title: DNA_1

value: DNA


title: PT_scion_21_5

status: Public on Dec 19 2024

type: SRA

city: Norwich

first: Hannah

middle: Rae

last: Thomas

address: Norwich Research Park, Colney Lane

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

library_source: transcriptomic

data_processing:
Fasta files were quality checked using FastQC 0.12.1.
TruSeq3 adaptors trimmed with Trimmomatic v0
39 with a head crop setting of 12, trailing setting of 3, minimum length of 52, and a sliding window of 4:20
The polyA tail was trimmed using Prinseq v0.20.4 with the left and right tail length (i.e. trim_trail_left) of 8 and the minimum length of 40.
Genome indexes were built for tomato and pepper using the ITAG4 and CM334 models respectively. Reads were aligned using STAR 2.7.10b  with two pass mode.
Files were sorted using Samtools 1.18.
Files were assembled using Strintie version 2.2.1.
Assembly: ITAG4.0 4081, Capsicum annuum 4072
Supplementary files format and content: raw reads matrix file for tomato and pepper

molecule: total RNA

organism: Capsicum annuum

source_name: Scion

growth_protocol: Solanum lycopersicum var. M82 (tomato) and Capsicum annuum var. California Wonder(pepper) seeds were straitified with 50% bleach. Tomato seeds were germinated in moist phytatrays and pepper seeds were germinated on soil on heatmaps. Tomato and pepper seedlings were grown in climate-controlled chambers set to 23 C with 16:8 day/night light cycles. 21 day old pepper and 14 day old tomato seedlings were grafted and allowed to heal in the dark for 3 days.

extract_protocol:
Tissue was flash frozen and hand ground with a mortal and pestle.  Total RNA was purified from Trizol-extracted samples using the Monarch Total RNA Miniprep Kit.
Libraries were built by the Cornell Institute of Biotechnology, Biotechnology Resource Centre using the Lexogen QuantSeq FWD prep kit and Poly(A) RNA Selection Kit V1
5 and subjected to high-throughput sequencing with the Illumina NextSeq 500/550 High-output kit

treatment_protocol: A 0.5 cm of tomato:tomato, pepper:pepper, tomato:pepper, and pepper tomato scion and stock were collected at 7, 14, and 21 days after grafting. Ungrafted tomato and pepper stems of the same age were also collected for tomato and pepper. Each sample had between 3-5 bioreplicates.

tag: time

value: 21 DAG

tag: tissue

value: Scion


title: Smartseq2_362

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

library_source: transcriptomic single cell

data_processing:
SmartSeq2 Analysis: Fastq files from SmartSeq2 libraries were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). Genome-mapped BAM files were quantified with RSEM (v1.3.1), and the resulting gene/UMI count matrix was processed in Seurat (v4.1.2). Data were normalized using the LogNormalize method, with mitochondrial gene expression and library size bias regressed out via the ScaleData function. Cells with >5% mitochondrial reads were excluded. Clustering, differential expression, and gene signature scoring were performed in Seurat. Differentially expressed genes were identified using the Wilcoxon Rank Sum test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.5 considered significant.
Bulk RNA-Seq raw Fastq files were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). The count matrix was processed in R with the DESeq2 package (v1.34). Genes with fewer than ten reads were filtered out, and sample normalization was applied using a negative binomial distribution model. Differential gene expression between conditions was assessed with the Wald test. Genes with adjusted P-values (FDR) < 0.1 were retained, and log2 fold changes were shrunk using the apeglm algorithm.
10x Genomics Analysis: Fastq files from cDNA and hashtag libraries generated on the Chromium platform (10x Genomics) were processed using Cell Ranger (v7.0.1). The resulting quantification matrix was processed in Seurat (v5.0) with normalization using the SCTransform function. Non-myeloid cell contaminants were removed based on the PanglaoDB_Augmented_2021 database and EnrichR package for R. Cells were classified by biological condition using the HTODemux function. Differentially expressed genes were identified with the Wilcoxon rank test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.3 considered significant. Signature scores were calculated using Seurat’s AddModuleScore function.
Assembly: mm10
Supplementary files format and content: Tab files from bulk RNA-Seq tab files containing the STAR gene quantification.
Supplementary files format and content: gene.results from RSEM quantification of Smartseq2 data
Supplementary files format and content: mtx, cellranger output from 10x genomics libraries.
Supplementary files format and content: rds, images of Seurat objects used in the analysis

molecule: polyA RNA

organism: Mus musculus

source_name: D-LN

extract_protocol:
Lymph nodes and gut tissue were dissected, finely chopped, and digested in RPMI medium with Collagenase D to obtain single-cell suspensions. For gut-associated lymph nodes, duodenal lymph nodes were identified using anatomical markers. Dendritic cells were isolated from the duodenal lamina propria by separating intestines, removing mucus with PBS and DTT, and stripping epithelium with EDTA. The tissue was further digested with DNaseI and collagenase, followed by Percoll gradient centrifugation to isolate DCs. Single-cell sorting of DCs was conducted into 96-well plates with TCL buffer and stored at –80°C.
Library Preparation for Single-cell RNA-seq (SmartSeq2). Single cells were sorted onto plates, covering all conditions in each replicate. RNA was extracted using RNAClean XP SPRI beads, then reverse-transcribed into cDNA with RT and TSO primers. The cDNA was amplified, cleaned with SPRI beads, and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Barcoded libraries were pooled and sequenced on the Illumina Nextseq 550 platform. Library Preparation for Single-cell RNA-Seq (10x Genomics). Cells were labeled with hashtag oligonucleotide (HTO)-tagged antibodies, sorted, and counted for viability. scRNA-seq libraries were generated using the 10x Genomics Chromium system, following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq SP flowcell at a minimum depth of 30,000 reads per cell. Library Preparation for Bulk RNA-seq. RNA was isolated using RNAClean XP beads. Reverse transcription was performed with specific primers, followed by cDNA amplification with KAPA HiFi HS Ready Mix. The amplified product was cleaned with RNAClean XP beads and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Libraries were pooled and sequenced as 75-base single-end reads on an Illumina NextSeq platform.

treatment_protocol: Mice were treated with dietary ovalbumin (OVA) to induce tolerance. For infection conditions, mice were infected with Heligmosomoides polygyrus (H.p.) or Strongyloides venezuelensis (S.v.) to model chronic and acute type 2 immune responses, respectively.

value: D-LN

value: Filtered

tag: number of_cells_sorted


title: Smartseq2_357

tag: treatment

value: SV


title: shLUC_1

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description: Library name: shLUC_1

data_processing:
Quality of RNA-seq FASTQ files was assessed with FastQC v0.11.9 (Babraham Bioinformatics, Cambridge, UK).
Adapter sequences were removed with the use of cutadapt v2.10.
miRNA read counts were obtained using miRDeep2 v2.0.1.2. miRbase v22.1 database was a source of reference miRNA sequences.
Assembly: GENCODE GRCh38.p13
Supplementary files format and content: counts.tsv – tab-delimited miRNA read counts table

organism: Homo sapiens

source_name: colon

growth_protocol: The human colon adenocarcinoma cell line HT-29 was purchased from the European Cell Culture Collection (Porton Down, Wiltshire, UK). Cells were grown in RPMI 1640 + L-Glutamine (Gibco, Thermo Fisher Scientific, MA, USA) supplemented with 10% fetal calf serum (Gibco), 1% penicillin and streptomycin (Gibco) and cultured under standard cell culture conditions (37°C, saturated humidity, 5% CO2). The HT-29 cells were additionally tested for mycoplasma contamination. CD44 knockdown in HT-29 cells was achieved by a shRNA-mediated approach. All animals used were pathogen-free Balb/c severe combined immunodeficient (SCID) mice aged 9-14 weeks with a weight of 25-30 g at the beginning of the experiment. Each animal was inoculated subcutaneously (s. c.) above the right scapula with 1 x 106 shLUC or shCD44 HT-29 cells in medium without supplements. The mice were euthanized when the tumors ulcerated or reached a size of ~1.5 cm³.

extract_protocol:
Approximately 50 mg of fresh-frozen xenograft PT tissue was crushed in liquid nitrogen in the presence of QIAzol Lysis Reagent (Qiagen, Hilden, Germany). The total RNA was isolated using miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. All RNA samples were treated with DNase I during the isolation procedure. The RNA yield was determined by UV absorbance using a NanoDrop 1000 spectrophotometer (Peqlab, Erlangen, Germany). The RNA quality was assessed by analyzing the ribosomal RNA integrity number (RIN) on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, Palo Alto, CA, USA). The RIN values of the isolated RNA samples ranged from 6.7 to 9.6.
Libraries for miRNA sequencing were prepared from total RNA samples using NEBNext Multiplex Small RNA Library Prep Kit for Illumina. Each sample was sequenced on the Illumina NextSeq 550 to generate single-end 50-nucleotide reads: 7 control samples (shLUC) and 8 samples with CD44 knockdown (shCD44).

value: colon

tag: cell line

tag: cell type

value: human colorectal adenocarcinoma

tag: origin

value: Xenograft

tag: strain

value: SCID

value: shLUC


title: PT_scion_21_3


title: PT_scion_21_4


title: PT_scion_21_1


title: Smartseq2_355


title: shCD44_8

description: Library name: shCD44_8


title: shCD44_7

description: Library name: shCD44_7


title: TP_stock_21_5

source_name: Stock

value: Stock


title: TP_stock_21_4


title: Smartseq2_354


title: shCD44_6

description: Library name: shCD44_6


title: TP_stock_21_3


title: TP_stock_21_2


title: shCD44_5

description: Library name: shCD44_5


title: PP_stock_21_5


title: Smartseq2_353


title: TP_stock_21_1


title: shLUC_2

description: Library name: shLUC_2


title: shCD44_4

description: Library name: shCD44_4


title: Smartseq2_352


title: PP_stock_21_4


title: Smartseq2_350


title: PP_stock_21_1


title: Smartseq2_351


title: shCD44_3

description: Library name: shCD44_3


title: PP_stock_21_2


title: PT_scion_21_2


title: PP_scion_21_4


title: shCD44_2

description: Library name: shCD44_2


title: Smartseq2_349


title: Smartseq2_356


title: shCD44_1

description: Library name: shCD44_1


title: PP_scion_21_3


title: PP_scion_21_2


title: TIRE-seq Human T cell library

city: Melbourne

first: Daniel

middle: Victor

last: Brown

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description:
Library name: TIRE_Tcell
Reverse transcription based sequencing
See feature_README.txt for sample metadata and barcodes.

data_processing:
Fastq data was processed into count matrices with v2.9.7 zUMIs.
Count matrices were converted into SingleCellExperiment objects with Bioconductor package SingleCellExperiment v1.29.1
Assembly: Reads were mapped against 10x Genomics pre-built references (July 7, 2020 version); GRCh38 v2-7-3a for human experiments mm10-2020-A for mouse experiments or hg19 and mm10 for mixed species experiments.
Supplementary files format and content: R Data Serialization (.rds) object that can be read into R with the readRDS() function

source_name: T cells

extract_protocol:
UHRR was a commerical source of RNA (ThermoFisher QS0639). Prime-seq was SPRI based RNA extraction. No extraction for TIRE-seq.
Prime-seq and TIRE-seq as described in protocols.io dx.doi.org/10.17504/protocols.io.j8nlk8rqdl5r/v1

value: T cells


title: Ungraft_P_21_5

source_name: Ungrafted stem

value: Ungrafted stem


title: PP_scion_21_1


title: Ungraft_P_21_4


title: PP_stock_21_3


title: Smartseq2_347


title: Ungraft_P_21_3


title: Prime-seq Human T cell library

description:
Library name: Prime_Tcell
Reverse transcription based sequencing
See feature_README.txt for sample metadata and barcodes.

value: CD3 and CD28


title: Prime-seq HEK293T library

description:
Library name: Prime_HEK
Reverse transcription based sequencing
See feature_README.txt for sample metadata and barcodes.


title: Smartseq2_346


title: Ungraft_P_21_2


title: PP_scion_21_5


title: PT_scion_14_5

value: 14 DAG


title: PT_scion_14_3


title: Prime-seq UHRR library

description:
Library name: Prime_UHRR
Reverse transcription based sequencing
See feature_README.txt for sample metadata and barcodes.

source_name: ThermoFisher QS0639

value: ThermoFisher QS0639


title: Smartseq2_345


title: TP_stock_14_3


title: PT_scion_14_1


title: TP_stock_14_2


title: Smartseq2_342


title: Smartseq2_343


title: PT_scion_14_2


title: TP_stock_14_1


title: TP_stock_14_4


title: Smartseq2_341


title: PP_stock_14_5


title: PP_stock_14_4


title: Donor1_2_CD4-LV_CD8-LV

city: Langen

first: Christian J.

last: Buchholz

state: Hessen

address: Paul-Ehrlich-Strasse 51-59

country: Germany

institute: Paul Ehrlich Institut

data_processing:
The raw reads allignment to the reference sequences and demultiplexing was performed with the Seven Bridges Genomics platform using  BD Rhapsody Targeted Analysis Pipeline Version 1.10, by using feature_README.fasta file as AbSeq reference, CAR_reference.fasta file as genome reference. Single-Cell Multiplex Kit- Human was used as sample Tag Version.
Assembly: BD_Rhapsody_Immune_Response_Panel_Hs_FASTA plus supplementary genes. Al l genes are listed in CAR_reference.fasta file.
Supplementary files format and content: SevenBridges output file: RSEC_MolsPerCell.csv
Library strategy: scRNA-seq and AbSeq

source_name: PBMCs

extract_protocol:
Activated PBMCs from two healthy donors were transduced with four different LVs, harvested 72 hours later, and processed for single-cell isolation using the BD Rhapsody system. Before single-cell isolation, all samples were enriched for viable cells using the Dead Cell Removal Kit (Miltenyi Biotec). The Pan T cell isolation kit (Miltenyi Biotec) was used for negative magnetic enrichment of CD3 T cells in the CD3-LV and VSV-LV treated groups, and the CD4 or CD8 isolation kits (Miltenyi Biotec) were used to enrich for CD4 or CD8 T cells in the CD4-LV and CD8-LV treated groups, respectively. Cells were labeled with AbSeqs and multiplexing sample tags and were mixed and loaded into three cartridges.
Library was generated acording to the protocol provided by BD biosciences 'mRNA Targeted, Sample Tag, and BD™ AbSeq Library Preparation with the BD Rhapsody™ Targeted mRNA and AbSeq Amplification Kit' (Doc ID: 214508 Rev. 3.0). Cellular mRNA, AbSeqs, and sample tag barcodes captured on poly(dT)-coated magnetic beads were reverse transcribed according to the manufacturer’s protocol. The cDNA was amplified using the immune response panel (Cat. No. 633750, BD Biosciences) and a panel of complementary custom primers to detect the CAR gene and several other genes of interest as listed in CAR_reference.fasta. The custom primers were designed and supplied by BD Biosciences. Libraries generated for different samples in a multiplex approach

value: PBMCs


title: Donor2_CD3-LV_VSV-LV


title: Smartseq2_340


title: Smartseq2_344


title: TIRE-seq UHRR library

description:
Library name: TIRE_UHRR
Reverse transcription based sequencing
See feature_README.txt for sample metadata and barcodes.


title: PP_stock_14_2


title: PP_scion_14_5


title: [01-018][TTm][p7]

city: Marseille

first: Pierre

last: Milpied

address: Parc Scientifique de Luminy, case 906

country: France

institute: Centre d'Immunologie de Marseille-Luminy (CIML)

data_processing:
Fastq files were generated with the DRAGEN software embedded on the Nextseq2000 sequencer. We then used a custom bioinformatics pipeline to process fastq files and generate single-cell gene expression matrices and TCR sequence files. Briefly, reads were processed with the zUMIs pipeline60 to generate the gene expression UMI count matrix, and with the TRUST4 pipeline61 to reconstruct TCR sequences.
Assembly: GRCh38 with additional artificial chromosome for 92 ERCC spike-in genes.
Supplementary files format and content: Seurat RDS object including umi counts and metadata (sample, cell type, stimulation condition)

source_name: Blood

extract_protocol:
mini-bulk Flash-FB5P-seq
For scRNA-seq of tetramer-stained CD4 T cells, we used an updated version of FB5P-seq (Flash-FB5P-seq) modified to implement advances developed by Hahaut et al. in the Flash-seq protocol59. Cells were sorted in 2 µl lysis mix composed of 0.1% Triton X-100 (0.02 µl), 1.2 U/µl recombinant RNAse inhibitor (0.06 µl), 6 mM dNTP mix (0.48 µl), 1.6 mM RT primer (5’-TGCGGTATCTAAAGCGGTGAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT*V*N-3’) (0.36 µl), 0.0125 pg/µl ERCC spike-in mix (0.05 µl), 9 mM dCTP (0.18 µl), 1 M betaine (0.4 µl), 1.2 mM DTT (0.024 µl) and PCR-grade H2O (0.426 µl). Plates were conserved at −80°C until sorting, thawed at RT for cell sorting, and immediately refrozen on dry ice then conserved at −80°C until further processing. Reverse transcription with template switching and cDNA amplification were performed in a single step. Each plate containing cells in lysis mix was thawed on ice, heated at 72°C for 3 min then immediately placed on ice. To each well containing 2 µl cell lysate, we added 8 µl of an RT-PCR mix composed of 2 U/µl Superscript IV reverse transcriptase (0.1 µl), 0.8 U/µl recombinant RNAse inhibitor (0.2 µl), 1X KAPA HiFi ReadyMix (5 µl), 4.8 mM DTT (0.48 µl), 0.8 M betaine (1.6 µl), 9.2 mM MgCl2 (0.092 µl), 0.1 µM forward PCR primer (5’-AGACGTGTGCTCTTCCGAT*C*T-3’) (0.1 µl), 0.1 µM reverse PCR primer (5’-TGCGGTATCTAAAGCGGTG*A*G-3’) (0.1 µl), 1.84 µM biotinylated barcoding template switching oligonucleotide (5’-biotin-AGACGTGTGCTCTTCCGATCTXXXXXXXXNNNNNNNNCAGCArGrGrG-3’, where XXXXXXXX are well-specific barcodes as published58, NNNNNNNN are random nucleotides serving as Unique Molecular Identifiers, and rG are riboguanosine RNA bases) (0.184 µl) and PCR-grade H2O (0.144 µl). Then plates were incubated in a thermal cycler 60 min at 50°C, 3 min at 98°C, and 22 cycles of 20 sec at 98°C, 20 sec at 67°C and 6 min at 72°C. We then pooled 5 µl amplified cDNA from all wells into one tube per plate, and performed 0.6X SPRI bead-based purification. Sequencing libraries were prepared from 800 pg cDNA per plate with the Illumina Nextera XT protocol, modified to target sequencing reads to the 5’ end of cDNA, as described 22,58. Before sequencing, pooled indexed libraries were depleted from ribosomal RNA-derived cDNA molecules by using the SEQoia RiboDepletion Kit (Biorad) according to the manufacturer’s instructions. Flash-FB5P-seq libraries were sequenced on an Illumina NextSeq2000 using P3 100 cycle kit and targeting 5×105-1×106 reads per cell in paired-end single-index mode with the following configuration: Read1 (gene template) 114 cycles, Read i7 (plate barcode) 8 cycles, Read2 (cell barcode and Unique Molecular Identifier) 16 cycles.
mini-bulk Flash-FB5P-seq

value: Blood

tag: sorting phenotype

tag: sampleID


title: PP_scion_14_4

value: Scion


title: Smartseq2_339

value: D-LN


title: PP_scion_14_3


title: [01-128][TTm][p6]


title: [01-004][TTm][p5]


title: PP_scion_14_2


title: PP_scion_14_1


title: Ungraft_P_14_5


title: Donor1_CD3-LV_VSV-LV


title: Smartseq2_338


title: PT_scion_7_4

value: 7 DAG


title: Ungraft_P_14_3


title: [01-140][TTm][p2]


title: Ungraft_P_14_2


title: [01-001 (1-2), 01-046 (3-96)][TTm][p1]


title: Ungraft_P_14_1


title: Ungraft_P_14_4


title: PT_scion_7_5


title: [01-061-02][stim]

tag: cell subset

tag: stimulation


title: Smartseq2_336

value: SV


title: Smartseq2_334

value: Filtered


title: Smartseq2_348


title: PP_stock_14_1


title: Smartseq2_335


title: [01-051][TTm][p3]


title: TP_stock_7_4


title: [01-018][TTm][p4]


title: [01-258-02][stim]


title: PT_scion_7_1


title: TP_stock_7_3


title: Smartseq2_337


title: Smartseq2_331


title: TP_stock_7_1


title: PP_stock_7_3


title: [01-135-04][stim]


title: PP_stock_7_2


title: PT_scion_7_3


title: Smartseq2_333


title: Smartseq2_330


title: PP_scion_7_5


title: PP_scion_7_4


title: [01-152-04][stim]


title: [01-140-07][stim]


title: PP_stock_7_1


title: Smartseq2_329


title: PP_scion_7_3


title: Smartseq2_328


title: PP_scion_7_2


title: PP_scion_7_1


title: [Ag-specific CD4 T cell][08 003 01][C.ALB][H9N063J4]

data_processing:
Base calls were processed to FASTQs by Dragen software onboard NextSeq2000; fastq files were processed as described in https://github.com/MilpiedLab/FB5P-seq. To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Assembly: GRCh38 with additional artificial chromosome for 92 ERCC spike-in genes.
Supplementary files format and content: comma separated values text file includes the UMI counts for all genes (columns) in all cells (rows) from the dataset.

tag: ag specificity

value: CD4 T cells


title: Ungraft_P_7_5


title: Ungraft_P_7_4


title: Smartseq2_327


title: Ungraft_P_7_1


title: [Ag-specific CD4 T cell][08 003 01][CYP2D6][H9N063J3]


title: Smartseq2_326


title: [Ag-specific CD4 T cell][UKELKM_6][CYP2D6][H9N063J2]


title: [Ag-specific CD4 T cell][01 247 01][SPIKE][H9N063J5]

value: SPIKE


title: Smartseq2_325


title: CS33 replicate 3

city: Toronto

first: yacine

last: touahri

address: 2075 Bayview Ave

country: Canada

institute: Sunnybrook Research Institute

data_processing:
Data were processed using Cell Ranger pipeline
Assembly: hg19 Human genome reference
Supplementary files format and content: tab separated values and matrix files

molecule: nuclear RNA

source_name: Human cerebral organoids

growth_protocol: Organoids were created using the STEMdiff Dorsal Forebrain Organoid Differentiation Kit (STEMCELL Technologies 08620) as per kit protocol, except that organoids were transferred to a 12-well plate with a miniaturized multiwell spinning bioreactor SpinΩ lid (PMID: 29470464) ≥day 14, matrigel (1% v/v) was added to all media ≥day 20 and Brain derived neurotrophic factor (20 ng/ml) was added to all media ≥day 30.

extract_protocol:
Four batches of 5 COs were pooled and flash frozen. Nuclei extraction was performed on frozen tissue as per manufacturer’s instructions (Nuclei isolation kit, 10x Genomics). Freshly isolated nuclei were counted using a Countess® II FL Automated Cell Counter (ThermoFisher Scientific) and immediately processed using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10X genomics, Cat # 1000263). For each reaction, 16500 nuclei were loaded onto GEM Chip K for an expected recovery of 10,000 nuclei.
For each reaction, 16500 nuclei were loaded onto GEM Chip K for an expected recovery of 10,000 nuclei. Gel Beads-in-emulsion were generated using the Chromium Controller followed by cDNA generation and amplification (13 cycles) as per manufacturer’s instructions. For each sample, 50ng of cDNA was used for library generation.

value: Human cerebral organoids

value: hESCs


title: CS31 replicate 1


title: CS34 replicate 4


title: [Ag-specific CD4 T cell][01 247 01][PDCE2 TOT][H9N063IG]

value: PDCE2 TOT


title: Smartseq2_324


title: Cerebellar organoid, mNeon-neg, differentiation 4

city: London

first: Elizabeth

last: Apsley

address: New Hunt's House, Guys campus

department: CDN

institute: Kings College London

description:
Library name: LCD19_neg
LCD19_neg

data_processing:
Read alignment and quantification was performed using Kallisto with Ensembl release 108.Transcripts were mapped to genes using tximport in R. Genes with more than 10 counts in 4 samples were included in analysis.
Variance stabilising transform (VST) from DESeq2 was applied to normalise expression
Assembly: Human genome Ensembl release 108
Supplementary files format and content: CbO_mNeonseq_counts.txt count matrix from DESeq2 object containing 8 columns of samples and 17884 rows of genes.

source_name: iPSC-derived cerebellar organoid

growth_protocol: Human iPSCs were differentiated to cerebellar organoids using established differentiation protocol (Tolonen, Apsley et al., 2024).

extract_protocol:
Total RNA was extracted from sorted cells using Qiagen RNeasy micro kit.
Libraries were prepared for sequencing using the NEBNext Ultra II Directional mRNA kit, with 22-58 ng input RNA.

treatment_protocol: At day 63 of differentiation, organoids were dissociated to single cells and flow cytometry performed to sort mNeon-positive and mNeon-negative populations of cells.

value: iPSC-derived cerebellar organoid

value: FOXP2-mNeon (AH017-3)

value: mNeon-neg


title: CS32 replicate 2


title: Smartseq2_323


title: Cerebellar organoid, mNeon-pos, differentiation 4

description:
Library name: LCD19_pos
LCD19_pos

value: mNeon-pos


title: [Ag-specific CD4 T cell][01 018 22][C.ALB][H9N063GK]


title: [Ag-specific CD4 T cell][01 018 22][SLA][H9N063IY]

value: SLA


title: Cerebellar organoid, mNeon-neg, differentiation 3

description:
Library name: LCD18_neg
LCD18_neg


title: Smartseq2_322


title: Cerebellar organoid, mNeon-pos, differentiation 3

description:
Library name: LCD18_pos
LCD18_pos


title: Cerebellar organoid, mNeon-pos, differentiation 2

description:
Library name: LCD17_pos
LCD17_pos


title: Cerebellar organoid, mNeon-neg, differentiation 2

description:
Library name: LCD17_neg
LCD17_neg


title: Smartseq2_321


title: [Ag-specific CD4 T cell][UKELKM_4][CYP2D6][H9N063IL]


title: Cerebellar organoid, mNeon-pos, differentiation 1

description:
Library name: LCD16_pos
LCD16_pos


title: Smartseq2_320


title: [Ag-specific CD4 T cell][01 239 01][C.ALB][H9H07JJN]


title: [Ag-specific CD4 T cell][01 239 01][PDCE2 TOT][H9N07JF2]


title: Smartseq2_319


title: [Ag-specific CD4 T cell][01 232 01][C.ALB][H9H07JJG]


title: A1

city: Nanjing

first: Shu

last: Xu

state: Jiangsu Province

address: China Pharmaceutical University

country: China

institute: China Pharmaceutical University

description:
Library name: Sample 1
ctrl-A1.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: human
Supplementary files format and content: raw. and txt.

source_name: Lung

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 µg/mL streptomycin at 37 °C with 5% CO2 incubation. Cells were seeded into 6-well plates (Corning) 24 h prior to transfection at a density of 200,000 cells per well.

extract_protocol:
Total RNA was prepared from transfection experiments after 48 h using a RNA Isolation Reagent (R701-01, Vazyme). 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

treatment_protocol: Cells were transfected by using TransIntro EL Transfection Reagent following the manufacturer’s recommended protocol. For each well of a 24-well plate, protein of FEN1 (2 pmol) and hpDNA (18 pmol) were transfected 24 h later.

value: Lung

value: A549 cells

value: Human non-small-cell lung carcinoma cell line

tag: genotype

value: TransIntro EL Transfection Reagent

tag: batch

value: total RNA


title: Smartseq2_316

value: D-LN

value: SV


title: Smartseq2_317


title: A3

description:
Library name: Sample 3
ctrl-A3.txt


title: B1

description:
Library name: Sample 4
text-B1.txt


title: B3

description:
Library name: Sample 6
text-B3.txt


title: B2

description:
Library name: Sample 5
text-B2.txt


title: [Ag-specific CD4 T cell][01 232 01][PDCE2 TOT][H9H07JJK]

value: Blood

value: CD4 T cells


title: scRNA-seq of ATRIP, HC1, HC2 and HC3 (2)

city: Gent

first: Evi

last: Duthoo

address: Molenaarsstraat 148

country: Belgium

institute: Ghent University

description:
Library name: LBA004_cDNA_S4
10X Genomics

data_processing:
After demultiplexing, we get 942.85M PF reads for our project, corresponding to 996.977M raw PF reads (41% of the lane). The pooling is in line with the expectations (according to M reads).
Further preprocessing was performed using the Cellranger v6.1.1 pipeline
Assembly: GRCh38.99
Supplementary files format and content: Filtered feature barcode matrices:
Supplementary files format and content: Format: Sparse matrix in Market Exchange format
Supplementary files format and content: Files: `LBAXXX_barcodes.tsv.gz`, `LBAXXX_features.tsv.gz`, `LBAXXX_matrix.mtx.gz`.
Supplementary files format and content: Content: Gene expression (cDNA) and feature barcode (FB5P: ADT/HTO) counts, processed using Cell Ranger v6.1.1.
Supplementary files format and content: TCR/BCR annotation files:
Supplementary files format and content: Format: CSV files.
Supplementary files format and content: Files: 'LBAXXX_XCR_filtered_contig_annotations.csv', 'LBAXXX_XCR_clonotypes.csv', 'LBAXXX_XCR_consensus_annotations.csv'.
Supplementary files format and content: Content: High-confidence TCR/BCR contigs, clonotypes and consensus sequences, processed using Cell Ranger v6.1.1.
Supplementary files format and content: Supplementary files:
Supplementary files format and content: The R scripts used to generate the visualisations in the publication will be available on GitHub from publication of the manuscript onwards: https://github.com/LeanderJonckheere/ATRIP_deficiency_JEM.git. The scripts start from the supplementary .rds files included in this repository.
Supplementary files format and content: ATRIP_merge_18062024.rds: This file contains all PBMC samples merged into a single Seurat object. It includes gene expression (RNA), ADT, and HTO data across all assays.
Supplementary files format and content: LBA001_LBA002_T_reclustered.rds: Reclustering of T cells derived from LBA001 and LBA002 samples, including integrated TCR sequencing data.
Supplementary files format and content: ATRIP_T_reclustered.rds, HC1_T_reclustered.rds, HC2_T_reclustered.rds, HC3_T_reclustered.rds: T cells subsetted and reclustered by sample, enabling detailed per-sample analysis.
Supplementary files format and content: CD8_TEM_all_patients.rds, CD8_TEM_ATRIP.rds, CD8_TEM_HC1.rds, CD8_TEM_HC2.rds, CD8_TEM_HC3.rds: Subsets of CD8 TEM cells, reclustered for both all patients and individual samples.
Supplementary files format and content: LBA003_LBA004_BCR_merge_Azimuth_subset.rds: Reclustering of B cells derived from LBA003 and LBA004 samples, with integrated BCR sequencing data.
Supplementary files format and content: ATRIP_B.rds, HC1_B.rds, HC2_B.rds, HC3_B.rds: B cell subsets reclustered by sample, enabling per-sample analysis.

source_name: Sorted viable CD19+ B cells

extract_protocol:
PBMCs and live B cells (following FACS) were resuspended and stored pending sequencing in buffer containing PBS + 0.04% BSA.
The cells were stained with TotalSeq antibodies (ADT's and HTOs). Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the Chromium controller 3. Single-cell cDNA, FB5P (TotalSeq C ADT/HTO), BCR-enriched and TCR-enriched libraries were prepared using the SI-TT-F11 sample index with 14 PCR cycles and a final reaction volume of 35 µL. Quality control (QC) was conducted using the cDNA Bioanalyzer. The run follows the standard expectations as described by Illumina as we get 2441M raw Passed Filter (PF) reads for the full lane, while the %>=Q30 is 95% for Read 1 and 92% for Read 2.

value: Sorted viable CD19+ B cells

tag: library type

value: mRNA


title: CITE-seq of ATRIP, HC1, HC2 and HC3 (2)

description:
Library name: LBA004_FB5P_S8
10X Genomics

library_source: other

data_processing:
After demultiplexing, we get 942.85M PF reads for our project, corresponding to 996.977M raw PF reads (41% of the lane). The pooling is in line with the expectations (according to M reads).
Further preprocessing was performed using the Cellranger v6.1.1 pipeline
Assembly: GRCh38.99
Supplementary files format and content: Filtered feature barcode matrices:
Supplementary files format and content: Format: Sparse matrix in Market Exchange format
Supplementary files format and content: Files: `LBAXXX_barcodes.tsv.gz`, `LBAXXX_features.tsv.gz`, `LBAXXX_matrix.mtx.gz`.
Supplementary files format and content: Content: Gene expression (cDNA) and feature barcode (FB5P: ADT/HTO) counts, processed using Cell Ranger v6.1.1.
Supplementary files format and content: TCR/BCR annotation files:
Supplementary files format and content: Format: CSV files.
Supplementary files format and content: Files: 'LBAXXX_XCR_filtered_contig_annotations.csv', 'LBAXXX_XCR_clonotypes.csv', 'LBAXXX_XCR_consensus_annotations.csv'.
Supplementary files format and content: Content: High-confidence TCR/BCR contigs, clonotypes and consensus sequences, processed using Cell Ranger v6.1.1.
Supplementary files format and content: Supplementary files:
Supplementary files format and content: The R scripts used to generate the visualisations in the publication will be available on GitHub from publication of the manuscript onwards: https://github.com/LeanderJonckheere/ATRIP_deficiency_JEM.git. The scripts start from the supplementary .rds files included in this repository.
Supplementary files format and content: ATRIP_merge_18062024.rds: This file contains all PBMC samples merged into a single Seurat object. It includes gene expression (RNA), ADT, and HTO data across all assays.
Supplementary files format and content: LBA001_LBA002_T_reclustered.rds: Reclustering of T cells derived from LBA001 and LBA002 samples, including integrated TCR sequencing data.
Supplementary files format and content: ATRIP_T_reclustered.rds, HC1_T_reclustered.rds, HC2_T_reclustered.rds, HC3_T_reclustered.rds: T cells subsetted and reclustered by sample, enabling detailed per-sample analysis.
Supplementary files format and content: CD8_TEM_all_patients.rds, CD8_TEM_ATRIP.rds, CD8_TEM_HC1.rds, CD8_TEM_HC2.rds, CD8_TEM_HC3.rds: Subsets of CD8 TEM cells, reclustered for both all patients and individual samples.
Supplementary files format and content: LBA003_LBA004_BCR_merge_Azimuth_subset.rds: Reclustering of B cells derived from LBA003 and LBA004 samples, with integrated BCR sequencing data.
Supplementary files format and content: ATRIP_B.rds, HC1_B.rds, HC2_B.rds, HC3_B.rds: B cell subsets reclustered by sample, enabling per-sample analysis.
Library strategy: CITE-seq

molecule: protein

value: ADT


title: [Ag-specific CD4 T cell][01 018 22][SLA][H9N063IZ]


title: Cerebellar organoid, mNeon-neg, differentiation 1

description:
Library name: LCD16_neg
LCD16_neg

value: iPSC-derived cerebellar organoid


title: Smartseq2_315


title: CITE-seq of ATRIP, HC1, HC2 and HC3 (1)

description:
Library name: LBA003_FB5P_S7
10X Genomics


title: scRNA-seq of ATRIP, HC1, HC2 and HC3 (1)

description:
Library name: LBA003_cDNA_S3
10X Genomics


title: BCR-seq of ATRIP, HC1, HC2 and HC3 (repeat)

description:
Library name: LBA004_BCR_S12
10X Genomics

value: BCR


title: [Ag-specific CD4 T cell][01-213-02][SPIKE][H9N063GG]

value: SPIKE


title: BCR-seq of ATRIP, HC1, HC2 and HC3

description:
Library name: LBA003_BCR_S11
10X Genomics


title: Smartseq2_318


title: [Ag-specific CD4 T cell][01-213-02][SPIKE][H9N063GN]


title: Smartseq2_313

value: Filtered


title: TCR-seq of HC2 and HC3

description:
Library name: LBA002_TCR_S10
10X Genomics

data_processing:
After demultiplexing, we get 942.85M PF reads for our project, corresponding to 996.977M raw PF reads (41% of the lane). The pooling is in line with the expectations (according to M reads).
Further preprocessing was performed using the Cellranger v6.1.1 pipeline
Assembly: GRCh38.99
Supplementary files format and content: Filtered feature barcode matrices:
Supplementary files format and content: Format: Sparse matrix in Market Exchange format
Supplementary files format and content: Files: `LBAXXX_barcodes.tsv.gz`, `LBAXXX_features.tsv.gz`, `LBAXXX_matrix.mtx.gz`.
Supplementary files format and content: Content: Gene expression (cDNA) and feature barcode (FB5P: ADT/HTO) counts, processed using Cell Ranger v6.1.1.
Supplementary files format and content: TCR/BCR annotation files:
Supplementary files format and content: Format: CSV files.
Supplementary files format and content: Files: 'LBAXXX_XCR_filtered_contig_annotations.csv', 'LBAXXX_XCR_clonotypes.csv', 'LBAXXX_XCR_consensus_annotations.csv'.
Supplementary files format and content: Content: High-confidence TCR/BCR contigs, clonotypes and consensus sequences, processed using Cell Ranger v6.1.1.
Supplementary files format and content: Supplementary files:
Supplementary files format and content: The R scripts used to generate the visualisations in the publication will be available on GitHub from publication of the manuscript onwards: https://github.com/LeanderJonckheere/ATRIP_deficiency_JEM.git. The scripts start from the supplementary .rds files included in this repository.
Supplementary files format and content: ATRIP_merge_18062024.rds: This file contains all PBMC samples merged into a single Seurat object. It includes gene expression (RNA), ADT, and HTO data across all assays.
Supplementary files format and content: LBA001_LBA002_T_reclustered.rds: Reclustering of T cells derived from LBA001 and LBA002 samples, including integrated TCR sequencing data.
Supplementary files format and content: ATRIP_T_reclustered.rds, HC1_T_reclustered.rds, HC2_T_reclustered.rds, HC3_T_reclustered.rds: T cells subsetted and reclustered by sample, enabling detailed per-sample analysis.
Supplementary files format and content: CD8_TEM_all_patients.rds, CD8_TEM_ATRIP.rds, CD8_TEM_HC1.rds, CD8_TEM_HC2.rds, CD8_TEM_HC3.rds: Subsets of CD8 TEM cells, reclustered for both all patients and individual samples.
Supplementary files format and content: LBA003_LBA004_BCR_merge_Azimuth_subset.rds: Reclustering of B cells derived from LBA003 and LBA004 samples, with integrated BCR sequencing data.
Supplementary files format and content: ATRIP_B.rds, HC1_B.rds, HC2_B.rds, HC3_B.rds: B cell subsets reclustered by sample, enabling per-sample analysis.
Library strategy: TCR-Seq

source_name: PBMC

value: PBMC

value: TCR


title: A2

description:
Library name: Sample 2
ctrl-A2.txt

value: Lung

value: A549 cells


title: [Ag-specific CD4 T cell][01-213-02][FLU][H9N063II]

value: FLU


title: Adult_CupRap_Forebrain_MERFISH_Biol2

type: RNA

city: Vancouver

first: Freda

middle: D.

last: Miller

state: BC

department: Michael Smith Laboratories, Department of Medical Genetics

institute: University of British Columbia

description:
Mouse brain gene panel
Vizgen MERSCOPE Instrument

hyb_protocol: Sections were processed in accordance with MERSCOPE guidelines for fresh frozen tissue prior to hybridization. Encoding probes were hybirdized for 36-48hours at 37°C. Following encoding probe hydribization, sections were processed in accordance with recommended protocols. Once loaded onto the MERSCOPE instrument, the sections were subjected to sequential rounds of readout probe hybridization.

scan_protocol: Full sections were imaged and analyzed using the Xenium Analyzer, software v1.7.6.0.

data_processing: Output files (cell_metadata, cell_by_gene, detected_transcripts, summary, and visualizer (.vzg) files) were generated directly by the Vizgen MERSCOPE onboard processing pipeline.

label: Gene targeting probes

label_protocol: Single cell spatial transcriptomics was performed using a panel targeting 300 mRNA transcripts. The 300 gene custom probe panel was designed to to include relevant cell type markers, ligands and receptors, all genes included in the panel are  documented in Willis et al. supplementary table 2 and in the MERSCOPEgene_panel.csv raw data file attached.

extract_protocol: Brains were dissected from adult CD-1 mice following exposure to 6 weeks of cuprizone-rapamycin or control (normal chow-vehicle injection) with 3 weeks recovery. Once dissected, brains were immediately embedded in O.C.T. compound (Tissue-Tek) on dry ice, stored at -70°C, and cryosectioned coronally onto VIzgen MERSCOPE slides to produce 10 μm sections.

treatment_protocol: Control animals were exposed to Vehicle I.P injection 5 consecutive days per week (5% PEG400; 5% Tween 80; and 5% ethanol, reconstituted in PBS), normal powdered chow - for 6 weeks. Cuprizone-rapamycin (CupRap) were exposed to rapamycin I.P injection 5 consecutive days per week (10 mg/kg rapamycin, R-5000, LC Laboratories; dissolved in 5% ethanol, 5% polyethylene glycol 400 (PEG400), Sigma; 5% Tween 80, Sigma; in PBS), ad libitum 0.3% cuprizone in powdered chow for 6 weeks. All animals had 3 weeks recovery prior to collection.

tag: sample type

value: CD-1, M/F, adult, brain, forebrain, cuprizone-rapamycin


title: CITE-seq of HC2 and HC3

description:
Library name: LBA002_FB5P_S6
10X Genomics


title: Smartseq2_311

value: D-LN


title: scRNA-seq of HC2 and HC3

description:
Library name: LBA002_cDNA_S2
10X Genomics


title: [Ag-specific CD4 T cell][01-213-02][FLU][H9N063IH]


title: Adult_Control_Forebrain_MERFISH_Biol1

value: CD-1, M/F, adult, brain, forebrain, control


title: [Ag-specific CD4 T cell][01-213-02][PDCE2 TOT][H9N063GL]

value: Blood

value: PDCE2 TOT


title: TCR-seq of ATRIP and HC1

description:
Library name: LBA001_TCR_S9
10X Genomics


title: CITE-seq of ATRIP and HC1

description:
Library name: LBA001_FB5P_S5
10X Genomics


title: HEPA-RG cell line treated with sEV from patient IHR3 after VLCKD

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

description: HEPA-RG+sEV from patient IHR3 at T1

data_processing:
Basecalling (Ion Torrent S5)
Alignment (Torrent mapping alignment program)
Quantification (Ion Torrent Ampliseq RNA plugin, unique mapping mode)
Count Normalizition (Transcriptome Analysis Console)
Assembly: hg19_Ampliseq transcriptome
Supplementary files format and content: Count Normalized in reads per million

source_name: HEPA-RG

growth_protocol: HEPA-RG human hepatoma cell line (Thermo Fisher Scientific, Waltham, MA, USA) was cultured using a hepatocyte bullet kit medium supplemented with 10% exosome-depleted FBS from Lonza Biowhittaker (Oslo, Norway) and 1% Antibiotic-Antimycotic (penicillin 10,000 U/mL, streptomycin 10,000 U/mL)

extract_protocol:
Total RNA from HEPA-RG treated with sEVs was extracted with miRNeasy® Mini kit (QIAGEN, Hilden, Germany)
Libraries were templated with the Ion Chef and sequenced using a 540 chip on the Ion GeneStudio S5 Prime system (Thermo Fisher Scientific,Waltham, MA, USA).

treatment_protocol: HEPA-RG were treated with sEVs cell line was cultured forming semi-confluent monolayers and then treated with sEVs derived from patients LR or IHR for chronic liver disease. The treatment concentration was 20 μg/μL of sEVs proteins for 8h

value: HEPA-RG

value: 20 μg/μL of Small Extracellular Vesicles

tag: disease

value: Obese Intermediate-Hight Risk patients after VLCKD


title: [Ag-specific CD4 T cell][01-213-02][PDCE2 TOT][H9N063GH]

tag: tissue

value: CD4 T cells


title: [Ag-specific CD4 T cell][01-192-02][FLU][H9N063Ik]


title: Smartseq2_314

tag: number of_cells_sorted

value: SV


title: Smartseq2_308

tag: treatment


title: HEPA-RG cell line treated with sEV from patient IHR3 before VLCKD

description: HEPA-RG+sEV from patient IHR3 at T0

tag: cell line

value: Obese Intermediate-Hight Risk patients before VLCKD


title: [Ag-specific CD4 T cell][01-192-02][FLU][H9N063IJ]

tag: cell type


title: [Ag-specific CD4 T cell][01-192-02][SLA][H9N063GC]

value: SLA


title: Adult_Control_Forebrain_MERFISH_Biol2


title: Smartseq2_312


title: Adult_CupRap_Forebrain_MERFISH_Biol1


title: HEPA-RG cell line treated with sEV from patient IHR2 before VLCKD

description: HEPA-RG+sEV from patient IHR2 at T0


title: Smartseq2_307


title: siSRBD1 48h Biological Repeat 2

city: Nashville

first: David

last: Cortez

state: TN

address: 2215 Garland Avenue

department: Biochemistry

institute: Vanderbilt University School of Medicine

description:
Library name: 5972-SW-6
column name in RNAseqSRWReadcounts.txt is 5972-SW-6

data_processing:
Reads were trimmed to remove adaptor sequences and aligned to hg38 using HiSat2. Feature Counts ws used to count the number of mapped reades to each gene.
Assembly: hg38
Supplementary files format and content: tab delimited text file contains raw readcounts for each sample

growth_protocol: Cells were grown in DMEM + 7.5% FBS

extract_protocol:
RNA was extracted with the Aurum total RNA mini kit (BioRad).
Library was prepared with the NEB stranded mRNA kit according to the manufacturer's instructions.

treatment_protocol: siRNA transfections were performed with Dharmafect-1 according to the manufacturers instructions.

value: osteosarcoma

value: SRBD1 knockdown

tag: time

value: 48 hours


title: Smartseq2_306


title: Smartseq2_310


title: Smartseq2_305


title: siSRBD1 24h Biological Repeat 2

description:
Library name: 5972-SW-4
column name in RNAseqSRWReadcounts.txt is 5972-SW-4

value: 24 hours


title: HEPA-RG cell line treated with sEV from patient IHR1 after VLCKD

description: HEPA-RG+sEV from patient IHR1 at T1


title: HEPA-RG cell line treated with sEV from patient IHR1 before VLCKD

description: HEPA-RG+sEV from patient IHR1 at T0


title: [Ag-specific CD4 T cell][01-214-02][SPIKE][H9N063G8]

value: SPIKE


title: siSRBD1 24h Biological Repeat 1

description:
Library name: 5972-SW-3
column name in RNAseqSRWReadcounts.txt is 5972-SW-3


title: scRNA-seq of ATRIP and HC1

description:
Library name: LBA001_cDNA_S1
10X Genomics

value: PBMC

value: mRNA


title: Smartseq2_303

value: D-LN


title: HEPA-RG cell line treated with sEV from patient LR3 after VLCKD

description: HEPA-RG+sEV from patient LR3 at T1

value: Obese Low Risk patients after VLCKD


title: [Ag-specific CD4 T cell][01-214-02][FLU][H9N063G6]

value: Blood

value: FLU


title: [Ag-specific CD4 T cell][01-214-02][PDCE2 TOT][H9N063G4]

value: PDCE2 TOT


title: HEPA-RG cell line treated with sEV from patient IHR2 after VLCKD

description: HEPA-RG+sEV from patient IHR2 at T1

value: HEPA-RG

value: 20 μg/μL of Small Extracellular Vesicles

value: Obese Intermediate-Hight Risk patients after VLCKD


title: Non-targeting Biological Repeat 1

description:
Library name: 5972-SW-1
column name in RNAseqSRWReadcounts.txt is 5972-SW-1

value: non-targeting knockdown


title: [Ag-specific CD4 T cell][01-176-03][SPIKE][H9N063GE]

value: CD4 T cells


title: [Ag-specific CD4 T cell][01-192-02][SLA][H9N063GI]

value: SLA


title: Smartseq2_309

value: SV


title: HEPA-RG cell line treated with sEV from patient LR2 after VLCKD

description: HEPA-RG+sEV from patient LR2 at T1


title: siSRBD1 48h Biological Repeat 1

description:
Library name: 5972-SW-5
column name in RNAseqSRWReadcounts.txt is 5972-SW-5

value: osteosarcoma

value: SRBD1 knockdown

value: 48 hours


title: Smartseq2_302


title: [Ag-specific CD4 T cell][01-176-03][FLU][H9N063GD]


title: Human iPS cells, Control 0.001% DMSO

city: Kanagawa

first: Tsunehiko

last: Hongen

address: Fujisawa Jyonan

country: Japan

institute: Yokohama University of Pharmacy

data_processing:
RNA-seq raw data was processed using Salmon version (1.10.3) on macOS (Apple Inc.). The raw sequencing reads (FASTQ files) were aligned to the reference transcriptome using Salmon’s quasi-mapping algorithm, which provides a robust and efficient method for transcript quantification. Subsequently, RStudio version (2024.04.2+764) was used for further data analysis.
Assembly: hg38
Supplementary files format and content: comma delimited file includes raw counts for each Sample

source_name: RCB0436 HUC-F2

growth_protocol: The cells were maintained in serum-free maintenance medium mTeSR Plus (Stemcell) on 35-mm2 dishes that were precoated with Matrigel as the cell basement membrane. Culture was performed at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). The quantity and quality of the RNA were measured using a Nano-Drop Lite (Thermo Fisher Scientific). Total RNA was used for the construction of sequencing libraries
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on MGI DNBSEQ-T7 sequencing platforms, according to effective library concentration and data amount.

treatment_protocol:
On the first day of cell thawing and passaging, the apoptosis inhibitor Y-27632 (Wako) was added at a final concentration of 10 μM.
hiPS cells were exposed to rotenone (0.3 μM, 1 μM, 25 μM) for 48 hours on the second day of differentiation. On day 4, total RNA was collected, RNA-seq data was obtained, and gene expression profiling analysis was conducted.

value: RCB0436 HUC-F2

value: human induced pluripotent stem cells

value: Neural Induction

value: Control 0.001% DMSO

value: 48 hour


title: Smartseq2_301

value: D-LN

value: Filtered


title: HEPA-RG cell line treated with sEV from patient LR2 before VLCKD

description: HEPA-RG+sEV from patient LR2 at T0

value: HEPA-RG

value: Obese Low Risk patients before VLCKD


title: Human iPS cells, Control 0.01% DMSO

value: Control 0.01% DMSO


title: Smartseq2_300


title: [Ag-specific CD4 T cell][01-188-02][C.ALB][H9N063G9]

value: Blood


title: HEPA-RG cell line treated with sEV from patient LR1 before VLCKD

description: HEPA-RG+sEV from patient LR1 at T0

value: 20 μg/μL of Small Extracellular Vesicles


title: HEPA-RG cell line treated with sEV from patient LR1 after VLCKD

description: HEPA-RG+sEV from patient LR1 at T1

value: Obese Low Risk patients after VLCKD


title: Smartseq2_304


title: Smartseq2_299


title: Smartseq2_298

value: SV


title: HEPA-RG cell line treated with sEV from patient LR3 before VLCKD

description: HEPA-RG+sEV from patient LR3 at T0


title: Human iPS cells, Control 0.1% DMSO

value: Control 0.1% DMSO


title: Non-targeting Biological Repeat 2

description:
Library name: 5972-SW-2
column name in RNAseqSRWReadcounts.txt is 5972-SW-2

value: osteosarcoma

value: non-targeting knockdown


title: [Ag-specific CD4 T cell][01-188-02][PDCE2 TOT][H9N063GA]

value: PDCE2 TOT

value: CD4 T cells


title: Human iPS cells, Rotenone, 0.3 μM

value: RCB0436 HUC-F2

value: human induced pluripotent stem cells

value: Neural Induction

value: Rotenone, 0.3 μM


title: [Ag-specific CD4 T cell][01-028-06 ][SPIKE][H9N063G3]

value: SPIKE


title: Human iPS cells, Rotenone, 1 μM

value: Rotenone, 1 μM

value: 48 hour


title: Smartseq2_297

value: D-LN

value: Filtered


title: 35dpt_Stereo-seq

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
After sequencing, the raw data of in-situ spatial transcriptomics were processed and unsupervised clustering was performed as described previously. Briefly, the expression profile matrices were generated using SAW, a pipeline available on GitHub (https://github.com/BGIResearch/SAW).
Assembly: GRCh38_GRCm38
Supplementary files format and content: the type of Stereo-seq data

organism:
Homo sapiens
Mus musculus

source_name: Mus musculus and Homo sapiens chimerism

extract_protocol:
Mouse lung tissue was perfused with 2% paraformaldehyde and fixed overnight at 4 °C. The fixed tissue samples were then embedded in Tissue-Teck OCT. Using a Leica CM1950 cryostat, tissue sections with a thickness of 10 μm were obtained and attached to Stereo-seq chips immediately. The spatial transcriptomics data was obtained using the STOmics technology. Briefly, the tissue sections were adhered to the Stereo-seq chip and heated for 3 minutes at 37 °C using a slide warmer. The chip was then incubated in -20 °C methanol for 30 minutes and stained with a nucleic acid dye (Thermo Fisher, Q10212). The stained chip was imaged using a Ti-7 Nikon Eclipse microscope.
The cDNA products were released and purified from the Stereo-seq chips after permeabilization for 26 minutes and reverse transcription. Indexed CDNA libraries were constructed following the manufacturer’s protocol. Finally, the CDNA libraries were sequenced on an MGI DNBSEQ-Tx sequencer, with 50 bp for read 1 and 100 bp for read 2.

value: Lung

value: epithelial cells

value: P63+ lung progenitor cells


title: Smartseq2_332

data_processing:
SmartSeq2 Analysis: Fastq files from SmartSeq2 libraries were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). Genome-mapped BAM files were quantified with RSEM (v1.3.1), and the resulting gene/UMI count matrix was processed in Seurat (v4.1.2). Data were normalized using the LogNormalize method, with mitochondrial gene expression and library size bias regressed out via the ScaleData function. Cells with >5% mitochondrial reads were excluded. Clustering, differential expression, and gene signature scoring were performed in Seurat. Differentially expressed genes were identified using the Wilcoxon Rank Sum test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.5 considered significant.
Bulk RNA-Seq raw Fastq files were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). The count matrix was processed in R with the DESeq2 package (v1.34). Genes with fewer than ten reads were filtered out, and sample normalization was applied using a negative binomial distribution model. Differential gene expression between conditions was assessed with the Wald test. Genes with adjusted P-values (FDR) < 0.1 were retained, and log2 fold changes were shrunk using the apeglm algorithm.
10x Genomics Analysis: Fastq files from cDNA and hashtag libraries generated on the Chromium platform (10x Genomics) were processed using Cell Ranger (v7.0.1). The resulting quantification matrix was processed in Seurat (v5.0) with normalization using the SCTransform function. Non-myeloid cell contaminants were removed based on the PanglaoDB_Augmented_2021 database and EnrichR package for R. Cells were classified by biological condition using the HTODemux function. Differentially expressed genes were identified with the Wilcoxon rank test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.3 considered significant. Signature scores were calculated using Seurat’s AddModuleScore function.
Assembly: mm10
Supplementary files format and content: Tab files from bulk RNA-Seq tab files containing the STAR gene quantification.
Supplementary files format and content: gene.results from RSEM quantification of Smartseq2 data
Supplementary files format and content: mtx, cellranger output from 10x genomics libraries.
Supplementary files format and content: rds, images of Seurat objects used in the analysis


title: MammaryTumor_Female_rep2

first: Ebony

last: Hargrove-Wiley

address: 2220 Pierce Ave 738 PRB

department: Cancer Biology

institute: Vanderbilt University

description: Library name: PyMT_MT_Female2

data_processing:
The sequencing data were analyzed and processed using PIPseeker (Fluent BioSciences)
Assembly: mm9
Supplementary files format and content: tsv.gv and mtx

source_name: mammary tumor

extract_protocol:
Matched tumors from MMTV-PyMT transgenic mice were harvested and incubated in RPMI media with collagenase (2mg/ml ) and Dnase (45 U/ml) and disassociated using the gentleMACS™ Tissue Dissociator.
Library construction was performed using the PIPseq™ T20 3ʹ Single Cell kit following the manufacturer instructions. RNA Kit v4.0 completed per the

value: mammary tumor

value: Male

value: FVB/n


title: [Ag-specific CD4 T cell][01-028-06][SLA][H9N063G5]

value: Blood

value: SLA


title: Smartseq2_295

source_name: D-LN

value: SV


title: Human iPS cells, Rotenone, 25 μM

value: RCB0436 HUC-F2

value: human induced pluripotent stem cells

value: Rotenone, 25 μM


title: [Ag-specific CD4 T cell][05-001-01][FLU][H9H07JJP]

value: FLU

value: CD4 T cells


title: Smartseq2_296


title: MammaryTumor_Female_rep1

description: Library name: PyMT_MT_Female1


title: [Ag-specific CD4 T cell][05-001-01][FLU][H9H07JJJ]


title: Smartseq2_294


title: MammaryTumor_Male_rep2

description: Library name: PyMT_MT_Male2

value: Female


title: MammaryTumor_Male_rep1

description: Library name: PyMT_MT_Male1


title: [Ag-specific CD4 T cell][05-001-01][SLA][H9H07JF6]


title: rnaInput_siSMARCAL1_hu_1

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human (hg19) using bwa (version 0.7.17). The output SAM files were converted to sorted BAM files using SAMtools (version 1.11).
Read1 was split into forward and reverse strand according to the SAM flag, using SAMtools view ‘-f 64 –F 16’ and ‘-f 80’, respectively.
Genome coverage bigwig files were generated by BEDtools (version 3.5.0) genomecov and bedGraphToBigWig (version 4) with the parameter ‘-scale 10,000,000/read1_number’.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample of RNA-seq

source_name: HeLa

extract_protocol:
DNA was labeled with EDU during replication, and clicked with Biotin-Azide. DNA as well as the combined RNA were caught by streptavidin beads.
Strand-specific DNA sequencing library was prepared by TABLE-seq. Strand-specific RNA sequencing library was prepared by the RNA-seq library prep kit (VAHTS, Cat. #NR604) following the manufacturer’s instructions.

treatment_protocol: Cells were crosslinked by 1% PFA at room temperature for 10 min, quenched with 1.25 mM glycine for 10 min with rotation. After washing with PBS, cells were permeabilized in PBS with 0.25% TritonX-100 at room temperature for 30 min, and Click reaction was performed at room temperature for 80 min. Then chromatin was fragmented by sonicating with Bioruptor under the condition of 30 s on and 30 s off for 5 cycles. The supernatants with fragmented chromatin were added to streptavidin beads and incubated at room temperature for 1 h with rotation. After beads washed, the nucleic acids were eluted with elution buffer (100 μl PBS with 1% SDS and 2 mg/mL proteinase K) by incubating at 55 °C for 2 h, followed by 70 °C for 20 min. The eluents were split for DNA and RNA purification, respectively. DNA was purified with Phenol/chloroform/isoamyl alcohol. RNA was extracted with Trizol.

value: HeLa

value: cervical carcinoma cell line

value: hydroxyurea


title: rnaInput_siSMARCAL1_hu_2


title: rnaInput_siRAD51_hu_2


title: Smartseq2_292

value: D-LN


title: [Ag-specific CD4 T cell][05-001-01][SLA][H9H07JF9]


title: rnaInput_siRAD51_hu_1


title: Smartseq2_291

value: Filtered


title: 10x VDJ sequencing for library P4_1_b

first: Gabriela

middle: S

last: Silva Santos

state: NY

description: 5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
For single-cell B cell receptor sequence reconstruction we used Cell Ranger (v.7.1.0) with mouse reference genome GRCm38. Hashtag-oligos (HTOs) UMI counts were processed using CITESeq-Count (v.1.4.5). We utilized MULTIseqDemux from Seurat (v4.1.1) to demultiplex, visualize and categorize cells as either GC or PC, based on the measured surface expression of CD138, CD95, CCR6 and CD86 by antibody-conjugated oligos.
Assembly: GRCm38
Supplementary files format and content: CiteSeq-Count and 10x Genomics output files

source_name: Lymph Node

extract_protocol:
S1PR2-CreERT2 R26 ZsG mice were immunized with the hapten-carrier NP-OVA followed by tamoxifen administration 5 days after immunization. ZsG labeled Fas+ GL7+ CD38- GC B cells and their progeny B220- CD138+ TACI+ were sorted 14 days after immunzation.
10X Genomics libraries were generated with the Chromium Single Cell 5′ Library as described in the 10X Genomics protocol and sequenced with NovaSeq 6000 S1.

value: Lymph Node

value: B cells


title: rnaInput_siCtrl_hu_2

value: siCtrl


title: Smartseq2_290

first: Tiago

last: Castro

extract_protocol:
Lymph nodes and gut tissue were dissected, finely chopped, and digested in RPMI medium with Collagenase D to obtain single-cell suspensions. For gut-associated lymph nodes, duodenal lymph nodes were identified using anatomical markers. Dendritic cells were isolated from the duodenal lamina propria by separating intestines, removing mucus with PBS and DTT, and stripping epithelium with EDTA. The tissue was further digested with DNaseI and collagenase, followed by Percoll gradient centrifugation to isolate DCs. Single-cell sorting of DCs was conducted into 96-well plates with TCL buffer and stored at –80°C.
Library Preparation for Single-cell RNA-seq (SmartSeq2). Single cells were sorted onto plates, covering all conditions in each replicate. RNA was extracted using RNAClean XP SPRI beads, then reverse-transcribed into cDNA with RT and TSO primers. The cDNA was amplified, cleaned with SPRI beads, and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Barcoded libraries were pooled and sequenced on the Illumina Nextseq 550 platform. Library Preparation for Single-cell RNA-Seq (10x Genomics). Cells were labeled with hashtag oligonucleotide (HTO)-tagged antibodies, sorted, and counted for viability. scRNA-seq libraries were generated using the 10x Genomics Chromium system, following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq SP flowcell at a minimum depth of 30,000 reads per cell. Library Preparation for Bulk RNA-seq. RNA was isolated using RNAClean XP beads. Reverse transcription was performed with specific primers, followed by cDNA amplification with KAPA HiFi HS Ready Mix. The amplified product was cleaned with RNAClean XP beads and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Libraries were pooled and sequenced as 75-base single-end reads on an Illumina NextSeq platform.


title: 10x VDJ sequencing for library P4_1_a


title: [Ag-specific CD4 T cell][01-165-03][SLA][H9H07JJL]

value: Blood


title: rnaInput_siCtrl_hu_1


title: Hashtag sequencing for library P4_1_a

description: 5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: [Ag-specific CD4 T cell][01-165-03][H1N1][H9H07JJO]


title: Smartseq2_289


title: Smartseq2_293


title: [Ag-specific CD4 T cell][01-165-03][SLA][H9H07JJR]

value: SLA


title: rnaInput_ko_hu_RH_2

value: DDX39A KO

value: hydroxyurea,RNaseH


title: rnaInput_ko_hu_RH_1


title: Smartseq2_288

value: SV


title: [Ag-specific CD4 T cell][01-004-08][H1N1][H990KHRS]


title: 10x_RNA-Seq

source_name: Lamina Propria

value: Lamina Propria


title: [Ag-specific CD4 T cell][01-004-08][SLA][H990KHRV]


title: rnaInput_ko_hu_DRB_2

value: hydroxyurea,DRB


title: 10x_HTO


title: Smartseq2_287


title: Hashtag sequencing for library P4_1_b


title: Smartseq2_286


title: [Ag-specific CD4 T cell][01-004-08][SLA][H990KHS1]

value: CD4 T cells


title: Smartseq2_285


title: [Ag-specific CD4 T cell][01-140-05][H1N1][H990KHRW]


title: Smartseq2_284


title: homo 3

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
A quality control check on the generated fastq ﬁles was performed using FastQC.
Peak analysis was conducted using HOMER software (v4.10; standard commands) after aligning fastq files to the mm10 mouse genome using bowtie2.
Assembly: mm10
Supplementary files format and content: bedgraph file of peaks (raw counts)

molecule: genomic DNA

source_name: liver

extract_protocol:
Livers were cryopowdered using a liquid nitrogen-cooled Retsch Cryomill. The cryopow-dered tissue was then fixed in 10 ml 1% PFA for 30 minutes at room temperature with gentle nutation. Fixation was quenched 1ml of 1.375M glycine (Cat # BP381-5, Fisher Scientific, Waltham, MA) with gentle nutation for 5 minutes at room temperature. After centrifugation at 3000g for 5 minutes at 4°C, the pellet was resuspended in cell lysis buffer as per reported conditions 69, supplementing the cell lysis buffer with 3mg/ml cytochalasin B and rotating for 10 minutes at 4°C.  Nuclei were pelleted at 300g for 10 min at 4°C, and subsequently processed fol-lowing the reported protocol with the adjustment of adding 3µg/ml cytochalasin B into all solutions for chromatin preparation and sonication, antibody incubation, and wash steps.  Chromatin was then sonicated for 15 cycles (30 sec, high power; 30 sec pause; 500µl volume) in a water bath sonicator set at 4°C (Bioruptor 300; Dia-genode, Denville, NJ).  After centrifuging at 10000g for 10 minutes at 4°C, sheared chromatin was checked on agarose gel for a shear band comprised between ~150 and ~600bp. Two µg of chromatin was kept for pooled input controls, whereas ~50µg chromatin were used for each pull-down reaction in a final volume of 2ml rotating at 4°C overnight. Primary antibody: rabbit polyclonal anti-GR (ABclonal #A2164). Chromatin complexes were precipitated with 100µl Dynabeads M-280 (sheep anti-rabbit #11203D; Thermo Scientific, Waltham, MA).  After washes and elution, samples were treated with proteinase K (cat #19131; Qiagen, Hilden, Germany) at 55°C and cross-linking was reversed through overnight incubation at 65°C. DNA was purified using the MinElute puri-fication kit (cat #28004; Qiagen, Hilden, Germany), quantitated using Qubit reader and reagents.
Library preparation and sequencing were conducted at the CCHMC DNA sequencing Core. Up to 30 ng of post-Immunoprecipitation dsDNA as measured by Invitrogen™ Qubit™ high- sensitivity spectroﬂuorometric measurement was made into Illumina-compatible NGS libraries using the ThruPLEX® DNA-Seq kit from Takara Bio Inc.
Each created library was dual-indexed with 8-base molecular barcodes for high level multiplexing. Libraries were made with 13 cycles of PCR ampliﬁcation.

value: liver

tag: age

tag: Sex

value: female


title: WT 2


title: batch2_rnaInput_ko_hu_1

value: HeLa

value: cervical carcinoma cell line


title: [Ag-specific CD4 T cell][01-140-05][H1N1][H990KHS0]

data_processing:
Base calls were processed to FASTQs by Dragen software onboard NextSeq2000; fastq files were processed as described in https://github.com/MilpiedLab/FB5P-seq. To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Assembly: GRCh38 with additional artificial chromosome for 92 ERCC spike-in genes.
Supplementary files format and content: comma separated values text file includes the UMI counts for all genes (columns) in all cells (rows) from the dataset.

tag: sampleID


title: WT 3


title: Smartseq2_282

institute: The Rockefeller University

value: D-LN


title: rnaInput_ko_hu_1

value: hydroxyurea


title: Smartseq2_283


title: [Ag-specific CD4 T cell][01-140-05][SLA][H9H07JFB]


title: rnaInput_ko_hu_2


title: rnaInput_ko_hu_DRB_1


title: Smartseq2_280


title: rnaInput_ctrl_hu_1

value: WT


title: [Ag-specific CD4 T cell][01-176-02][PDCE2][H9H07JF8]


title: WT 1


title: input


title: WT liver 3

data_processing:
A quality control check on the fastq files was performed using FastQC.
Upon passing basic quality metrics, the reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic 75 [Version 0.33].
The trimmed reads were then mapped to mm10 reference genome using default parameters with strandness (R for single-end and RF for paired-end) option in Hisat2 76 [Version 2.0.5].
In the next step, transcript/gene abundance was determined using kallisto 77 [Version 0.43.1].
We first created a transcriptome index in kallisto using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and counts per million (CPM).
Assembly: mm10
Supplementary files format and content: csv table containing isoform CPM

extract_protocol:
RNA-seq was conducted on RNA extracted from liver tissue. Total RNA was extracted from cryo-pulverized liver tissues with Trizol (#15596026; Thermo Fisher Scientific, Waltham, MA) and re-purified using the RNeasy Mini Kit (Cat #74104; Qiagen, Germantown, MD). RNA-seq was performed at the DNA Core (CCHMC) blinded to treatment groups.
150 to 300 ng of total RNA determined by Qubit (Cat#Q33238; Invitro-gen, Waltham, MA) high-sensitivity spectrofluorometric measurement was poly-A selected and reverse tran-scribed using Illumina’s TruSeq stranded mRNA library preparation kit (Cat# 20020595; Illumina, San Diego, CA).
Each sample was fitted with one of 96 adapters containing a different 8 base molecular barcode for high level multiplexing. After 15 cycles of PCR amplification, libraries were sequenced.

value: 4 months-old

value: WT/WT


title: rnaInput_ctrl_hu_2


title: rnaInput_ctrl_2


title: [Ag-specific CD4 T cell][01-176-02][PDCE2][H9H07JF4]

value: Blood


title: ATAC-seq_Day8_RAS_siTPR_Rep2

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

institute: MRC Human Genetics Unit, The University Of Edinburgh

data_processing:
Reads were trimmed to reomve adaptor sequences and to allow high quality bases but with atleast 30 bp read length with cutadapt.
Reads were aligned in paired-end mode with bowtie2 --no-discordant --no-mixed --no-unal --very-sensitive  -X 2000.
Duplecates removed with Picard and bigwig generated with HOMER succh that each fragment is centred at Tn5 insertion site.
Assembly: Hg19
Supplementary files format and content: bigwig format

source_name: Cell line

growth_protocol: Early passage IMR90-STOP and IMR90-RAS cell lines (PMID: 23770676) were used to induce oncogene induced senescence (OIS) by Ras translocation to the nucleus by addition of 100nM 4-hydroxytamoxifen (4-OHT, Sigma-Aldrich) for either 3 or 8 days. Cells were transfected with a 30nM final concentration of predesigned control or TPR siRNAs (Dharmacon). Transfections were carried out on day 0 of 4-OHT treatment and on every third subsequent day. Cells are used for RNAs-seq and ATAC-seq library preperation.

extract_protocol:
We used the Omni-ATAC protocol (Corces et al., 2017, PMID: 28846090) with some modifications. Briefly, IMR90 cells were harvested by trypsinization and washed with cold PBS. One million cells were resuspended in ice cold ATAC resuspension buffer (ATAC-RSB; 20 mM Tris HCl pH 7.6, 10 mM MgCl2, 20% dimethyl formamide) and 40 strokes in a 1 ml Dounce using a rounded pestle were applied. Debris was pre-cleared by spinning at 100 g for 3 mins. The supernatant was collected and spun again at 1000 g for 5 min to collect the nuclear pellet. The pellet was resuspended in 1 ml ATAC-RSB buffer with 0.1% Tween-20 and spun at 1000 g for 5 min. The nuclear pellet was resuspended in 100 μl TD buffer (10 mM Tris HCl pH 7.6, 5 mM MgCl2, 10% dimethyl formamide) and the Omni-ATAC protocol performed on 50000 nuclei.
ATAC-seq libraries were made using adaptor sequences as described previously (Buenrostro et al., 2013, PMID: 24097267). Libraries were assessed for quality and fragment size using the Agilent Bioanalyzer.

value: Cell line

value: siTPR


title: [Ag-specific CD4 T cell][01-176-02][H1N1][H990KHRZ]


title: homo 1


title: Smartseq2_281

city: New York

address: 1230 York Avenue


title: rs6190 liver 3


title: rnaInput_ctrl_1


title: Smartseq2_278


title: rna_siSMARCAL1_hu_2


title: ATAC-seq_Day8_RAS_siCTRL_Rep2

value: siControl


title: WT liver 2


title: Smartseq2_277

value: SV


title: Smartseq2_276


title: rs6190 liver 2


title: rna_siSMARCAL1_hu_1


title: Smartseq2_279


title: rs6190 liver 1


title: Smartseq2_275


title: ATAC-seq_Day8_RAS_siTPR_Rep1


title: batch2_rnaInput_ko_hu_2

value: DDX39A KO


title: [Ag-specific CD4 T cell][01-176-02][H1N1][H9H07JF3]


title: rna_siRAD51_hu_2


title: ATAC-seq_Day8_RAS_siCTRL_Rep1


title: WT liver 1


title: rna_siRAD51_hu_1


title: ATAC-seq_Day8_STOP_siTPR_Rep1


title: Smartseq2_273


title: IMQ treated, KO #5

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
bcl2fastq was used to convert Illumina BCL files to FastQ
STAR 2.7.8a was used to map paired end reads to mm10
htseq 2.0.1 was used to generate raw counts
Assembly: mm10
Supplementary files format and content: tab delimited text file containing raw counts

source_name: Bone marrow neutrophil

growth_protocol: Neutrophil were obtained from mouse bone marrow by negative selection and processed immediately.

extract_protocol:
Cells were lysed by TRIzol reagent immediately after isolation and stored in -80  ֯C. RNA was purified by using Direct-zol RNA kits (Zymo Research) following the manufacturer’s instructions and quantified by NanoDrop Microvolume Spectrophotometer (Thermo-Fisher Scientific).
Illumina RNA libraries were prepared with NEBNext Ultra II RNA library preparation kit for Illumina (NEB #E7490) according to manufacturer’s instructions

treatment_protocol: Mice were treated with topical imiquimod cream for 6 weeks.

value: Bone marrow neutrophil

value: Bmal1 myeloid conditional KO

value: IMQ treated


title: IMQ treated, KO #4


title: ATAC-seq_Day8_STOP_siCTRL_Rep1


title: rna_siCtrl_hu_1

value: siCtrl


title: ATAC-seq_Day8_RAS_siCTRL_Rep4


title: IMQ treated, KO #3


title: rna_ko_hu_RH_2

value: HeLa

value: hydroxyurea,RNaseH


title: Smartseq2_271

value: D-LN


title: IMQ treated, KO #2


title: ATAC-seq_Day8_RAS_siCTRL_Rep3


title: Smartseq2_270


title: ATAC-seq_Day8_STOP_siTPR_Rep2


title: rna_ko_hu_RH_1

value: cervical carcinoma cell line


title: Smartseq2_274


title: IMQ treated, KO #1


title: Smartseq2_269


title: rna_ko_hu_DRB_2

value: hydroxyurea,DRB


title: rna_ko_hu_DRB_1


title: rna_siCtrl_hu_2

value: hydroxyurea


title: Smartseq2_268

value: Filtered


title: ATAC-seq_Day3_RAS_siTPR_Rep2


title: IMQ treated, WT #4

value: WT


title: batch2_rna_ko_hu_2


title: Smartseq2_267


title: Smartseq2_272


title: ATAC-seq_Day3_RAS_siCTRL_Rep2

value: Cell line


title: batch2_rna_ko_hu_1


title: Smartseq2_266


title: ATAC-seq_Day3_STOP_siTPR_Rep2

value: siTPR


title: IMQ treated, WT #2


title: treated

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

description: 10X Genomics

data_processing:
Sequenced reads were mapped to the CellRanger human genome build GRCh38 with CellRanger (v8.0.1) using the Gencode human transcript GTF (v32) and the following parameter: --expect-cells=8000.
Background removal was performed using CellBender (v0.3), and the resulting samples imported into Seurat (v4.3.0) objects.
Each object was filtered per cell requiring at least 2000 genes identified (nFeature_RNA > 2000), fewer than 10,000 genes identified (nFeature_RNA < 10000), and less that 1% of the reads from a mitochondrial origin (mito.genes < 1). Mitochondrial genes were identified with the following command: PercentageFeatureSet(my_initial_object, pattern = "^MT-")
Each Seurat object was normalized (NormalizeData) using the LogNormalize method and a scale factor of 10000, and the set of variable genes identified (FindVariableFeatures) using the VST method and 2000 genes.
The resulting objects were then integrated using FindIntegrationAnchors and IntegrateData, scaled and centered (ScaleData), had dimensionality reduction performed (RunPCA and RunUMAP), and clusters identified (FindNeighbors and FindClusters with a granularity resolution of 0.9). Clusters judged to represent the same cell type (e.g. RPE and fibroblast) were merged into a single cluster each.
Assembly: GRCh38
Supplementary files format and content: Comma-separated matrices of metadata per cell (all_metadata.csv.gz) and counts per cell per gene (all_expression_data.csv.gz)

source_name: RPE/choroid

extract_protocol:
Frozen tissue samples were prepared for single nuclei RNA sequencing using the Chromium Nuclei Isolation Kit (PN-1000493 10x Genomics). In brief, frozen tissue samples were dissociated in lysis buffer with a sterile plastic pestle. During the dissociation samples were stored on ice. Dissociated tissue was pipette mixed and incubated for 10 minutes on ice. Dissociated tissue was passed through a 100 µm filter prior to transferring to a nuclei isolation column. Samples were centrifuged and the flowthrough which contained nuclei was collected. Nuclei were washed and resuspended in 25-50 µL. Nuclei were counted using a hemocytometer.
Following manufacturers protocols, nuclei were prepared for single nuclei RNA sequencing using the Chromium GEM-X single cell 3’ Kit (10X Genomics).

treatment_protocol: Paired 4 mm biopsy punches of human donor RPE/choroid tissue were collected into 24 well plates in DMEM with Primocin(TM) containing either 20µg/ml of recombinant monomeric CRP or media alone containing vehicle (PBS) and were maintained at 37°C, 5% CO2. After 22 hours of incubation the tissue was snap frozen and stored at -80°C.

value: RPE/choroid

value: CRP


title: [Ag-specific CD4 T cell][01-176-03][PDCE2 TOT][H9N063GB]

first: Pierre

last: Milpied

institute: Centre d'Immunologie de Marseille-Luminy (CIML)

source_name: Blood

value: Blood

value: PDCE2 TOT

value: CD4 T cells


title: ATAC-seq_Day8_STOP_siCTRL_Rep2

value: siControl


title: ATAC-seq_Day3_STOP_siCTRL_Rep2


title: Smartseq2_265

value: SV


title: IMQ treated, WT #1

value: Bone marrow neutrophil

value: IMQ treated


title: IMQ treated, WT #5


title: control

description: 10X Genomics

value: PBS


title: ATAC-seq_Day3_RAS_siTPR_Rep1


title: SAMPLE_02_000038_W0_HC

city: Kiel

first: Rashmi

last: Tandon

address: Rosalind-Franklin-Strasse 9

institute: UKSH

data_processing:
Illumina standard primers were trimmed using trim_galore (version 0.6.6)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 103) using hisat2 (version 2.2.1)
Mapped reads were cleaned and sorted using samtools (version 1.11)
Number of reads for each gene was counted using rsubread (version 2.2.6)
Assembly: GRCh38, Ensembl release 103
Supplementary files format and content: Comma-separated text file including raw counts of sequencing reads for each gene and sample

source_name: skin

extract_protocol:
Total RNA was isolated using the mirVanaTM miRNA Isolation Kit (Lifetechnologies, Carlsbad,CA)
RNA samples were prepared for sequencing using the Illumina stranded mRNA protocol and sequenced on the NovaSeq6000 with 2x100bp

value: skin

tag: cohort number

tag: subject number

tag: timepoint

value: HC


title: ATAC-seq_Day3_RAS_siCTRL_Rep1


title: Smartseq2_263

value: D-LN


title: Smartseq2_264


title: Untreated, KO #4

tag: genotype

value: Bmal1 myeloid conditional KO

value: Untreated


title: SAMPLE_02_000037_W0_HC


title: Smartseq2_262


title: Untreated, KO #3


title: ATAC-seq_Day3_STOP_siTPR_Rep1

value: Cell line


title: Smartseq2_260


title: IMQ treated, WT #3

value: WT


title: Untreated, KO #5


title: Untreated, KO #2


title: Day3_RNA-seq_STOP_siTPR_Rep-2

data_processing:
Reads were trimmed to reomve adaptor sequences and to allow high quality bases but with atleast 30 bp read length with cutadapt.
Raw Fastq files for each sample were merged and aligned to the human genome assembly hg19 using HISAT2 (Kim et al., 2019) with default parameters
Reads were assigned to genomic features using the featureCounts tool from the subread package (Liao et al., 2014).
Assembly: Hg19
Supplementary files format and content: tab-delimited format
Supplementary files format and content: RNAs-seq feature counts per gene

source_name: cell line

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen).
Libraries were prepared from 500ng of each RNA sample using the NEBNext Ultra II Directional RNA library kit with PolyA enrichment module (New England Biolabs).  Libraries were assessed for quality and fragment size using the Agilent Bioanalyser and sequenced on NextSeq-2000 platform

value: cell line

value: siTPR


title: SAMPLE_02_000035_W0_HC


title: Untreated, KO #1


title: Day3_RNA-seq_STOP_siTPR_Rep-1


title: SAMPLE_02_000034_W0_HC


title: SAMPLE_02_000036_W0_HC


title: Smartseq2_259


title: Untreated, WT #5


title: ATAC-seq_Day3_STOP_siCTRL_Rep1


title: Smartseq2_261


title: Smartseq2_258


title: Day3_RNA-seq_STOP_siCTRL_Rep-2

value: siCTRL


title: homo 2

value: liver

value: female


title: Untreated, WT #4


title: Smartseq2_257


title: Untreated, WT #3


title: SAMPLE_02_000031_W0_HC


title: Day3_RNA-seq_STOP_siCTRL_Rep-1


title: Day3_RNA-seq_RAS_siTPR_Rep-2


title: Smartseq2_255


title: Untreated, WT #2


title: Day3_RNA-seq_RAS_siTPR_Rep-1


title: SAMPLE_02_000030_W0_HC


title: Untreated, WT #1


title: Smartseq2_256


title: SAMPLE_02_000032_W0_HC


title: Smartseq2_254


title: Smartseq2_253


title: Day3_RNA-seq_RAS_siCTRL_Rep-2


title: SAMPLE_02_000029_W0_HC


title: SAMPLE_02_000028_W0_HC


title: SAMPLE_02_000033_W0_HC


title: short-term HSCs, Wild Type, rep-4

city: Shang Hai

first: Yin

last: Wang

address: Dong An street

institute: Fudan university

data_processing:
Raw data were trimmed by Trim Galore (v0.6.7) with default setting.
The clean data were mapped to mm10 reference genome using Hisat2 (v7.5.0) in paired-end mode with default parameters.
Gene count matrices were calculated by featureCounts (v2.0.1) with parameters -M -O.
TE transcripts (v.2.2.3) was applied to count TE and gene with the parameter mode multi.
Differentially expressed Gene and TE analysis was performed by using DESeq2 (v1.34.0) package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw gene and TE counts

source_name: bone marrow

extract_protocol:
the reverse-transcribed RNA was amplified to obtain enough cDNA by a modified SMART-Seq2 protocol and 5 ng cDNA was used for cDNA library construction with TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme).
SmartSeq2

value: bone marrow

value: short-term HSCs

value: Wild Type


title: Smartseq2_252

value: SV


title: Day3_RNA-seq_RAS_siCTRL_Rep-1


title: SAMPLE_02_000027_W0_HC


title: short-term HSCs, Wild Type, rep-3


title: HCT116, 50nM SY5609 75min IFN 45min 2

city: Boulder

first: Taylor

middle: K

last: Jones

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

data_processing:
Mapping of PRO-seq data was performed using the NascentFlow Pipeline (DOI 10.17605/OSF.IO/NDHJ2)
Assembly: hg38
Supplementary files format and content: sva_corrected_counts.csv contains the 3' end normalized, batch corrected counts used in this study
Supplementary files format and content: hct116_sy5609_metadata_clean.txt is additional metadata information used in data processing
Library strategy: PRO-seq

growth_protocol: HCT116 cells were grown in McCoy’s 5A media (10% fetal bovine serum, 1% Penicillin/streptomycin) to ~75% confluency on 500cm^2 plates

extract_protocol:
At time 30 minutes, the media was aspirated from the plate and the cells were washed in ice cold 1x D-PBS three times. 40mL of ice-cold Lysis Buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1x Protease Inhibitors (1mM Benzamidine (Sigma B6506-100G), 1mM Sodium Metabisulfite (Sigma 255556-100G), 0.25mM Phenylmethylsulfonyl Fluoride (American Bioanalytical AB01620), and 4U/mL SUPERase-In) was then added to the plate and cells were scraped with a cell-lifter (Costar) and the resuspended cells were transferred into a conical and put on ice. Resuspended cells were allowed to swell in lysis buffer, on ice, for 0.5-1hour (while the other cells were being harvested). Cells were then pelleted in a fixed-angle rotor centrifuge at 1000xg for 15 minutes. Pelleted cells were resuspended in 10mL of Lysis Buffer with a wide-bore P1000 tip and the centrifugation step was repeated. Being mostly nuclei and cell debris, the pellet was resuspended in 500uL of Freezing Buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 4U/ml SUPERase-In) and moved to a low-retention 1.5mL tube and pelleted at 2000xg for 4 minutes. The final pellet was resuspended in Freezing Buffer, checked for purity and counted under a microscope, and brought to a concentration of 10million nuclei/100uL then aliquoted and snap frozen.
Nuclear run-on was conducted as described (Mahat et al., 2016) with the following modifications: the final concentration of non-biotinylated CTP was raised from 0.25mM to 25mM, and the final library clean-up and size selection was accomplished using 1X AMPure XP beads (Beckman A63881).

treatment_protocol: At time 0 minutes, 50uM SY-5609 (1000x stock), 1mM Palbociclib (1000x stock), or DMSO was added to the conditioned media and mixed thoroughly.

value: Human colorectal carcinoma

tag: treatment time

value: 75 minutes

value: 10ng/mL IFN, 50nM SY5609


title: short-term HSCs, Wild Type, rep-2


title: SAMPLE_02_000026_W0_HC

value: skin

value: HC


title: HCT116, 50nM SY5609 75min IFN 45min 1


title: Smartseq2_251

value: D-LN


title: short-term HSCs, Wild Type, rep-1


title: SAMPLE_02_000025_W0_HC


title: Smartseq2_250


title: HCT116, DMSO 75min IFN 45min 2

value: 10ng/mL IFN


title: Smartseq2_249


title: SAMPLE_02_000024_W0_HC


title: short-term HSCs, DNMT3A knockout, rep-4

value: DNMT3A knockout


title: short-term HSCs, DNMT3A knockout, rep-3


title: SAMPLE_02_000023_W0_HC


title: Smartseq2_248


title: short-term HSCs, DNMT3A knockout, rep-2


title: SAMPLE_02_000022_W0_HC


title: HCT116, DMSO 75min 2

value: DMSO


title: HCT116, DMSO 75min IFN 45min 1


title: short-term HSCs, DNMT3A knockout, rep-1


title: HCT116, DMSO 75min 1


title: Smartseq2_246


title: MEPs, Wild Type, rep-4

value: MEPs


title: Smartseq2_247


title: SAMPLE_02_000021_W0_HC


title: HCT116, 1uM Palbociclib 30min 2

value: 30 minutes

value: 1uM Palbociclib


title: Smartseq2_245


title: MEPs, Wild Type, rep-3


title: HCT116, 1uM Palbociclib 30min 1


title: Smartseq2_244


title: SAMPLE_02_000020_W0_HC


title: SAMPLE_02_000019_W0_HC


title: HCT116, 50nM SY5609 30min 2


title: MEPs, Wild Type, rep-1


title: Smartseq2_243


title: SAMPLE_02_000018_W0_HC


title: MEPs, DNMT3A knockout, rep-4


title: Smartseq2_242


title: SAMPLE_02_000017_W0_HC


title: MEPs, DNMT3A knockout, rep-3


title: SAMPLE_02_000016_W0_HC


title: HCT116, DMSO 30min 2


title: Smartseq2_241


title: HCT116, DMSO 30min 1


title: Smartseq2_240


title: MEPs, DNMT3A knockout, rep-2


title: MEPs, DNMT3A knockout, rep-1


title: SAMPLE_02_000015_W0_HC


title: Smartseq2_239


title: long-term HSCs, Wild Type, rep-4

value: long-term HSCs


title: HCT116, DMSO 75min 3


title: SAMPLE_02_000014_W0_HC


title: HCT116, DMSO 75min 4


title: SAMPLE_02_000013_W0_HC


title: SAMPLE_02_000012_W0_HC


title: Smartseq2_237


title: long-term HSCs, Wild Type, rep-2

value: bone marrow


title: Smartseq2_238


title: long-term HSCs, Wild Type, rep-3


title: long-term HSCs, Wild Type, rep-1


title: SAMPLE_02_000011_W0_HC


title: Pt9_TIL-FB

city: Tampa

first: Dongliang

last: Du

address: 111 Magnolia

institute: Moffitt

description:
Pt9_TIL_barcodes.tsv.gz
Pt9_TIL_features.tsv.gz
Pt9_TIL_matrix.mtx.gz

data_processing:
For single-cell RNA-seq data, Cell Ranger (v3.0, 10X Genomics) was used for sequencing reads mapping against GRCh38 human transcriptome, UMI counting, and barcodes filtering. Only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.070 for analysis. Then cells with less than 200 genes detected or greater than 10% mitochondrial UMIs were filtered out; genes detected in less than three cells were also excluded. Doublets were detected using Scrublet71, doubletCells implemented in scran72, DoubletFinder73, and scDblFinder74, assuming 0.08% doublet rate for every 1000 cells sequenced in 10X experiments. Cells identified as doublets by >=2 methods were removed from further analysis. Raw UMI counts were log normalized and top 500 variable genes were detected in each sample independently. T cell receptor and immunoglobulin genes were removed from the variable gene list to prevent clustering based on V(D)J transcripts. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring() function. To remove batch effects between samples, individual patient samples were further integrated using FindIntegrationAnchors() and IntegrateData() functions75 with parameter anchor.features =8000. Scaled z-scores for each gene were calculated using ScaleData() function by regressing against % of mitochondrial UMIs, cell cycle phases score, and total reads count. Principal component analysis was performed on the integrated data. A shared nearest neighbor (SNN) graph was constructed based on the first 30 principle components. A total of 23 clusters were identified using the FindClusters() function by Louvain clustering76 at resolution=0.9. Uniform manifold approximation and projection (UMAP) was used to visualize clustering and gene expression.
Assembly: GRCh38
Supplementary files format and content: tsv and matrix files

source_name: Tumor

growth_protocol: TIL was cultured at Moffitt Cell Therapy Facility, following a previously described protocol (https://doi.org/10.1038/s41591-021-01462-y).

extract_protocol:
1. For isolated TIL: Tumor was minced and carefully mixed in digestion medium with collagenase (type II and type IV), hyaluronidase and DNAase (Thermo Fisher Scientific). Then undigested tumor was filtered from the cell suspension to generate a single-cell suspension. Intact cells were enriched with a Ficoll-Hypaque (GE Healthcare Bio-Sciences) gradient and viable tumor cells were enumerated by trypan blue exclusion. The tumor digested was stained with anti-human CD3 and Zombie NIR. Isolated TIL was sorted as the CD3+ Zombie NIR- population and sent for single cell sequencing.  2. For cultured TIL: Samples were stained with anti-human CD3 and Zombie NIR, and flow sorting was conducted to sort CD3+Zombie NIR- TIL for single cell sequencing.
The cell suspension was loaded onto the 10X Genomics Chromium Single Cell Controller (10X Genomics, Inc., Pleasanton, CA) at a concentration of about one thousand cells per microliter and the single cells, reagents, and 10x Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs).  Revers transcription of poly-adenylated mRNA was performed inside each droplet, and cDNA generated from cells encapsulated with a 10X Genomics Chromium NextGEM Single Cell V(D)J Reagent Kit was enriched using VDJ primers provided in the kit.  A portion of the DNA library generated from antibody-labeled cells was amplified using primers provided by 10X Genomics to prepare a cell surface protein library, and the cDNA, feature barcoding and VDJ-enriched libraries were completed in bulk reactions using the 10X Genomics Chromium NextGEM Single Cell 3’ or 5’ V(D)J Reagent Kits.

value: Tumor

value: TIL

value: T cells

value: cultured


title: Pt7_TIL-FB

description:
Pt7_TIL_barcodes.tsv.gz
Pt7_TIL_features.tsv.gz
Pt7_TIL_matrix.mtx.gz


title: HCT116, 50nM SY5609 30min 1

value: Human colorectal carcinoma


title: Smartseq2_236

value: SV


title: Pt9_Baseline_Tumor-FB

description:
Pt9_Baseline_Tumor_barcodes.tsv.gz
Pt9_Baseline_Tumor_features.tsv.gz
Pt9_Baseline_Tumor_matrix.mtx.gz

value: isolated


title: SAMPLE_02_000010_W0_HC

value: skin

value: HC


title: Smartseq2_235

value: D-LN


title: Pt3_TIL-FB

description:
Pt3_TIL_barcodes.tsv.gz
Pt3_TIL_features.tsv.gz
Pt3_TIL_matrix.mtx.gz


title: Pt31_TIL-FB

description:
Pt31_TIL_barcodes.tsv.gz
Pt31_TIL_features.tsv.gz
Pt31_TIL_matrix.mtx.gz


title: SAMPLE_02_000008_W0_HC


title: Pt31_Baseline_Tumor-FB

description:
Pt31_Baseline_Tumor_barcodes.tsv.gz
Pt31_Baseline_Tumor_features.tsv.gz
Pt31_Baseline_Tumor_matrix.mtx.gz


title: Smartseq2_233


title: long-term HSCs, DNMT3A knockout, rep-1

value: DNMT3A knockout


title: Smartseq2_231


title: SAMPLE_02_000006_W0_HC


title: SAMPLE_02_000007_W0_HC


title: Pt9_TIL-VDJ


title: long-term HSCs, DNMT3A knockout, rep-2


title: CMPs and GMPs, Wild Type, rep-4

value: CMPs and GMPs

value: Wild Type


title: Pt9_Baseline_Tumor-VDJ


title: SAMPLE_02_000005_W0_HC


title: Smartseq2_230


title: Pt7_TIL-VDJ


title: CMPs and GMPs, Wild Type, rep-2


title: SAMPLE_02_000003_W0_HC


title: long-term HSCs, DNMT3A knockout, rep-4


title: Smartseq2_228


title: Pt5_TIL-VDJ


title: SAMPLE_02_000009_W0_HC


title: long-term HSCs, DNMT3A knockout, rep-3


title: Smartseq2_227

value: Filtered


title: SAMPLE_02_000002_W0_HC


title: CMPs and GMPs, DNMT3A knockout, rep-4


title: Smartseq2_232


title: Pt3_TD-VDJ


title: Smartseq2_226


title: CMPs and GMPs, DNMT3A knockout, rep-3


title: Smartseq2_234


title: SAMPLE_02_000027_W0_TL

value: TL


title: Smartseq2_224


title: SAMPLE_02_000004_W0_HC


title: CMPs and GMPs, Wild Type, rep-3


title: Smartseq2_229


title: CMPs and GMPs, DNMT3A knockout, rep-1


title: Pt3_TIL-VDJ


title: SAMPLE_02_000025_W0_TL


title: Smartseq2_222


title: Smartseq2_223


title: c-kit+ bone marrow cells, Wild Type, rep-2

value: c-kit+ bone marrow cells


title: SAMPLE_02_000024_W0_TL


title: Pt31_Baseline_Tumor-VDJ


title: Pt25_TIL-VDJ


title: Pt16_TIL-VDJ


title: c-kit+ bone marrow cells, Wild Type, rep-1

value: bone marrow


title: Smartseq2_221


title: SAMPLE_02_000001_W0_HC


title: Pt3_Aph-VDJ

source_name: blood

value: blood

value: Apheresis


title: c-kit+ bone marrow cells, STING knockout, rep-2

value: STING knockout


title: Pt14_TIL-VDJ

value: Tumor

value: TIL

value: T cells

value: cultured


title: Pt9_TIL-RNA


title: Smartseq2_225

value: SV


title: SAMPLE_02_000023_W0_TL

value: skin


title: SAMPLE_02_000022_W0_TL


title: c-kit+ bone marrow cells, STING knockout, rep-1


title: Pt31_TIL-VDJ


title: CMPs and GMPs, DNMT3A knockout, rep-2


title: Smartseq2_219

value: D-LN


title: SAMPLE_02_000026_W0_TL


title: SAMPLE_02_000021_W0_TL


title: Smartseq2_220


title: SAMPLE_02_000020_W0_TL


title: c-kit+ bone marrow cells, DNMT3A/STING double knockout, rep-3

value: DNMT3A/STING double knockout


title: Pt7_TIL-RNA


title: SAMPLE_02_000019_W0_TL


title: Smartseq2_217


title: Pt5_TIL-RNA


title: c-kit+ bone marrow cells, DNMT3A/STING double knockout, rep-2


title: Smartseq2_216


title: Pt9_Baseline_Tumor-RNA

value: isolated


title: c-kit+ bone marrow cells, DNMT3A/STING double knockout, rep-1


title: SAMPLE_02_000018_W0_TL


title: Pt3_TIL-RNA


title: Smartseq2_215


title: c-kit+ bone marrow cells, DNMT3A knockout, rep-2

value: DNMT3A knockout


title: c-kit+ bone marrow cells, DNMT3A knockout, rep-1


title: SAMPLE_02_000017_W0_TL


title: CMPs and GMPs, Wild Type, rep-1

value: CMPs and GMPs

value: Wild Type


title: Pt3_TD-RNA


title: SAMPLE_02_000015_W0_TL

value: TL


title: SAMPLE_02_000016_W0_TL


title: Smartseq2_212


title: CD-1 distal ileum, HA35-treated pup 6

city: Oklahoma City

first: Kathryn

last: Burge

state: OK

address: 800 Research Parkway

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

description: Fresh frozen bulk transcriptome sequencing

data_processing:
Sequences were analyzed through a custom computational pipeline on the OSCER HPC (high performance computing) consisting of the open-source gSNAP, Cufflinks, and R for sequence alignment and evaluation of differential gene expression.
Reads generated were mapped to the mouse genome (mm10) by gSMAP, expression (fragments per kilobase of transcript per million mapped reads, FPKM) derived by Cufflinks, and differential expression analyzed using R.
Assembly: mm10
Supplementary files format and content: Comma separated values file including FPKM values for all genes for each sample
Supplementary files format and content: Comma separated values file including FPKM values for differentially expressed genes (p<0.05) for each sample

source_name: distal ileum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen), and quality and quantity evaluated by a NanoDrop Lite spectrophotometer. Sequencing libraries were constructed using 200-500 ng of high-quality RNA.
RNA libraries for RNA-seq were prepared using the CORALL Total RNA-Seq Library Prep Kit v2 (Lexogen), following manufacturer's protocols.

treatment_protocol: CD-1 pups were treated once daily with 30 mg/kg body weight HA35 dissolved in sterile water (HA35) or an equal volume of sterile water (control) from P7-P14.

value: distal ileum

value: M

value: wild-type


title: Smartseq2_218


title: Smartseq2_213


title: Smartseq2_214


title: SAMPLE_02_000014_W0_TL


title: CD-1 distal ileum, HA35-treated pup 9

value: F


title: Pt31_TIL-RNA

value: Tumor


title: Pt31_Baseline_Tumor-RNA

value: TIL


title: Pt3_Aph-RNA

value: blood

value: Apheresis

value: T cells


title: SAMPLE_02_000013_W0_TL

value: skin


title: Smartseq2_211

value: D-LN

value: SV


title: CD-1 distal ileum, HA35-treated pup 1


title: CD-1 distal ileum, HA35-treated pup 3


title: CD-1 distal ileum, control pup 8

value: Control


title: SAMPLE_02_000012_W0_TL


title: Pt16_TIL-RNA

value: cultured


title: Smartseq2_210


title: SAMPLE_02_000011_W0_TL


title: Pt14_TIL-RNA


title: CD-1 distal ileum, control pup 6


title: Smartseq2_208


title: Smartseq2_207


title: CD-1 distal ileum, control pup 4