEZ

address: Husargatan 3

country: Sweden

institute: UPPSALA UNIVERSITY

description: Sample taken 6 months after treatment

hyb_protocol: Following fragmentation, sscDNA were hybridized on human Clariom™ S Array according to standard Affymetrix protocol.'

scan_protocol: GeneChips were scanned using Affymetrix Scanner at the Bioinformatics and Expression Analysis Core Facility.

data_processing: Transcriptome Analysis Console (TAC) software (Thermofisher Scientific) was used for the analysis of the microarray data.

label: biotin

source_name: Sorted MCps

label_protocol: Biotinylated  sscDNA were prepared according to the GeneChip WT Pico protocol (Affymetrix) by the Bioinformatics and Expression Analysis Core Facility at Karolinska Institutet.

growth_protocol: MC progenitors were sorted from PBMCs (FACSAria III cell sorter) into 96 well plates (Sarsted) containing 200 μL of RTL buffer (Qiagen), and kept at -80°C until analysis

extract_protocol: For RNA isolation, the single cell RNA purification kit from Norgen Biotek Corp was used according to the manufacturer's instructions

treatment_protocol: PBMCs were collected before and after anti- IL-5Rα therapy.


title: MCp before the treatment patient 2011

description: Sample taken before the treatment


title: 11 SAM24413601


title: REC cells, R782

description: 20220516_0952_MC-111565_FAT27400_8372c8be.barcode01


title: 09 SAM24413599


title: ZF_72_hpf_7.8_µM_Acetochlor_III

city: Bloomington

first: Jason

last: Tennessen

state: IN

address: 1001 E. Third St

department: Department of Biology

institute: Indiana University

data_processing:
The quality of RNA reads was assessed with FastQC [Andrews 2010] and MultiQC [Ewels 2016]
Salmon v1.6.0 used to quantify read count
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Danio rerio

source_name: Whole Larva (pooled)

extract_protocol:
Trizol Extraction. Qiagen RNeasy purification
PolyA selected libraries

value: Whole Larva (pooled)

tag: age

value: 72 hpf

value: WT

value: 7.8 µM Acetochlor treated larvea

tag: replicate

value: rep III


title: 08 SAM24413598

value: Brain Cerebral Cortex

tag: agent

tag: time point


title: 07 SAM24413597

tag: animal id


title: ZF_72_hpf_7.8_µM_Acetochlor_I

tag: tissue

value: rep I


title: Pancreatic Islet, D2_H_LY

description: 10x Genomics


title: Pancreatic Islet, D3_H

description: 10x Genomics


title: Pancreatic Islet, D3_D

description: 10x Genomics


title: ZF_72_hpf_7.8_µM_Acetochlor_II

value: rep II


title: Pancreatic Islet, D2_H_GLP

description: 10x Genomics


title: ZF_72_hpf_780_nM_Acetochlor_III

value: 780 nM Acetochlor treated larvea


title: MCp after the treatment patient 2009

description: Sample taken 13 months after treatment

value: Male


title: ZF_72_hpf_780_nM_Acetochlor_II


title: 05 SAM24413595

tag: cell type


title: Pancreatic Islet, D2_D

description: 10x Genomics

tag: treatment


title: MCp before the treatment patient 2009

description: Sample taken before the treatment

tag: Sex


title: MCp after the treatment patient 2016

description: Sample taken 6 months after treatment

value: Female


title: MCp before the treatment patient 2012

description: Sample taken before the treatment


title: 04 SAM24413594


title: 34640_W4_S56

city: Duarte

first: Zhenlong

last: Li

address: 1500 East Duarte Road

institute: City of hope

description: Library name: Sample 9

data_processing:
Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling.
Sequencing was performed using the single-read mode of 51 cycles of read1 and 7 cycles of index read with V4 reagents on a Hiseq 2500 system (Illumina).

organism: Mus

source_name: Ncr1-WT ILC1

extract_protocol:
Ncr1+/+ or Ncr1gfp/gfp ILC1s were sorted from the liver of mice using BD FACSAriaTM Fusion. Total RNA was isolated from ILC1s using a miRNeasy Mini Kit (QIAGEN).
SMART-Seq® Ultra Low Input RNA Kit for Sequencing–v4 (Takara Bio) was used for getting double-strand cDNA from each sample with 2 ng of input total RNA. The resulting cDNA was sheared using a Covaris LE220 sonicator. The sheared DNA was used for to prepare a sequencing library, using a KAPA HyperPrep Kit. The final libraries were quantified using the Qubit Assay Kit (Thermo Fisher Scientific) and Bioanalyzer (Agilent). Sequencing was performed using the single-read mode of 51 cycles of read1 and 7 cycles of index read with V4 reagents on a Hiseq 2500 system (Illumina). Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling.

value: Liver


title: 34641_W5_S57

description: Library name: Sample 10


title: Pancreatic Islet, D1_H_LY

description: 10x Genomics

value: Pancreatic Islet


title: ZF_72_hpf_780_nM_Acetochlor_I


title: MCp after the treatment patient 2012

description: Sample taken 6 months after treatment


title: MCp before the treatment patient 2016

description: Sample taken before the treatment


title: 34639_W3_S55

description: Library name: Sample 8


title: 03 SAM24413593


title: ZF_72_hpf_Ctrl_III

value: Control Untreated


title: 34638_W2_S54

description: Library name: Sample 7


title: 02 SAM24413592


title: 06 SAM24413596


title: 34637_W1_S53

description: Library name: Sample 6


title: ZF_72_hpf_2.3_µM_Tefluthrin_III

value: 2.3µM Tefluthrin treated larvae


title: 01 SAM24413591


title: ZF_72_hpf_Ctrl_II


title: Pancreatic Islet, D1_H

description: 10x Genomics

value: wild-type

value: H


title: Pancreatic Islet, D2_H

description: 10x Genomics


title: Pancreatic Islet, D1_D

description: 10x Genomics

value: D


title: ZF_72_hpf_2.3_µM_Tefluthrin_II

value: Whole Larva (pooled)

value: 72 hpf


title: 34636_K5_S66

description: Library name: Sample 5

source_name: Ncr1-KO ILC1


title: HIC_WT_rep2

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer runnning with default parameter
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: hic

growth_protocol: Cells were cultured using McCoy’s 5A media with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100ug/ml streptomycin. Cells were grown at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Chipseq: Cultured cells were fixed with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 125 mM glycine. Twenty million fixed cells were washed with PBS, snap-frozen and stored at -80°C until further processing. Before use, the cells were resuspended in 1 ml of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100 and freshly added Complete Mini EDTA free proteinase inhibitor. Sonication was performed using Branson sonicator at amplitude 35%, 12 cycles of 20 sec sonication followed by 30 sec of pause or using Covaris ME220 sonicator at duty factor 20%, peak incident power 75, cycle/burst 1000 for 6 min at 4°C. The antibody-protein solution was then incubated with 40 ml of Dynabeads Protein A for 40 min at room temperature under agitation. Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with LiCl buffer (0.25M LiCl, 0.5% NP-40, 0.5% NaDOC), once with TE pH 8.0 containing 0.2% Triton X-100, and once with TE pH 8.0. Crosslinks were reversed by incubating the beads at 65°C for 4 hours in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column.
HiC: Cultured cells were fixed with 1% formaldehyde and the reaction was quenched with 200 mM glycine. Cells were then lysed and digested with the MboI restriction enzyme. DNA ends were then marked with biotin-14-dATP and ligated by proximity. After reverse crosslinking, DNA was sheered to an average size of 200-400 bp. This DNA was then pulled down using MyOne Streptavidin T1 beads and washed.
Chipseq: Ovation Ultralow Library System V2 kit , Hi-C library were amplified directly from of the beads with 4-6 cycles of PCR, using Illumina primers (Bioo Scientific) and Q5 Hi-Fidelity DNA polymerase

treatment_protocol: HCT116-Rad21-mAID-clover cells were grown for 3 days before addition of media containing 750uM indole-3-acetic acid (IAA). For AsiSI induction, HCT-116 cells containing the nAsiSI-T2A-BFP construct show efficient induction of breaks 4-8 hours following treatment with 1M 4OHT. In experiments where DNA damage was induced for 72h, fresh 4OHT was added every 24h. Inhibition of ATM was achieved by incubating cells with 1M KU-55933 for 1 hour prior to induction of DSBs

tag: cell line

value: Human colorectal carcinoma cell


title: 34635_K4_S52

description: Library name: Sample 4

tag: strain


title: HIC_WT_rep1


title: 5504C SAM24398702

data_processing:
Reads were aligned to the genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package.
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: Each sample has a TSV data file with counts

source_name: Brain Frontal Cortex

value: Brain Frontal Cortex

tag: animalsample

value: C

tag: animalid


title: 5503C SAM24398700


title: ZF_72_hpf_60_nM_Tefluthrin_III

value: WT

value: 60 nM Tefluthrin treated larvae

value: rep III


title: Pancreatic Islet, D1_H_GLP

description: 10x Genomics


title: 5504A SAM24398701

value: A


title: HIC_WT_DSBATMi_rep2

value: DSB(4OHT), ATMi


title: ZF_72_hpf_2.3_µM_Tefluthrin_I

value: rep I


title: 5503A SAM24398699


title: 34632_K1_S49

description: Library name: Sample 1

value: Liver


title: 5502C SAM24398698


title: HIC_WT_DSBATMi_rep1


title: ZF_72_hpf_60_nM_Tefluthrin_I


title: 34634_K3_S51

description: Library name: Sample 3


title: HIC_WT_Auxin_rep2

value: IAA


title: 34633_K2_S50

description: Library name: Sample 2


title: ZF_72_hpf_Ctrl_I

value: Control Untreated


title: HIC_WT_Auxin_rep1


title: 4504C SAM24398690


title: HIC_Pdef_DSB_rep2

value: Rad21_AIDdegron, SMC1AS957AHz/S966AHz


title: Female mouse spinal cord tissue, Input

city: Houston

first: Zhung-Fu

last: Lee

state: Texas

address: 2300 Old Spanish Trl, Apt1013

institute: Baylor College of Medicine

description: Library name: Female_input

data_processing:
For Nkx6.1 ChIP-seq, reads were aligned to the mm10 reference genome using BWA. Duplicate reads were marked with Picard's MarkDuplicates function, and peaks were called using the MACS peak caller. Blacklisted regions were excluded to remove signal-artifact. Separate peak lists were created for male and female samples, and to identify sex-specific binding regions, bedtools intersect -v was used to remove overlapping peaks between the two conditions, generating male-specific and female-specific peak sets. These sex-specific binding regions were annotated using HOMER's annotatePeaks.pl function. Motif enrichment analysis was conducted with HOMER's findMotifsGenome.pl, which identified enriched transcription factor motifs within the sex-specific regions.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: spinal cord

extract_protocol:
Cell pellets were collected by centrifugation at 3500 rpm for 5 min at 4°C, washed with PBS, and frozen at 80°C until further processing. Pellets were resuspended with PBS–phenylmethylsulfonyl fluoride (PMSF) containing 0.5% Igepal to release nuclei followed by washing with cold ChIP-Buffer (0.25% Triton-X100, 10 mM EDTA, 0.5 mM EGTA, 10 mM HEPES pH 6.5), and nuclei were lysed with ChIP lysis buffer (0.5% SDS, 5 mM EDTA, 25 mM Tris-HCl pH 8) for 15 to 20 min at room temperature
ChIP libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina no. IP-202-1012), according to the manufacturer’s instructions. Libraries ranging from 250 to 350 bp were extracted from gel incisions using the QIAquick Gel Extraction Kit (Qiagen no. 28706),

value: spinal cord

tag: chip antibody


title: human A549 cells, PR8/H1N1 influenza virus infected, 24 hpi

city: Beijing

first: Zhimin

last: Jiang

address: Yuanmingyuang west road 2

institute: Chinese Agricultural University

description: Library name: Sample 2

data_processing:
Identification of putative vcircRNA junctions derived from the linear PR8 virus RNA genome. Aligning with the viral genome  generates the start and the end of read positions. To ensure that the junction originates from vcircRNAs, it is essential to validate the exact order of nucleotide positions, specifically the 5′ breakpoint, end of read, start of read, and finally the 3′ breakpoint
Assembly: Reference sequence is PR8/H1N1 virus genome
Supplementary files format and content: The processed data from each sample including the backsplicing site analysis and the viral circRNA sequence information. For the backsplicing site analysis, The annotation-independent algorithms, find_circ, vircircRNA and CIRI2 with downstream analysis tool CIRI-full for de novo reconstruction of circRNAs, were employed to analyze sequencing data. For vcircRNA information, by alignment with the viral genome, a putative vcircRNA was defined by the presence of a discontinuous reading with two breakpoints in the junction region, and additional two nucleotides located at the start and end of junction-spanning reads.

source_name: human A549 cells

extract_protocol:
1 mL Tri-reagent (Sigma) was added to each sample, and RNA was harvested according to the manufacturer’s instructions. The ribosomal RNA is removed and linear RNA was digested by RNase treatment.  RNA was reverse transcribed using random primers and then was detected by  RNA-seq.
RNA libraries were prepared for sequencing using standard  TruSeq DNA PCR-Free Library Preparation Kit  protocols.

value: human A549 cells

value: Lung epithelial cells

value: PR8/H1N1 infection


title: 5502A SAM24398697


title: 4504A SAM24398689


title: human A549 cells, PR8/H1N1 influenza virus infected, 12 hpi

description: Library name: Sample 1


title: HIC_Pdef_DSB_rep1

value: Human colorectal carcinoma cell

tag: genotype


title: Male mouse spinal cord tissue, Input

description: Library name: Male_input


title: ZF_72_hpf_60_nM_Tefluthrin_II

value: Whole Larva (pooled)

value: 72 hpf

value: rep II


title: HIC_WT_DSB_rep2


title: HL+187-24hrs-_R-3 [M_19_2074_42_AD019_L006]

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

data_processing:
Illumina next generation sequencing platform
The reads were aligned to the reference genomes with Tophat v2.0.13. The obtained bam files were further converted in to gff files to analyse the data further. The number of reads in the alignments that overlap with gene features were counted with feature Counts 1.4.6.
Gene expression levels were normalized using log2 transform count Normalization
Arabidopsis thaliana
Assembly: Arabidopsis thaliana
Supplementary files format and content: Excel, log2 transform count based Normalization

organism: Arabidopsis thaliana

source_name: plant seedling

growth_protocol: Arabidopsis thaliana plants were grown at 22⁰C under 16 h light and 8 h dark period

extract_protocol:
Total RNA was extracted using Nucleospin RNA plant kit (Macherey-Nagel), we further followed with DNaseI treatment to remove gemomic DNA as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Ribo-zero Illumina protocol

treatment_protocol: Two different light stress regimes (normal light 130 μmol m-2 s-1 and high light 1050 μmol m-2 s-1 ) were implemented on SA187 colonized plants

value: plant seedling


title: 4503A SAM24398687

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
NGS Lab

value: Brain Frontal Cortex


title: HIC_WT_DSB_rep1


title: LUHMES H116, D15, Rep4

city: Edinburgh

first: Aleksandra

last: Helwak

address: Max Born Crescent

department: Wellcome Centre for Cell Biology

institute: The University of Edinburgh

data_processing:
Flexbar (version 3.4.0) - adapter trimming and quality fitering (quality threshold 30)
Reads were mapped to the genome (GRCh38 downloaded from Ensembl) using STAR (version 2.7.3a, --outMultimapperOrder Random)
Reads were aligned to the genomic features from annotation from GENECODE (gencode.v34.annotation.gtf; evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100) from 2020-03-24) using featureCounts (version: 2.0.0, parameters: -p -t exon -g gene_id -Q 10 -s 2).
Assembly: hg38
Supplementary files format and content: tab-delimited output files from featureCounts with raw counts for each genomic feature; one processed file per sample

source_name: Brain; Mesencephalon

growth_protocol: Proliferating cells were grown on poly-L-ornithine and fibronectin coated dishes in Advanced DMEM/F12 with addition of L-Glutamine, N2 supplement and βFGF at 37C and 5% CO2.

extract_protocol:
Cells were lysed in Trizol and after the phase separation, aqueous phase was further purified using Zymo Direct-Zol Plus kit. Total RNA was treated with DNase RQ1 and the integrity was tested on Bioanalyzer.
Ribosomal RNA was depleted with NEBNext rRNA Depletion kit. RNAseq libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturers protocol and sequenced by BGI Genomics.

treatment_protocol: Cells were differentiated in two steps: for pre-differentiation proliferating cells were seeded in proliferation medium. The next day proliferation medium was exchanged for differentiation medium:  advanced DMEM/F12 with addition of L-Glutamine, N2, GDNF, cAMP and doxycycline for two days. On day 2 of differentiation cells were trypsinized, counted and seeded on 10 cm dish, starting second step of differentiation.  During the subsequent differentiation process, half of the medium was changed every second day. Cells were taken for analysis, 6 (D06), 10 (D10) and 15 (D15) days after the initial exchange to differentiation medium.

value: Brain; Mesencephalon

value: LUHMES

value: immortalized embryonic neuronal progenitor

value: heterozygous deletion of SNORD116 cluster

tag: clone

value: differentiation

tag: time


title: 4502C SAM24398686

value: C


title: LUHMES H116, D15, Rep3


title: Female mouse spinal cord tissue, Nkx6.1 ChIP

description: Library name: Female_Nkx6.1


title: HL-24hr-R-3 [M_19_2072_39_AD015_L006]


title: HIC_WT_DSBAuxin_rep2

value: DSB(4OHT), IAA


title: HL+187-24hrs-_R-1 [M_19_2073_40_AD016_L006]


title: 4502A SAM24398685

value: A


title: Male mouse spinal cord tissue, Nkx6.1 ChIP

description: Library name: Male_Nkx6.1

value: spinal cord


title: HL-24hr-R-2 [M_19_2071_38_AD014_L006]


title: LUHMES H116, D15, Rep5


title: LUHMES H116, D10, Rep5


title: 4501C SAM24398684


title: HL-24hr-R-1 [M_19_2070_37_AD013_L006]


title: HIC_WT_DSBAuxin_rep1


title: Chipseq_Pdef_Rad21_UTR

value: Rad21 (abcam, Ab992)

value: Rad21_AIDdegron, SMC1AS957AHz/S966AHz


title: 4501A SAM24398683


title: LUHMES H116, D10, Rep3


title: NL+187-24hr-R-3 [M_19_2069_36_AD012_L005]


title: Chipseq_Pdef_Rad21_DSB

value: Human colorectal carcinoma cell


title: LUHMES H116, D10, Rep2


title: 4503C SAM24398688


title: NL+187-24hr-R-2 [M_19_2068_35_AD011_L005]


title: 1503A SAM24398673


title: P10

city: Shanghai

first: ln

last: wang

address: Room 309, C building No. 154, Jianchuan Road 953 Nong, Minhang District

institute: shanghai

description: proc data header: Cy76

data_processing:
Bioinformatics data analysis was performed by Newcore Biotechnology (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference genome (hg38).
mRNA：featureCounts software (v2.0) was used to get the raw gene level mRNA read counts as the mRNA expression profile. DESeq2 software (v1.30.1) was used to normalize and calculate the fold change and Pvalue between two groups. Ensembl GTF gene annotation database (v104) was used to annotate the mRNA.
LncRNA: HTSeq software (v0.13.5) was used to get the raw transcript level lncRNA read counts as the lncRNA expression profile. DESeq2 software (v1.30.1) was used to normalize and calculate the fold change and Pvalue between two groups. Ensembl human GTF gene annotation database (v104) was used to annotate the lncRNA.
circRNA: DCC software (v0.5.0) was used to identified circRNAs and calculate the raw junction reads as the circRNA expression profile. DESeq2 software (v1.30.1) was used to normalize and calculate the fold change and Pvalue between two groups. Ensembl human GTF gene annotation database (v104) and circBase database were used to annotating the circRNA by circAnno software.
Assembly: human hg38
Supplementary files format and content: raw counts of mRNA, LncRNA in excel
Supplementary files format and content: raw junction counts of circRNA in excel

source_name: Left renal tissue

growth_protocol: The senescence-related marker proteins P53 and P21waf were detected by immunohistochemistry

extract_protocol:
RNA-seq libraries were constructed by NewCore Biotech (Shanghai, China). Firstly, RNA was isolated with TRIZOL reagent (Invitrogen, Grand Island, NY), total RNA was purified by the Qiagen RNeasy mini kit (Qiagen, Valencia, CA). Purified RNA was analyzed on an ND-8000 spectrophotometer (Nanodrop Technologies, Wilmington, DE).
High quality total RNA was used as the starting material. Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer's instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina NovaSeq 6000 instrument with paired end reads

treatment_protocol: Operation.We collected a total of 76 discarded renal tissue samples from patients who underwent radical nephrectomy for urological tumors or trauma in The First Affiliated Hospital of China Medical University from March 12,2018 to August 15,2018.

value: Left renal tissue

value: Mesangial cell

value: Young

value: Operation


title: 1502C SAM24398672

city: South San Francisco

last: Friedman

address: 1 DNA Way

institute: Genentech, Inc.

value: Brain Frontal Cortex


title: LUHMES H116, D06, Rep4

value: Brain; Mesencephalon


title: NL-24hr-R-3 [M_19_2066_33_AD009_L005]

value: plant seedling


title: 1502A SAM24398671


title: 1501C SAM24398670


title: LUHMES H116, D06, Rep2

value: LUHMES

value: immortalized embryonic neuronal progenitor


title: P8

description: proc data header: Cy72

source_name: Right renal tissue

value: Right renal tissue


title: NL-24hr-R-1 [M_19_2064_31_AD007_L005]


title: NL-24hr-R-2 [M_19_2065_32_AD008_L005]


title: NL-5Days-R-3 [M_19_2063_30_AD006_L005]


title: 5504B SAM24395527

value: B


title: P6

description: proc data header: Cy52


title: 1503C SAM24398674

value: C


title: LUHMES H116, D06, Rep1

value: heterozygous deletion of SNORD116 cluster

value: differentiation


title: 1501A SAM24398669

value: A


title: Chipseq_Pdef_Mre11

value: Mre11 (Novus Biologicals NB100-142)

value: Rad21_AIDdegron, SMC1AS957AHz/S966AHz


title: LUHMES H116, D00, Rep4


title: P7

description: proc data header: Cy54

value: Left renal tissue


title: NL-5Days-R-2 [M_19_2062_29_AD005_L004]


title: P5

description: proc data header: Cy49

value: Mesangial cell

value: Aging


title: 5503B SAM24395526


title: LUHMES H116, D00, Rep3


title: LUHMES H116, D10, Rep1


title: NL+187-24hr-R-1 [M_19_2067_34_AD010_L005]


title: LUHMES H116, D10, Rep4


title: P9

description: proc data header: Cy26

value: Young

value: Operation


title: NL-5Days-R-1 [M_19_2061_28_AD004_L004]


title: LUHMES H116, D06, Rep3

value: Brain; Mesencephalon


title: LUHMES H116, D00, Rep2


title: P3

description: proc data header: Cy59


title: P4

description: proc data header: Cy24


title: 5502B SAM24395525

value: Brain Frontal Cortex


title: LUHMES H116, D00, Rep1

value: LUHMES


title: NL+187-5Days-R-2 [M_19_2059_26_AD002_L004]

value: plant seedling


title: P2

description: proc data header: Cy44


title: 5501B SAM24395523


title: 5501C SAM24395524


title: P1

description: proc data header: Cy7

value: Right renal tissue


title: NL+187-5Days-R-1 [M_19_2058_25_AD001_L004]


title: NL+187-5Days-R-3 [M_19_2060_27_AD003_L004]


title: 5501A SAM24395522


title: HL-5days-R-3 [M_19_2057_24_AD027_L004]


title: MCF7 - CMO Multiplexing Capture

data_processing:
Sequenced fastq files were aligned, filtered, barcoded and UMI counted using Cell Ranger Chromium Single Cell RNA-seq version 7.1.0, by 10X Genomics with Cell Ranger, GRCh38 database (version 2020-A) as the human genome reference
Cells were demultiplexed into separate datasets by sample using the Seurat HTODemux function, and cells without a CMO tag or multiple tags were filtered out
XZ_53333 is the gene expression library. XZ_53336 is the CMO Multiplexing Capture library. All 5 samples are in these files
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For single cell RNA sequencing experiment, 2x105 cells were seeded in triplicate in 6 well plates for 24 hours. Next, we collected cells using trypsin, washed them twice with PBS containing 3% BSA before adding 100ul of multiplexing oligos to each pellet. Following dissociation, cells were incubated for 5 min at room temperature before subsequent washes with 2 ml of PBS containing 3% BSA. Cells were resuspended in 500 ul of PBS containing 1% BSA, counted, and 1.5x105 cells from individual samples were pooled into one library. After cells viability assessment, the library was centrifuged (1200 RPM for 5 min), the supernatant removed, and the pellet was suspended to a final concentration of 1.5 million cells per ml.  We found that most samples had over 90% cell viability, therefore, samples were directly processed for library preparation without the need for cell sorting based on DAPI. For multiplexing, we used CellPlex, a cholesterol-modified oligonucleotide (CMO) cell tagging based approach from 10x Genomics.  We barcoded each sample (MCF7 and bone-derived MCF7) before pooling samples for single cell library preparation.
CellPlex (10x Genomics)

value: parental (CMO305), mammary (CMO309), bone (CMO312), lung (CMO311), ovary (CMO310)

value: NO TREATMENT


title: 4504B SAM24395515

value: B


title: HL-5days-R-2 [M_19_2056_23_AD025_L004]


title: MCF7 - single cell gene expression


title: LUHMES H115, D15, Rep1

value: immortalized embryonic neuronal progenitor

value: heterozygous deletion of SNORD115 cluster

value: differentiation


title: LUHMES H115, D15, Rep2


title: HL-5days-R-1 [M_19_2055_22_AD023_L003]


title: LUHMES D115, D10, Rep2

value: homozygous deletion of SNORD115 cluster


title: LUHMES D115, D15, Rep1


title: HL+187-5days-R-3 [M_19_2054_21_AD022_L003]