title: UPN827 cells, TN472 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN472 TrailNet Baseline T1D plasma


title: LINC01399_1_C_LP3

status: Public on Jun 01 2026

type: SRA

city: Ghent

first: Xin

last: Wang

address: Corneel Heymanslaan 10, B

country: Belgium

institute: University Gent

description: Library name: RNA017457

library_source: other

data_processing:
High performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

molecule: other

organism: Homo sapiens

growth_protocol: HEK293T-dCas9 cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37 °C in the incubator with 5% CO₂.

extract_protocol:
Cells were lysed directly in the culture plate using the SingleShot™ Cell Lysis Kit (Bio-Rad) according to the manufacturer’s instructions. Cell lysates were used directly for downstream RNA-seq library preparation.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) .

treatment_protocol: Cells were transfected with a total of 40 ng purified sgRNA per well using Lipofectamine™ CRISPRMAX™ Cas9 Transfection Reagent (Invitrogen, Cat. #CMAX00003).

tag: cell line

tag: cell type

value: embryonic kidney cell

tag: genotype

tag: treatment

tag: batch


title: GMB7-1_GMB5_Hypoxia treated

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

description:
Library name: GMB5_HI.bam
GMB_HI.txt

library_source: transcriptomic

data_processing:
RNA-seq data analysis was performed using the Torrent Mapping Alignment Program (TMAP) (https://github.com/iontorrent/TMAP). Alignment of the raw sequencing reads generated by the Ion Torrent sequencing data against reference sequence derived from the hg19 (GRCh37) assembly was carried out using nested alignment. Each of the short alignment algorithm generates contigs of certain size which is then passed to the next alignment algorithm generating longer contigs and eventually applying de novo alignment using SMEM algorithm. Raw read counts of the targeted genes were extrapolated using samtools (samtools view –c –F 4 –L bed_file bam_file). RNA-seq data was normalized using Fragments Per Kilobase Million (FPKM) normalization prior to quality control check. Differentially expressed gene (DEGs) analysis was performed using DESeq2.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

source_name: RCNSi003-A (RRID:CVCL_E4ER)

extract_protocol:
RNA were isolated  from GMB7-1 organoids in healthy and hypoxia-treated conditions. Three sample from each group were used. For gene expression analysis, the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit was utilized, enabling the simultaneous measurement of over 20,000 human RefSeq genes.
Genomic DNA removal from RNA samples was ensured by treating the RNA with Turbo DNase (ThermoFisher Scientific, USA). Next, whole transcriptome sequencing was performed using targeted RNA-Seq with Ion AmpliSeq whole transcriptome human gene expression kit (ThermoFisher Scientific, USA). Briefly, cDNA was synthesized using a SuperScript VILO cDNA Synthesis kit (ThermoFisher Scientific, USA) and amplified using Ion AmpliSeq human gene expression core panel primers. The amplified products were subjected to enzymatic shearing to get amplicons of ~200 bp, then ligated with the adapter and the unique barcodes. Next, the constructed library was purified using Agencourt AMPure XP Beads (Beckman Coulter, USA), quantified using an Ion Library TaqMan™ quantitation kit (Applied Biosystems, USA), further diluted to 100 pM, and pooled equally with 16 individual samples. The diluted library was amplified and enriched in Ion Chef System (ThermoFisher Scientific) according to the manufacturer’s instructions. Ion 540 Chip was used to sequence the prepared template libraries using an Ion S5 XL Semiconductor sequencer (ThermoFisher Scientific).

treatment_protocol: Hypoxia treated cell lines were exposed to 1% oxygen for 24h followed by 24h of normoxia step (reoxygenation). Healthy cell line were kept at normoxic condition.

value: RCNSi003-A (RRID:CVCL_E4ER)

value: Human induced pluripotent stem cell (hiPSC)


title: UPN827 cells, TN471 TrailNet Baseline T1D plasma

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

source_name: UPN827 cells stimulated with TN471 TrailNet Baseline T1D plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

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

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: TrailNet Baseline


title: LINC01399_1_B_LP3

description: Library name: RNA017456


title: LSP_biorep2_techrep1

city: Palo Alto

first: Reema

last: Baskar

address: 3373 Hillview Ave

institute: Stanford University

library_source: genomic

data_processing:
FASTQ files from Illumina nextseq runs were obtained from primer de-barcoding using the bcl2fastq2 application. Else, they were obtained directly from novogene sequencing service. FASTQ files were input into pepATAC pipeline to check sequencing quality (fastqc), trim (Skewer), and align (bowtie2) to the hg38 genome for cell line data and hg19 for BM and BALL data. Duplicated reads were marked and removed using Picard MarkDuplicates tool. Peaks were called using MACS2 under parameters ‘-q 0.01 ‐‐shift 0 –nomodel’. The signal-to-noise ratio between transcription start sites and flanking regions was calculated and plotted to check data quality. All samples had TSS scores of 10 and above, as well as expected fragment length distributions as plotted for all 3 sequencing experiments with 2 technical and 2 biological replicates each.
Consensus bed file was created for each experiment across technical and biological replicates using Chraccr package. Exact code in github and zenodo as referred to in paper.
Assembly: hg19
Supplementary files format and content: Peak set output from pepATAC pipeline (bed file format)
Library strategy: InTAC-seq (variation of ATAC-seq)

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: After BM processing and lineage depletion as described in paper methods section, 1 million BMMC from 2 separate donors were washed and resuspended in PBS. Cells were stained with LIVE/DEAD Aqua kit (Invitrogen, #L34965) and incubated at RTP for 30 min protected from light. Cells were then washed and pelleted before resuspending in 100ul of PBS with Human TruStain Fc blocker (Biolegend, #422302) for 10min at RTP. Cells were then incubated with our surface marker antibody cocktail for 30min in dark and on ice (Table S5). Wash cells with 2ml CSM at 300G for 10min. Fix cells with 1.6% paraformaldehyde in PBS for 5min at RTP. Wash cells twice with 1X permeabilization buffer (from eBioscience Foxp3/Transcription Factor staining buffer set, #00-5523-00) at 600G for 5min. Add intracellular marker (TdT) into cells resuspended in 100ul of 1X permeabilization buffer and incubate for 45min at RTP. Wash cells with CSM at 600G for 5min. Cells were filtered for clumps before sorting. Cells were then washed and resuspended in 1ml CSM for FACS sorting. Cells were gated for cell size and viability on Aqua before defined epigenetic switch point populations were sorted.

extract_protocol:
Sorted cells were counted and split into 50K cells per replicate, including live, unsorted control. Samples were then processed using the InTAC-seq protocol. Briefly, cells were washed once with cold PBS at 300G for 5 minutes and then once with cold PBS+0.1% Tween-20 at 300G for 5 minutes. Transposition and lysis were carried out in 1 step with each sample cell pellet being suspended with 25ul 2x TD buffer, 2.5ul Tn5 enzyme, 0.5ul 1% digitonin, 0.5ul of 10% NP40 and 21.5ul of nuclease-free water. Cell suspensions were incubated at 37C for 30 minutes on a shaker at 800RPM. After transposition, 50ul of 2X reverse crosslinking buffer (100mM N,N-Dimethylethylenediamine, pH 6.5 (Sigma Aldrich D158003), 2% SDS, 1ul Proteinase K (NEB #P8107S) in nuclease-free water) was added to cells with an overnight incubation at 37C on a shaker at 800RPM.
DNA extracted from samples using QIAGEN MiniElute PCR purification columns and subsequent library preparation and next-generation sequencing were carried out as previously described in the InTAC-seq paper and this protocol is optimized from the published InTAC-seq method. For the preparation of live ATAC-seq samples from fresh cells as a comparison, samples were prepared as above, except DNA was purified immediately after transposition rather than performing crosslink reversal.

tag: tissue

value: Bone marrow

value: Developing B cell


title: GMB7-1_GMB4_Hypoxia treated

description:
Library name: GMB4_HI.bam
GMB_HI.txt


title: UPN827 cells, TN470 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN470 TrailNet Baseline T1D plasma


title: LSP_biorep1_techrep3


title: LINC01399_1_A_LP3

description: Library name: RNA017455


title: GMB7-1_GMB6__Healthy

description:
Library name: GMB6_HE.bam
GMB_HE.txt


title: UPN827 cells, TN469 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN469 TrailNet Baseline T1D plasma


title: MIR4458HG_D_LP3

description: Library name: RNA017454


title: S4_biorep2_techrep2


title: LSP_biorep1_techrep2


title: GMB7-1_GMB5__Healthy

description:
Library name: GMB5_HE.bam
GMB_HE.txt


title: LSP_biorep1_techrep1


title: MIR4458HG_C_LP3

description: Library name: RNA017453


title: UPN827 cells, TN468 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN468 TrailNet Baseline T1D plasma


title: DO iPSC line 6608, triphenyl phosphate treated

city: Bar Harbor

first: Madison

last: Armstrong

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: Library name: DO_iPSC_6608_TPHP

data_processing:
Raw RNA-seq reads were combined across lanes for each sample to obtain over 30 million raw reads per sample. Combined RNA-seq reads were processed using the Jackson Laboratory Data Science Nextflow DSL2 Workflows (version 24.10.6, https://github.com/TheJacksonLaboratory/jds-nf-workflows/wiki). Reads were aligned and quantified using EMASE (Expectation Maximization for Allele-Specific Expression)[Munger, S.C., et al., RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics, 2014. 198(1): p. 59–73.]
Raw gbrs expected read counts were compiled into a counts matrix. Raw transcript per million counts were compiled into a tpm matrix.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Count tsv file with counts per gene (rows) for each sample (columns)
Supplementary files format and content: Transcript per million tsv with tpm per gene (rows) for each sample (columns)

organism: Mus musculus

source_name: DO iPSC 6608

growth_protocol: 218 Diversity Outbred iPSC lines were thawed from early passage aliquots, plating ~1 million cells onto gelatinized 60mm tissue culture treated plates with mESC medium +2i/LIF (DMEM supplemented with 15% ES cell grade FBS [Gibco, 16141079], 1X GlutaMAX [100X, Gibco, 35050061], 1X penicillin/streptomycin [100X, Gibco, 15140], 1X nonessential amino acids [100X, Gibco, 11140], 1X sodium pyruvate [100X, Gibco, 11360], 0.1 mM β‐mercaptoethanol [55 mM, Gibco 21985023], and 1,000 U/ml leukemia inhibitory factor [Chemicon ESG1106 or 1107], supplemented with 2i [3 uM CHIR99021, Stemgent 04-0004, GSK3 inhibition and 1 uM PD0325901, Stemgent 04-0006, MEK/ERK inhibition]). Cells were grown to confluency in 5% CO2 at 37°C before passaging for a minimum of three passages before beginning the treament protocol.

extract_protocol:
Total RNA was isolated from tissue using the NucleoMag RNA Kit (Macherey-Nagel) and the KingFisher Flex purification system (ThermoFisher). Cells were homogenized in MR1 buffer (Macherey-Nagel) by vortexing.  RNA isolation was performed according to the manufacturer’s protocol. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA ScreenTape Assay (Agilent Technologies).
Stranded libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: Density plating experiments identified plating with 75,000 cells produced optimal numbers of cells following treatment. Cells were plated on gelatinized 12-well tissue culture treated glass-like bottom plates to reduce chemical precipitation. Following plating with 75,000 cells per well in mESC medium +2i/LIF, cells were allowed to recover from passaging and expand for 24 hours at 5% CO2 at 37°C. After 24 hours of recovery, control sample cell media was replaced with fresh mESC medium +2i/LIF while treated sample cell media was replaced with mESC medium +2i/LIF with added 80μM triphenyl phosphate (TPHP, dissolved in DMSO, Acros Organics 147672500). Cells were treated for 24 hours at 5% CO2 at 37°C. Cells were collected using trypsin (0.05%, Gibco 25300-054) and cell pellets were store at -80°C until RNA extraction.

value: DO iPSC 6608

value: iPSC

value: triphenyl phosphate

tag: Sex

value: female

tag: do generation

tag: run


title: MIR4458HG_A_LP3

description: Library name: RNA017451


title: UPN827 cells, TN467 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN467 TrailNet Baseline T1D plasma


title: GM12878_H3K27ac_Low_rep2

data_processing:
*library strategy: InTAC-seq (variation of ATAC-seq)
FASTQ files from Illumina nextseq runs were obtained from primer de-barcoding using the bcl2fastq2 application. Else, they were obtained directly from novogene sequencing service. FASTQ files were input into pepATAC pipeline to check sequencing quality (fastqc), trim (Skewer), and align (bowtie2) to the hg38 genome for cell line data and hg19 for BM and BALL data. Duplicated reads were marked and removed using Picard MarkDuplicates tool. Peaks were called using MACS2 under parameters ‘-q 0.01 ‐‐shift 0 –nomodel’. The signal-to-noise ratio between transcription start sites and flanking regions was calculated and plotted to check data quality. All samples had TSS scores of 10 and above, as well as expected fragment length distributions as plotted for all 3 sequencing experiments with 2 technical and 2 biological replicates each.
Consensus bed file was created for each experiment across technical and biological replicates using Chraccr package. Exact code in github and zenodo as referred to in paper.
Count matrix contains raw insertion counts across samples for all peaks in consensus peakset and can be used for any relevant downstream analysis.
Assembly: hg38
Supplementary files format and content: peak set output from pepATAC pipeline (bed file format)

growth_protocol: GM12878 cell line was grown to a low passage number (<10) and stained for viability (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, L34957) before being washed with CSM. Cells were then fixed with 1ml of 1.6% paraformaldehyde for 5 minutes at RTP and washed twice with permeabilization buffer (1:10 diluted eBioscience transcription factor permeabilization buffer, 00-5521-00). Cells were incubated with H3K37ac (CST D5E4) antibody for 30min at RTP before washing with permeabilization buffer and doing a secondary stain with anti-rabbit FITC-conjugated antibody for 15 minutes at RTP. Cells were then washed and resuspended in 1ml CSM for FACS sorting. Cells were gated for cell size and viability before high and low H3K27ac populations were sorted.

value: Lymphoblastoidcells

tag: sorted fraction

tag: biomaterial provider


title: GMB7-1_GMB4_Healthy

description:
Library name: GMB4_HE.bam
GMB_HE.txt


title: MIR4458HG_B_LP3

description: Library name: RNA017452


title: GM12878_H3K27ac_Low_rep1


title: DO iPSC line 6608, untreated

description: Library name: DO_iPSC_6608_CTRL

value: untreated


title: GM12878_H3K27ac_High_rep2


title: LINC01315_1_D_LP3

description: Library name: RNA017450


title: UPN827 cells, TN465 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN465 TrailNet Baseline T1D plasma


title: UPN827 cells, TN466 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN466 TrailNet Baseline T1D plasma


title: DO iPSC line 6606, triphenyl phosphate treated

description: Library name: DO_iPSC_6606_TPHP

source_name: DO iPSC 6606

value: DO iPSC 6606


title: GM12878_H3K27ac_High_rep1


title: UPN827 cells, TN464 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN464 TrailNet Baseline T1D plasma


title: LINC01315_1_C_LP3

description: Library name: RNA017449


title: DO iPSC line 6606, untreated

description: Library name: DO_iPSC_6606_CTRL


title: GM12878_LiveCellCtrl_rep2


title: LINC01315_1_B_LP3

description: Library name: RNA017448


title: UPN827 cells, TN463 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN463 TrailNet Baseline T1D plasma


title: DO iPSC line 6604, triphenyl phosphate treated

description: Library name: DO_iPSC_6604_TPHP

source_name: DO iPSC 6604

value: DO iPSC 6604


title: UPN827 cells, TN462 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN462 TrailNet Baseline T1D plasma


title: LINC01315_1_A_LP3

description: Library name: RNA017447


title: GM12878_LiveCellCtrl_rep1


title: DO iPSC line 6604, untreated

description: Library name: DO_iPSC_6604_CTRL


title: MIR222HG_D_LP3

description: Library name: RNA017446


title: UPN827 cells, TN461 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN461 TrailNet Baseline T1D plasma


title: Bulk_PtenSmad4_VP

city: Notre Dame

last: Lu

state: IN

address: 109 Galvin Life Science Center

institute: University of Notre Dame

description: Bulk tumor from PB-Cre⁺ PtenL/L Smad4L/L mouse, ventral lobe prostate

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Bulk tumor, Prostate-specific deletions of Pten and Smad4, ventral lobe prostate

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: ventral lobe prostate

value: PB-Cre+ PtenL/L Smad4L/L mTmG

tag: age

value: 25.9 weeks

value: bulk tumor


title: UPN827 cells, TN460 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN460 TrailNet Baseline T1D plasma


title: DO iPSC line 6600, triphenyl phosphate treated

description: Library name: DO_iPSC_6600_TPHP

source_name: DO iPSC 6600

value: DO iPSC 6600


title: MIR222HG_C_LP3

description: Library name: RNA017445

value: embryonic kidney cell


title: DO iPSC line 6600, untreated

description: Library name: DO_iPSC_6600_CTRL


title: Bulk_PtenSmad4_DLP

description: Bulk tumor from PB-Cre⁺ PtenL/L Smad4L/L mouse, dorsolateral prostate

source_name: Bulk tumor, Prostate-specific deletions of Pten and Smad4, dorsolateral prostate

value: dorsolateral prostate


title: PKP2 control hiPSC-cardiomyocytes rep2

city: Utrecht

first: Su Ji

last: Han

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: Sample 2

library_source: transcriptomic single cell

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cell barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA. Data was demultiplexed.Raw read counts (included as count tables "ReadCounts") were converted to umi counts (referred to as "barcode counts"); an additional correction was performed based on binominal statistics, resulting in "transcript counts".
Assembly: hg19
Supplementary files format and content: Count tables of raw reads ("readcounts"). Columns are single cells, rows indicate genes and chromosomal origin using HGNC symbols and "chrX" where X indicates chromosome of origin. Files are labeled by identifiers described above, R1 and R2 indicate to read 1 and read 2. s001-2 and s006-7 enumerates the samples. (HUB = Hubrecht, SH = Su Ji Han)
Supplementary files format and content: umi counts ("barcode counts") Columns are single cells (and each file corresponds to one sample), rows indicate genes and chromosomal origin using HGNC symbols and "chrX" where X indicates chromosome of origin. Files are labeled by identifiers described above, R1 and R2 indicate to read 1 and read 2. s001-2 and s006-7 enumerates the samples. (HUB = Hubrecht, SH = Su Ji Han)
Supplementary files format and content: corrected umi counts ("transcript counts"): Columns are single cells (and each file corresponds to one sample), rows indicate genes and chromosomal origin using HGNC symbols and "chrX" where X indicates chromosome of origin. Files are labeled by identifiers described above, R1 and R2 indicate to read 1 and read 2. s001-2 and s006-7 enumerates the samples. (HUB = Hubrecht, SH = Su Ji Han)

molecule: polyA RNA

source_name: hiPSC-derived cardiomyocytes

growth_protocol: The hiPSCs were cultured on Geltrex™ LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix-coated wells (Gibco: A1413302) in Essential 8™ Medium (Gibco: A1517001). For directed differentiation to cardiomyocytes, hiPSCs were cultured until they reached 80-90% cell confluency. Differentiation was started (day 0) using RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with 4µM CHIR99021, 0.5 mg/mL human recombinant albumin and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate. After 48 hours, the medium was aspirated and cells were incubated in RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with 5µM IWP2, 0.5 mg/mL human recombinant albumin and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate for another 48 hours. On day 4 and 6 the medium was changed to RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with 0.5 mg/mL human recombinant albumin and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate. On day 8, cells were refreshed with RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with B-27™Supplement (50x)-serum free (Gibco: 17504001). When spontaneously beating cardiomyocytes were observed cells were dissociated using TrypLE™ Select Enzyme (10x), no phenol red (Gibco: A1217703) and seeded for experiments in Geltrex-coated plates using RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with B-27™Supplement (50x)-serum free (Gibco: 17504001) and 2μM Thiazovivin. The day after the cells were maintained in RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with B-27™Supplement (50x)-serum free (Gibco: 17504001) until they were used for experiments.

extract_protocol:
hiPSC-cardiomyocytes were dissociated using TrypLE™ Select Enzyme (10x), no phenol red (Gibco: A1217703) and single-cell sorted using the FACSJazz™ Cell Sorter (BD Biosciences) into 384-well plates provided by Single Cell Discoveries. After sorting, plates were centrifuged at 4 °C, put on dry ice and stored at -80 °C until they were processed for library preparation.
The plates were prepared for single-cell mRNA sequencing by Single Cell Discoveries according to an adapted version of the SORT-seq protocol.

value: hiPSC-derived cardiomyocytes


title: MIR222HG_B_LP3

description: Library name: RNA017444


title: WT_PN3_RNA-seq_r3

city: Shanghai

first: Xinyu

address: Siping Road 1239

country: China

institute: Tongji University

description:
Library name: Sample8
WT PN3 RNA-seq replicate3

data_processing:
RNA-seq: For raw paired-end RNA-seq reads, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. HISAT2 was used to align the clean sequence data to the mouse reference genome (mm10). StringTie was used to quantify gene expression from the aligned sequences for each gene, and htseq-count was used to count reads number for each gene. The mouse gene annotation file was obtained from the mouse GENCODE release (GRCm38.99).
Assembly: mm10
Supplementary files format and content: gene fpkm file

source_name: PN3 stage zygote

growth_protocol: Specific pathogen-free (SPF) mice were housed in the animal facility at Tongji University,Shanghai, China, and they were fed a standard diet. The temperature and light were strictly controlled (24 °C; 12 h light and 12 h dark). Smarca4flox/flox mice are from previous study(Qi et al. 2021). All animal experiments were performed in accordance with the University of Health Guide for the Care and Use of Laboratory Animals and were approved by the Biological Research Ethics Committee of Tongji University. To get MII oocytes for ICSI, B6D2F1 or Smarca4flox/flox Gdf9 Cre C57BL/6 female mice (8–12-weeks old) were superovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical) 48 h later.

extract_protocol:
20-30 blastomere per replicate were isolated and washed before they were placed into 1.4 μL of lysis buffer (10 mM Tris-HCl, pH 8.5, 5 mM MgCl2, 0.6% NP-40) for individual reactions. Then, 1.8 μL of MNase master mix (MNase buffer, 0.125 U/μL MNase (NEB, M0247S), 2 mM DTT, and 5% PEG 6000) was added into each tube, and the reaction was incubated at 25 °C for 10 min for chromatin fragmentation. The reaction was stopped by the addition of 0.4 μL of 100 mM EDTA, and then 0.4 μL of 2% Triton X-100 was added to the reaction to release the fragmented chromatin. Then, 0.2 μL of 20 mg/mL protease (Qiagen) was added, and the reaction was incubated at 50 °C for 90 min for protein digestion followed by incubation at 75 °C for 30 min for protease inactivation. The sequencing libraries were prepared using the KAPA Hyper Prep kit for the Illumina platform (Roche, kk8504) following the manufacturer’s instructions. After standard procedures including end repair and A-tailing, adapter ligation, post-ligation cleanup, and library amplification, the resulting products were subjected to a second round of PCR amplification with the same provided primers to generate sufficient DNA materials for highthroughput sequencing.
For mouse embryos, the sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase(Kapa Biosystems, KK8483) and KAPA HyperPrep Kit for the Illumina platform (Roche, kk8504) following manufacturer’s protocol. Paired-end sequencing with 150-bp read length was performed on the HiSeq X Ten (Illumina) platform.

value: PN3 stage zygote

value: wild type


title: UPN827 cells, TN459 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN459 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: DO iPSC line 6594, triphenyl phosphate treated

description: Library name: DO_iPSC_6594_TPHP

source_name: DO iPSC 6594

value: DO iPSC 6594

value: iPSC

value: triphenyl phosphate

value: female


title: Bulk_PtenSmad4_AP

description: Bulk tumor from PB-Cre⁺ PtenL/L Smad4L/L mouse, anterior lobe prostate

source_name: Bulk tumor, Prostate-specific deletions of Pten and Smad4, anterior lobe prostate

value: anterior lobe prostate


title: UPN827 cells, TN458 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN458 TrailNet Baseline T1D plasma


title: MIR222HG_A_LP3

description: Library name: RNA017443


title: Bulk_PtenApc_VP

description: Bulk tumor from PB-Cre⁺ PtenL/L ApcL/L mouse, ventral lobe prostate

source_name: Bulk tumor, Prostate-specific deletions of Pten and Apc, ventral lobe prostate

value: ventral lobe prostate

value: PB-Cre+ PtenL/L ApcL/L mTmG

value: 19.6 weeks


title: DO iPSC line 6594, untreated

description: Library name: DO_iPSC_6594_CTRL

value: untreated


title: LINC01234_1_D_LP3

description: Library name: RNA017442


title: UPN827 cells, TN457 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN457 TrailNet Baseline T1D plasma


title: Bulk_PtenApc_DLP

description: Bulk tumor from PB-Cre⁺ PtenL/L ApcL/L mouse, dorsolateral prostate

source_name: Bulk tumor, Prostate-specific deletions of Pten and Apc, dorsolateral prostate

value: bulk tumor


title: PVT1_B_LP4

description: Library name: RNA017484

value: embryonic kidney cell


title: DO iPSC line 6586, triphenyl phosphate treated

description: Library name: DO_iPSC_6586_TPHP

source_name: DO iPSC 6586

value: DO iPSC 6586


title: LINC01234_1_C_LP3

description: Library name: RNA017441


title: UPN827 cells, TN456 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN456 TrailNet Baseline T1D plasma


title: DO iPSC line 6586, untreated

description: Library name: DO_iPSC_6586_CTRL


title: Bulk_PtenApc_AP

description: Bulk tumor from PB-Cre⁺ PtenL/L ApcL/L mouse, anterior lobe prostate

source_name: Bulk tumor, Prostate-specific deletions of Pten and Apc, anterior lobe prostate


title: LINC01234_1_B_LP3

description: Library name: RNA017440


title: UPN827 cells, TN455 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN455 TrailNet Baseline T1D plasma


title: DO iPSC line 6584, triphenyl phosphate treated

description: Library name: DO_iPSC_6584_TPHP

source_name: DO iPSC 6584

value: DO iPSC 6584


title: Bulk_Pten_VP_rep2

description: Bulk tumor from PB-Cre⁺ PtenL/L mouse, ventral lobe prostate (biological replicate 2)

source_name: Bulk tumor, Prostate-specific deletions of Pten, ventral lobe prostate

value: PB-Cre+ PtenL/L mTmG


title: LINC01234_1_A_LP3

description: Library name: RNA017439


title: UPN827 cells, TN454 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN454 TrailNet Baseline T1D plasma


title: T3095

city: Ann Arbor

first: Adam

last: Abraham

state: MI

address: 2800 Plymouth Rd

department: Orthopaedic Surgery

institute: University of Michigan

description:
Library name: 3T
Column name in TENDONseq__counts.tsv: T3095

data_processing:
The reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure the quality of data
Fastq Screen v0.13.0 was used to screen for various types of contamination
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a  and assigned count estimates to genes with RSEM v1.3.3.  Alignment options followed ENCODE standards for RNA-seq.
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Tendon

extract_protocol:
RNA extraction was performed using RNeasy Mini Fibrous Tissue Kit with on-column deoxyribonuclease I treatment according to manufacturer’s instructions
The NEBNext Ultra II RNA Library Preparation for Illumina Kit was used to prepare the samples for sequencing following the manufacturer protocol.

value: Tendon

value: H


title: DO iPSC line 6584, untreated

description: Library name: DO_iPSC_6584_CTRL


title: MIATNB_1_D_LP3

description: Library name: RNA017438


title: Bulk_Pten_DLP_rep2

description: Bulk tumor from PB-Cre⁺ PtenL/L mouse, dorsolateral prostate (biological replicate 2)

source_name: Bulk tumor, Prostate-specific deletions of Pten, dorsolateral prostate

value: dorsolateral prostate


title: UPN827 cells, TN453 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN453 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: Bulk_Pten_VP_rep1

description: Bulk tumor from PB-Cre⁺ PtenL/L mouse, ventral lobe prostate (biological replicate 1)

value: 25.0 weeks


title: DO iPSC line 6562, triphenyl phosphate treated

description: Library name: DO_iPSC_6562_TPHP

source_name: DO iPSC 6562

value: DO iPSC 6562

value: iPSC

value: triphenyl phosphate

value: female


title: MIATNB_1_C_LP3

description: Library name: RNA017437


title: Bulk_Pten_DLP_rep1

description: Bulk tumor from PB-Cre⁺ PtenL/L mouse, dorsolateral prostate (biological replicate 1)


title: DO iPSC line 6562, untreated

description: Library name: DO_iPSC_6562_CTRL


title: UPN827 cells, TN452 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN452 TrailNet Baseline T1D plasma


title: MIATNB_1_B_LP3

description: Library name: RNA017436


title: DO iPSC line 6560, triphenyl phosphate treated

description: Library name: DO_iPSC_6560_TPHP

source_name: DO iPSC 6560

value: DO iPSC 6560


title: GFP_PtenApc_rep4

description: GFP⁺ cells from PB-Cre⁺ PtenL/L ApcL/L mouse (biological replicate 4)

source_name: GFP+ cells, Prostate-specific deletions of Pten and Apc

value: prostate

value: PB-Cre+ PtenL/L ApcL/L mTmG

value: 15.2 weeks

value: GFP+ cells


title: UPN827 cells, TN451 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN451 TrailNet Baseline T1D plasma


title: GFP_PtenApc_rep3

description: GFP⁺ cells from PB-Cre⁺ PtenL/L ApcL/L mouse (biological replicate 3)

value: 23.5 weeks


title: MIATNB_1_A_LP3

description: Library name: RNA017435

value: embryonic kidney cell


title: UPN827 cells, TN450 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN450 TrailNet Baseline T1D plasma


title: UPN827 cells, TN449 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN449 TrailNet Baseline T1D plasma


title: DO iPSC line 6560, untreated

description: Library name: DO_iPSC_6560_CTRL

value: untreated


title: LINC01021_1_D_LP3

description: Library name: RNA017434


title: DO iPSC line 6556, triphenyl phosphate treated

description: Library name: DO_iPSC_6556_TPHP

source_name: DO iPSC 6556

value: DO iPSC 6556


title: GFP_PtenApc_rep2

description: GFP⁺ cells from PB-Cre⁺ PtenL/L ApcL/L mouse (biological replicate 2)


title: LINC01021_1_C_LP3

description: Library name: RNA017433


title: GFP_PtenApc_rep1

description: GFP⁺ cells from PB-Cre⁺ PtenL/L ApcL/L mouse (biological replicate 1)

value: 22.6 weeks


title: DO iPSC line 6556, untreated

description: Library name: DO_iPSC_6556_CTRL


title: UPN827 cells, TN448 TrailNet Baseline T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN448 TrailNet Baseline T1D plasma

value: UPN827 cells


title: LINC01021_1_B_LP3

description: Library name: RNA017432


title: CD8 T cell, rim-enriched, KO (F322)

city: Leuven

first: Lisa

middle: M

last: Becker

address: Herestraat 49

institute: VIB KU Leuven Center for Cancer Biology

data_processing:
Quality trimming: We trimmed low quality ends (< Q20) with FastX 0.0.14. Reads that are shorter than 35bp after trimming are removed.
Adapter trimming: The adapters are trimmed only at the end (at least 10bp overlap and 90% match) with cutadapt 3.2. Reads that are shorter than 35bp after adapter trimming are removed.
Quality filtering: Using FastX 0.0.14 and ShortRead 1.52.0, we remove polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type).
Removal of contaminants: Using bowtie 2.4.5, we identify reads that align to phix illumina and remove them
Assembly: GRCm3882
Supplementary files format and content: Counts.csv coma separated file containing raw counts. Fastq files were aligned with HISAT2 vesrsion 2.1.0 for the M.musculus reference GRCm38 downloaded from HISAT2 website, Counting was done with subread-2.0.0 FeatureCounts for the reference mm10.ncbiRefSeq.gtf

source_name: lung tumor (rim-enriched)

extract_protocol:
RNA was harvested using the Qiagen RNeasy Micro Kit
Libraries were prepared with the TruSeq RNA Library Prep Kit (Illumina) following manufacturer's protocols

value: lung tumor (rim-enriched)

value: CD8 T cells

value: KO


title: UPN827 cells, TN447 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN447 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: Monocytes, resting state, person 48

city: Boston

first: Zachary

middle: D

last: Nagel

state: MA

address: 655 Huntington Avenue

department: Environmental Health

institute: Harvard University

description: Library name: M_48

data_processing:
RNA-seq data were processed using the bcbio-nextgen pipeline with the hg38 genome build. The FASTQ files underwent pre-processing, where UMIs were incorporated into R2, and R1 was discarded, resulting in single FASTQ files per library. Reads were quality trimmed with Trim Galore and aligned to hg38 using TopHat2. Transcript quantification was performed with DEXSeq to produce a count matrix.
Assembly: hg38
Supplementary files format and content: csv file in .gz containing raw read counts for each sample

source_name: Blood

growth_protocol: RPMI 1640 medium supplemented with 20% FBS at 37C/5%CO2

extract_protocol:
RNA isolation was performed using PureLinkTM RNA Mini Kit protocol (Invitrogen, Cat no. 12183018A). 25 ng of isolated total RNA was used for constructing sequencing libraries
RNA samples were quantified and assessed using the Advanced Analytical Fragment Analyzer. Libraries were prepared using the 3’ Digital Gene Expression (DGE) sequencing protocol, following established methods. Custom 3’ DGE primers with barcodes and Unique Molecular Identifiers (UMIs) were incorporated to tag transcripts uniquely. After reverse transcription and template switching, cDNA was pooled, cleaned, amplified, and tagmented using Nextera tagmentation. Libraries were sequenced on an Illumina NextSeq500 platform. For more details on library construction, refer to the published protocol in the reference (doi: https://doi.org/10.1101/003236)

treatment_protocol: PBMCs and T cells were stimulated by 10ng/ml of Phytohemagglutinin-L and B cells were stimulated by human B cell Expansion kit for 3 days

value: Blood

value: Primary Monocytes

value: Monocytes


title: DO iPSC line 6538, triphenyl phosphate treated

description: Library name: DO_iPSC_6538_TPHP

source_name: DO iPSC 6538

value: DO iPSC 6538

value: iPSC

value: triphenyl phosphate

value: female


title: LINC01021_1_A_LP3

description: Library name: RNA017431


title: UPN827 cells, TN446RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN446RH2 TrailNet Baseline T1D plasma


title: liver_EEC+TMA treatment

city: Kumjeong-ku

first: Dae Youn

last: Hwang

state: --- Select One ---

address: Samnangjin-ro, 1268-50

country: South Korea

institute: Pusan National University

description: Gene expression data from 10-weeks-old EEC+TMA treatment ICR mice

hyb_protocol: Approximately 5.5 μg of the labeled DNA target was hybridized to the Affymetrix GeneChipTM Mouse 2.0 ST Array (ThermoFisher Scientific Inc.) at 45°C for 16 h.

scan_protocol: The hybridized arrays were washed, stained on a GeneChipTM Fluidics Station 450 (ThermoFisher Scientific Inc.), and scanned on a GCS3000 Scanner (Affymetrix, Santa Clara, CA, USA).

data_processing: The signal values were calculated using the Affymetrix® GeneChip™ Command Console® Software (AGCC).

label: Biotin

source_name: ICR mice liver tissue, EEC+TMA treatment

label_protocol: The sense cDNA was fragmented and biotin-labeled with terminal deoxynucleotidyl transferase (TdT) using the GeneChipTM HT WT Terminal Labeling Kit (ThermoFisher Scientific Inc.).

growth_protocol: The experimental protocol for mice treated with Ecklonia cava + TMA was reviewed and approved by Pusan National University's Animal Care and Use Committee (PNU-IACUC; approval number PNU-2025-0593)

extract_protocol: The total RNAs were purified from the frozen liver tissue (100 mg) using TransZol (TransGen Biotech Co. LTD, Beijing, China) (1 mL) solution based on the manufacturer’s protocol.

treatment_protocol: Ecklonia cava ethanol extract was orally administered to 8-week-old ICR mice for 2 weeks, and TMA was treated for 24 h.

value: Liver

value: 10 weeks


title: DO iPSC line 6538, untreated

description: Library name: DO_iPSC_6538_CTRL

value: untreated


title: liver_TMA treatment

description: Gene expression data from 10-weeks-old TMA treatment ICR mice

source_name: ICR mice liver tissue, TMA treatment


title: LINC01515_1_D_LP3

description: Library name: RNA017430

value: embryonic kidney cell


title: DO iPSC line 6536, triphenyl phosphate treated

description: Library name: DO_iPSC_6536_TPHP

source_name: DO iPSC 6536

value: DO iPSC 6536


title: UPN827 cells, TN445 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN445 TrailNet Baseline T1D plasma

value: UPN827 cells


title: liver_No treatment

description: Gene expression data from 10-weeks-old No treatment ICR mice

source_name: ICR mice liver tissue, No treatment


title: CAF133_5FU

city: Suwon-si

first: in-hye

last: Ham

address: 169 Worldcup-ro, Yeongtong-gu

department: surgery

institute: Ajou University School of medicine

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: Fibroblasts

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: CAF cells (CAF47, CAF51, CAF98, CAF133) were cultured in DMEM supplemented with [10%] fetal bovine serum (FBS) and [1%] penicillin/streptomycin. Cells were aintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted from CAF cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: To induce senescence, CAF cells were treated with 50 uM of 5-Fluorouracil (5-FU) for 72 hours. Control cells were treated with an equal volume of DMSO as a vehicle control.


title: DO iPSC line 6536, untreated

description: Library name: DO_iPSC_6536_CTRL


title: LINC01515_1_C_LP3

description: Library name: RNA017429


title: CAF133_Ctrl


title: UPN827 cells, TN444 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN444 TrailNet Baseline T1D plasma


title: LINC01515_1_B_LP3

description: Library name: RNA017428


title: DO iPSC line 6532, triphenyl phosphate treated

description: Library name: DO_iPSC_6532_TPHP

source_name: DO iPSC 6532

value: DO iPSC 6532


title: UPN827 cells, TN443 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN443 TrailNet Baseline T1D plasma


title: CAF98_5FU


title: LINC01515_1_A_LP3

description: Library name: RNA017427


title: UPN827 cells, TN442 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN442 TrailNet Baseline T1D plasma


title: LINC00882_1_D_LP3

description: Library name: RNA017426


title: DO iPSC line 6532, untreated

description: Library name: DO_iPSC_6532_CTRL


title: CAF51_5FU


title: LINC00882_1_C_LP3

description: Library name: RNA017425


title: DO iPSC line 6530, triphenyl phosphate treated

description: Library name: DO_iPSC_6530_TPHP

source_name: DO iPSC 6530

value: DO iPSC 6530


title: CAF98_Ctrl


title: UPN827 cells, TN441 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN441 TrailNet Baseline T1D plasma


title: Pancreas from obese donor D332

city: NYC

first: Alexey

last: Koshkin

state: New York

department: Department of Pathology and Cell Biology

institute: Columbia University Medical center, department of Pathology and Cell Biology

description:
Library name: DS026_library
Bulk RNA-seq from pancreas of obese donor D332 in batch B

data_processing:
Data Preprocessing Whole-Transcriptome Profiling by RNA-Seq D8+ TRM (DAPI- CD45+ CD3+ CD8+ CD45RA- CCR7- CD69+ 70 cells) from pancreas, small  intestine, lymph node and spleen were individually sorted. Analysis was restricted to CD8 TRM  because they are the predominant TRM lineage in pancreas. RNA was isolated from cell pellets  using the RNeasy Mini Kit (QIAGEN) and quantitated using an Agilent 2100 Bioanalyzer (Agilent  Technologies), and library preparation and RNA-seq was performed by the Columbia Genome Center as previously described4. To analyze the effect of obesity on TRM gene expression, RNA-Seq reads from sorted CD8+ 259 TRM were mapped, filtered and read counts computed as we previously described7 260 . Data from samples that were included in our previous study7 261 (GEO: GSE135582) were merged with 24 additional samples and batch correction was performed using ComBat-seq21  4. Kumar, B.V., et al. Human Tissue-Resident Memory T Cells Are Defined by Core  Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. Cell Rep 20, 2921-  2934 (2017) 7. Weisberg, S.P., et al. Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the  Human Pancreas through the PD-1/PD-L1 Pathway. Cell Rep 29, 3916-3932 e3915 (2019) . 21. Zhang, Y., Parmigiani, G. & Johnson, W.E. ComBat-seq: batch eject adjustment for RNA-seq  count data. NAR Genom Bioinform 2, lqaa078 (2020).
Assembly: Homo sapiens
Supplementary files format and content: Counts_Table_bulkRNAseq_GEO.txt

source_name: spleen/PLN

extract_protocol:
Human Tissue Samples Human samples Tissues were obtained from deceased organ donors as part of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement with LiveOnNY as described previously (Carpenter et al., 2018, Gordon et al., 2017, Granot et al., 2017, Kumar et al., 2017, Miron et al., 2018, Senda et al., 2019). Donors were free of cancer, chronic diseases, seronegative for hepatitis B, C, and HIV, and represented diverse ages. Use of organ donor tissues does not qualify as “human subjects” research, as confirmed by the Columbia University IRB as tissue samples were obtained from brain-dead (deceased) individuals.
library preparation and RNA-seq was performed by the Columbia Genome Center as previously described

value: spleen/PLN

tag: sample group

value: obese

value: B


title: DO iPSC line 6530, untreated

description: Library name: DO_iPSC_6530_CTRL


title: UPN827 cells, TN440 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN440 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: CAF51_Ctrl


title: LINC00882_1_B_LP3

description: Library name: RNA017424


title: UPN827 cells, TN439 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN439 TrailNet Baseline T1D plasma


title: DO iPSC line 6518, triphenyl phosphate treated

description: Library name: DO_iPSC_6518_TPHP

source_name: DO iPSC 6518

value: DO iPSC 6518


title: UPN827 cells, TN438 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN438 TrailNet Baseline T1D plasma


title: CAF47_5FU


title: LINC00882_1_A_LP3

description: Library name: RNA017423


title: NT_B_LP2

description: Library name: RNA017422

value: NT


title: DO iPSC line 6518, untreated

description: Library name: DO_iPSC_6518_CTRL

value: iPSC


title: CAF47_Ctrl


title: DO iPSC line 6470, triphenyl phosphate treated

description: Library name: DO_iPSC_6470_TPHP

source_name: DO iPSC 6470

value: DO iPSC 6470

value: triphenyl phosphate

value: male


title: DO iPSC line 6470, untreated

description: Library name: DO_iPSC_6470_CTRL


title: NT_A_LP2

description: Library name: RNA017421


title: ChIP-seq H3K27me3

city: Barcelona

first: Marian

last: Martínez-Balbás

state: Barcelona

address: Baldiri Reixac 4-8, EDIFICI HELIX

country: Spain

institute: IBMB-CSIC

data_processing:
Read quality check was performed using FASTQ (Babraham Bioinformatics)
Reads were mapped to the Gallus gallus genome galGal4 with BWA (Li and Durbin, 2009)
Peak calling was performed using MACS2 (Zhang et al., 2008). Effective genome size 8e8, q-value 0.1
Bigwigs were generated from wigs obtained in MACS2 (Zhang et al., 2008)
Genome_build: galGal4
Supplementary_files_format_and_content: Bed files contain genomic coordinates of called peaks. Bigwig files contain the information  for displaying graphs.

organism: Gallus gallus

source_name: Neural tube

growth_protocol: Not applicable

extract_protocol:
To perform ChIP-seq experiment, chicken neural tubes of stage HH30 were trypsinized for 5-10 min in Trypsin-EDTA 0.5%. From these disaggregated neural tubes, approximately 5x106 cells were fixed with formaldehyde 1% during 10 minutes and then, fixation was stopped by addition of 0.125M glycine. Cells were lysed in 1% SDS lysis buffer (1% SDS; 10mM EDTA pH8.0; 50mM Tris-HCl pH8.1). Sonication step was performed in a Bioruptor sonicator and shredded chromatin was used for each immunoprecipitation with H3K4me3 (Abcam ab8580) and H3K27me3 (Millipore, 07449) antibodies. The antibody-protein complex was captured using magnetic beads (Magna ChIP™ Protein A Magnetic Beads Millipore 16-661). After decrosslinking, DNA was purified using phenol/chloroform extraction followed by ethanol precipitation. Purified DNA from the input and the immunoprecipitations were used to prepare the library that was sequenced in a HiSeq 2500 sequencer (Illumina)
Libraries were prepared using the NEBNext® Ultra DNA Library Prep for Illumina® kit (ref. E7370) according to the manufacturer's protocol.

treatment_protocol: Eggs from White-Leghorn chickens were incubated at 38.5ºC and 70% humidity. Embryos were staged following Hamburger and Hamilton (HH) (Hamburger and Hamilton, 1992).

value: Neural tube

tag: strain

value: White Leghorn

tag: developmental stage

tag: chip antibody

value: H3K27me3 - Millipore 07-449

value: WT


title: UPN827 cells, TN437 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN437 TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN436 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN436 TrailNet Baseline T1D plasma


title: Mock_B_LP2

description: Library name: RNA017420

tag: cell line

tag: cell type

value: embryonic kidney cell

value: Mock


title: INPUT

tag: genotype


title: UPN827 cells, TN435 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN435 TrailNet Baseline T1D plasma


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 044 | Full ROI

first: Emmanuel

last: Ogbonna

address: 200 Longwood Ave

department: Laboratory of Systems Pharmacology

institute: Harvard Medical School; Tufts University School of Medicine

description:
Library name: LSP16102_B5_scan1 | 044 | Full ROI
FFPE

data_processing:
Raw sequencing data were processed to generate FASTQ files
demultiplexed fastqs according to nanostring pipeline
Process FASTQ files through GeoMx NGS pipeline and convert to DCC files
Retreive DCC files
Transfer DCC files to GeoMx DSP for QC and normalisation by DSP software
Then we have Q3 normalised count matrix file (available with the publication as Supplementary File)
Supplementary files format and content: DCC files are digital count files which have been processed from FASTQ files by nanostring pipeline
Library strategy: Spatial Transcriptomics

source_name: tuberculosis-infected human lung tissue

extract_protocol:
5uM thickness section was processed according to GeoMx protocol provided by Nanostring
the libraries were prepared according to manufacturer's protocol (Nanostring)

value: tuberculosis-infected human lung tissue

tag: batch

tag: histopathological region

value: TLS

tag: patient id


title: DO iPSC line 6458, triphenyl phosphate treated

description: Library name: DO_iPSC_6458_TPHP

source_name: DO iPSC 6458

value: DO iPSC 6458

tag: treatment


title: ChIP-seq H3K4me3

tag: tissue

value: H3K4me3 - Abcam ab8580


title: UPN827 cells, TN434 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN434 TrailNet Baseline T1D plasma

tag: responder cells

tag: sample timepoint

value: TrailNet Baseline


title: Mock_A_LP2

description: Library name: RNA017419

data_processing:
High performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables


title: PoolCTL_B_LP2

description: Library name: RNA017418

value: PoolCTL


title: DO iPSC line 6458, untreated

description: Library name: DO_iPSC_6458_CTRL

value: iPSC

value: untreated

tag: Sex

tag: do generation

tag: run


title: Phthalate-injected GV oocyte, Rep3

city: Urbana

first: Huanyu

last: Qiao

state: Illinois

address: 2001 South Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois Urbana-Champaign

description:
Library name: Phthalate_GV_Oocyte_Rep3
Phthalates-injected CD-1 mouse GV oocyte, Smart-seq3 scRNA-seq

data_processing:
Sequencing adapters and low-quality bases were removed using Cutadapt and Trimmomatic. Cleaned reads were aligned to the mouse reference genome (mm10) via Hisat2. Differential expression analysis was conducted using DESeq2. Genes with pvalue < 0.05 and |log₂ fold change| > 1 were considered significantly differentially expressed. Gene Ontology (GO) and KEGG pathway analysis were performed using the ClusterProfiler.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Ovary

growth_protocol: Female CD-1 mice (4-6 weeks old) were maintained under controlled environmental conditions (12 h light/12 h dark cycle, 22 ± 1 °C) with free access to food and water.

extract_protocol:
For each experimental group, a single GV oocyte were transferred into lysis buffer supplemented with RNase inhibitor to preserve RNA integrity.
Reverse transcription was initiated using an oligo(dT) primer containing a 5′ anchor sequence, and a template-switching oligonucleotide (TSO) enabled generation of full-length cDNA. The synthesized cDNA was subsequently amplified by PCR and purified with magnetic beads. The concentration of amplified cDNA was measured using the Qubit dsDNA HS Assay Kit, and size distribution of fragments was determined using an Agilent 4200 TapeStation system. Libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s guidelines and sequenced on the Illumina MiSeq platform with 150 bp paired-end (PE150) setting.

treatment_protocol: Cumulus-oocyte complexes (COCs) were released by puncturing antral follicles with sterile needles and collected into fresh M2 droplets. The COCs were microinjected with either water or phthalate metabolite mixtures, washed three times, and transferred into pre-warmed in vitro maturation (IVM) medium consisting of α-minimum essential medium (α-MEM) supplemented with 10% fetal bovine serum (FBS), 200 mIU/mL follicle-stimulating hormone (FSH), and 50 µg/mL sodium pyruvate. The injected COCs were cultured at 37 °C in a 5% CO₂ incubator, and oocytes were collected at GV stage.

value: Ovary

value: Oocyte

value: Phthalates-injected


title: DO iPSC line 5468, untreated

description: Library name: DO_iPSC_5468_CTRL

source_name: DO iPSC 5468

value: DO iPSC 5468

value: female


title: DO iPSC line 5468, triphenyl phosphate treated

description: Library name: DO_iPSC_5468_TPHP

value: triphenyl phosphate


title: Phthalate-injected GV oocyte, Rep1

description:
Library name: Phthalate_GV_Oocyte_Rep1
Phthalates-injected CD-1 mouse GV oocyte, Smart-seq3 scRNA-seq


title: UPN827 cells, TN432 TrailNet Baseline T1D plasma

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN827 cells stimulated with TN432 TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN433 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN433 TrailNet Baseline T1D plasma


title: DO iPSC line 5463, triphenyl phosphate treated

description: Library name: DO_iPSC_5463_TPHP

source_name: DO iPSC 5463

value: DO iPSC 5463


title: GAL4_B_LP2

institute: University Gent

description: Library name: RNA017416

value: embryonic kidney cell


title: Phthalate-injected GV oocyte, Rep2

description:
Library name: Phthalate_GV_Oocyte_Rep2
Phthalates-injected CD-1 mouse GV oocyte, Smart-seq3 scRNA-seq


title: Pancreas from lean donor D453

description:
Library name: DS019_library
Bulk RNA-seq from pancreas of lean donor D453 in batch B

source_name: pancreas

value: pancreas

tag: sample group

value: lean

value: B


title: PoolCTL_A_LP2

description: Library name: RNA017417


title: GAL4_A_LP2

description: Library name: RNA017415


title: Water-injected GV oocyte, Rep3

description:
Library name: WT_GV_Oocyte_Rep3
Water-injected CD-1 mouse GV oocyte, Smart-seq3 scRNA-seq

value: Water-injected


title: UPN827 cells, TN431 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN431 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 5463, untreated

description: Library name: DO_iPSC_5463_CTRL


title: Water-injected GV oocyte, Rep2

description:
Library name: WT_GV_Oocyte_Rep2
Water-injected CD-1 mouse GV oocyte, Smart-seq3 scRNA-seq


title: NEAT1_B_LP2

description: Library name: RNA017414


title: UPN827 cells, TN430RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN430RH2 TrailNet Baseline T1D plasma


title: DO iPSC line 5454, triphenyl phosphate treated

description: Library name: DO_iPSC_5454_TPHP

source_name: DO iPSC 5454

value: DO iPSC 5454


title: UPN827 cells, TN429 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN429 TrailNet Baseline T1D plasma


title: Water-injected GV oocyte, Rep1

description:
Library name: WT_GV_Oocyte_Rep1
Water-injected CD-1 mouse GV oocyte, Smart-seq3 scRNA-seq


title: NEAT1_A_LP2

description: Library name: RNA017413


title: DO iPSC line 5454, untreated

description: Library name: DO_iPSC_5454_CTRL

value: iPSC


title: EpiDrug_0714

city: Tarrytown

first: Qingqing

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description:
Library name: EpiDrug_0714
scATAC-seq data

data_processing:
Cellranger-atac v2.1.0 (10x Genomics) was used to perform demultiplexing and read alignment of scATAC-seq raw data from all treatments and timepoints
Single cell data were filtered based on the number of unique fragments per cell and enrichment of ATAC-seq accessibility at TSSs, as described in Satpathy et al, 2019. TSS positions were acquired from the TxDb.Hsapiens.UCSC.hg38.knownGene Bioconductor package.
Cell clustering based on cell genome accessibility were performed as described in ref.Kourtis et al, 2022, with the minimum cluster size set to 150 for the first round of clustering, and a final resolution of 0.8. For subclustering of T cells, the minimum cluster size was set to 100 and a final resolution of 0.8.
Gene activity score, TF motif enrichment calculation and pseudotime analyses were performed as described in Kourtis et al, 2022
Assembly: mm10
Supplementary files format and content: MetaData.txt file, phenotypic metadata for cells in dataset
Supplementary files format and content: peakSet.txt file, peaks called from the datasets
Supplementary files format and content: fragments.tsv.gz files; ATAC-seq fragments captured by the assay, analyzed by Cell ranger

source_name: Tumor

growth_protocol: hCD3/hPSMA humanized male mice (8-12 week old) were implanted with 2.5x106 TrampC2/hPSMA tumor cells by subcutaneous injection in the right flank. hCD3/hCD20 humanized female mice (8-12 weeks old) were implanted with 0.5x106 MC38/hCD20 tumor cells by subcutaneous injection in the right flank.

extract_protocol:
Freshly sorted, live mouse T cells were washed with PBS containing 0.04% BSA, and the cell count was determined. Nuclei were isolated using the 10x Genomics Low Cell Input Nuclei Isolation protocol. Briefly, cells were centrifuged at 300×g for 5 min at 4°C and resuspended in 50µL PBS + 0.04% BSA. After centrifugation, 45µL of the supernatant was removed, and 45µL of chilled Lysis Buffer was added. The suspension was gently mixed and incubated on ice for 3-5 min. Chilled Wash Buffer was added without mixing, followed by centrifugation at 500×g for 5 min. Supernatant was removed, and 45 µL of chilled Diluted Nuclei Buffer was added. After a second centrifugation, the pellet was resuspended in 7µL of chilled Diluted Nuclei Buffer. Nuclei concentration was counted and used immediately for transposition
Single-cell ATAC-seq libraries were prepared using the Chromium Next GEM Single Cell ATAC Reagent Kits v2 (10x Genomics, Pleasanton, CA) per manufacturer’s instructions. Transposed nuclei were loaded with gel beads and reagents onto a Chromium Next GEM Chip H and processed on the Chromium X instrument to generate barcoded Gel Beads-in-emulsion (GEMs). GEMs underwent thermal cycling for barcoding, followed by recovery, Dynabead and SPRIselect cleanup, sample indexing PCR, and dual-sided SPRI size selection. Final libraries were quantified with the Qubit dsDNA HS assay (Thermo Fisher Scientific) and assessed using the TapeStation (Agilent Technologies, Santa Clara, CA). Libraries were sequenced on a NovaSeq (Illumina, San Diego, CA), producing approximately 200 million paired-end 150 bp reads per sample.

treatment_protocol: On indicated timepoints, mice were euthanized and tumors excised. Tumors were weighed and processed using the mouse tumor dissociation kit (Miltenyi 130-096-730) per manufacturer’s protocol with the following modifications: Enzyme R was used at 40% of the recommended volume. Tumors were minced in petri dishes using razors (VWR 55411-050), transferred to 5mL tubes containing enzyme mix, and incubated in a 37oC water bath for 40 min vortexing every 5 min. Dissociated tumors were forced through a 70uM mesh filter (Miltenyi 130-098-462) to generate single cell suspension for flow cytometry.

value: Tumor

value: T cells

value: hCD3/hPSMA humanized

value: Decitabine


title: DPH1_B_LP2

city: Ghent

first: Xin

address: Corneel Heymanslaan 10, B

description: Library name: RNA017412

extract_protocol:
Cells were lysed directly in the culture plate using the SingleShot™ Cell Lysis Kit (Bio-Rad) according to the manufacturer’s instructions. Cell lysates were used directly for downstream RNA-seq library preparation.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) .


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 036 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 036 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue

value: TLS


title: DO iPSC line 5433, triphenyl phosphate treated

description: Library name: DO_iPSC_5433_TPHP

data_processing:
Raw RNA-seq reads were combined across lanes for each sample to obtain over 30 million raw reads per sample. Combined RNA-seq reads were processed using the Jackson Laboratory Data Science Nextflow DSL2 Workflows (version 24.10.6, https://github.com/TheJacksonLaboratory/jds-nf-workflows/wiki). Reads were aligned and quantified using EMASE (Expectation Maximization for Allele-Specific Expression)[Munger, S.C., et al., RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics, 2014. 198(1): p. 59–73.]
Raw gbrs expected read counts were compiled into a counts matrix. Raw transcript per million counts were compiled into a tpm matrix.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Count tsv file with counts per gene (rows) for each sample (columns)
Supplementary files format and content: Transcript per million tsv with tpm per gene (rows) for each sample (columns)

source_name: DO iPSC 5433

value: DO iPSC 5433

value: triphenyl phosphate

value: male


title: UPN827 cells, TN428 TrailNet Baseline T1D plasma

institute: Medical College of Wisconsin

source_name: UPN827 cells stimulated with TN428 TrailNet Baseline T1D plasma

value: UPN827 cells


title: mouse ES cells, replicate 3

city: Yayoi, Bunkyo-ku

first: Hiroki

last: Ono

state: Tokyo

department: Research Division for Applied Life Sciences

country: Japan

institute: Institute for Quantitative Biosciences, The University of Tokyo

description: Library name: mESC_R3_S5_R1_001

data_processing:
Adapter sequences were trimmed from raw reads using cutadapt 1.16 with options: cutadapt -a TGGAATTCTCGGGTGCCAAGG -o ${library_name}_trim1.fastq ${library_name}.fastq.gz
Four-nt long degenerate sequences at the 3′ and 5′ end were trimmed using cutadapt 1.16 with options: cutadapt -u 4 -u -4 -m 18 -o ${library_name}_trim2.fastq ${library_name}_trim1.fastq
Low-quality reads (Phred quality score <20 in >95% of the bases) were removed using FASTX-Toolkit 0.0.14 with options: fastq_quality_filter -q 20 -p 95 -Q 33 -i ${library_name}_trim2.fastq -o ${library_name}_trim3.fastq
Low-quality reads (Phred quality score <30 in >50% of the bases) were removed using FASTX-Toolkit 0.0.14 with options: fastq_quality_filter -q 30 -p 50 -Q 33 -i ${library_name}_trim3.fastq -o ${library_name}_trim4.fastq
Artifact reads were eliminated with FASTX-Toolkit 0.0.14 with options: fastx_artifacts_filter -v -i ${library_name}_trim4.fastq -o ${library_name}_trim5.fastq
Raw read counts and normalized abundance (RPM) of miRNAs were obtained using miRge 2.0 (ver. 2.0.6) with options: (for HeLa) miRge2.0 annotate -s ${library_name}_trim5.fastq -d miRBase -pb ${path_to_bowtie} -lib ${path_to_library} -sp human -ai -gff -cpu 4 (for mouse ES cells) miRge2.0 annotate -s ${library_name}_trim5.fastq -d miRBase -pb ${path_to_bowtie} -lib ${path_to_library} -sp mouse -ai -gff -cpu 4
Assembly: miRBase v22
Supplementary files format and content: csv files including raw read counts
Supplementary files format and content: csv files including normalized abundance (RPM)

source_name: mouse ES cells

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol
miRNA-seq libraries were prepared according to the AQ-seq method (Kim et al., Nucleic Acids Res. 2019, doi: 10.1093/nar/gky1293) with some modifications.

value: mouse ES cells


title: UPN827 cells, TN427 TrailNet Baseline T1D plasma

city: Milwaukee

first: Martin

source_name: UPN827 cells stimulated with TN427 TrailNet Baseline T1D plasma

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


title: UPN827 cells, TN426 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN426 TrailNet Baseline T1D plasma


title: DPH1_A_LP2

last: Wang

description: Library name: RNA017411

value: embryonic kidney cell


title: Sham Dorsal root ganglion

city: Winston Salem

first: Yusuke

last: Shiozawa

address: 1 Medical Center Blvd

institute: Wake Forest University School of Medicine

description:
Library name: Sample 1
10x Genomics

data_processing:
The Cell Ranger Single-Cell Software Suite v7.2 were used to perform sample de‐multiplexing, alignment, filtering, and UMI (i.e., unique molecular identifier) counting. The data for each respective subpopulation were aggregated for direct comparison of single-cell transcriptomes. Low‐quality cells identified as having less than 200 expressed genes were discarded. Cells with low viability were also removed if their proportions of mitochondrial gene expression are larger than 40%.
Assembly: Mouse mm10
Supplementary files format and content: Tab seperated values files and matrix files

source_name: Dorsal root ganglion

extract_protocol:
Lumbar DRGs (L2-L4) of male C57BL/6 mice (8–12 weeks of age) were dissected and directly placed into a 15 mL conical tube, containing 14 mL of ice-cold HBSS. Isolated DRGs were enzymatically digested in 3 mL of papain solution (30 U/mL papain, 0.1% saturated NaHCO3 solution, 0.3 mg/mL L-Cys) in HBSS for 30 min at 37°C with 5% CO2, and then incubated in 3 mL of collagenase type II and Dispase II solution (4 mg/mL CLS2  and 4.7 mg/mL dispase) in HBSS for 30 min at 37°C with 5% CO2. The resulting DRGs were centrifuged at 200 × g for 2 min and washed with HBSS. The pellet was transferred to a 15 mL conical tube, containing 500 μL of neuronal growth medium with 1% N2, 2% B-27, 2 mM L-glutamine, 1% penicillin-streptomycin, and 0.4% glucose. The DRGs were triturated and filtered through a stainless mesh sieve (40 μm) to obtain single-cell suspensions and remove undigested tissue debris. BSA purification 3.5% (W/V) was performed by centrifugation at 14 × g for 20 min at room temperature to separate sensory neurons and debris.
Cells with >80% viability were loaded into wells of a 10X Chromium single-cell capture chip targeting a cell recovery rate of 2,000‐4,000 cells. Single‐cell gel beads in emulsion were created on a Chromium Single-Cell Controller and scRNA‐seq libraries were prepared using the Chromium Single-Cell 3’ Library and Gel Bead kit according to the manufacturer's protocol (10X Genomics). Sequencing libraries were loaded at 1.3 PM on an Illumina NextSeq500 with High Output 150 cycle kit for paired‐end sequencing using the following read length: 26 bp Read1, 8 bp i7 Index, 0 bp i5 Index, and 98 bp Read2.

value: Dorsal root ganglion

value: dorsal root ganglion


title: DO iPSC line 5433, untreated

city: Bar Harbor

first: Madison

institute: The Jackson Laboratory

description: Library name: DO_iPSC_5433_CTRL

extract_protocol:
Total RNA was isolated from tissue using the NucleoMag RNA Kit (Macherey-Nagel) and the KingFisher Flex purification system (ThermoFisher). Cells were homogenized in MR1 buffer (Macherey-Nagel) by vortexing.  RNA isolation was performed according to the manufacturer’s protocol. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA ScreenTape Assay (Agilent Technologies).
Stranded libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

value: untreated


title: mouse ES cells, replicate 2

description: Library name: mESC_R2_S4_R1_001


title: LINC00857_1_D_LP2

description: Library name: RNA017410


title: UPN827 cells, TN425 TrailNet Baseline T1D plasma

last: Hessner

address: 8701 Watertown Plank Road

source_name: UPN827 cells stimulated with TN425 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: mouse ES cells, replicate 1

description: Library name: mESC_R1_S3_R1_001


title: UPN827 cells, TN424 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN424 TrailNet Baseline T1D plasma


title: DO iPSC line 5421, untreated

description: Library name: DO_iPSC_5421_CTRL

source_name: DO iPSC 5421

value: DO iPSC 5421

value: iPSC

value: female


title: DO iPSC line 5421, triphenyl phosphate treated

description: Library name: DO_iPSC_5421_TPHP


title: CD8 cells, Na Lactate and Oxyrase treatment, mRNA replicate 3

first: Christopher

middle: Lee

last: Baker

address: 600 Main Street

department: Research

description: Library name: 4-3

data_processing:
RNA-seq reads were filtered and trimmed for quality scores >30 using trimmomatic for nextera adapters. The filtered reads were aligned to Gencode (M25) reference transcripts using RSEM (v1.2.12) equipped with Bowtie2 (v2.2.0) (command: rsem-calculate-expression  --bowtie2 --paired-end). RSEM calculates expected counts and transcript per million (TPM). The expected counts from RSEM were used in the Bioconductor edgeR 3.20.9 package to determine differentially expressed genes.
ATAC-seq reads were trimmed with Trimmomatic to remove adapters and low-quality bases, then aligned to the mouse genome (mm10) using BWA. Duplicate reads were removed using picard tools, and reads adjusted for Tn5 insertion using custom script from Greenleaf lab. Peak calling was performed with MACS2, and regions present in at least three biological replicates were retained as high-confidence accessible sites. Read counts across regions were quantified using bedtools, filtered to exclude low-abundance regions, and normalized using the TMM method in edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each sample (ATAC-seq), and batch corrected counts for RNA-seq (tpm)
Supplementary files format and content: bigWig files for each ATAC-seq sample and replicate

source_name: CD8 T cells

growth_protocol: CD8 T cells were isolated from mouse spleens and lymph nodes using MACS microbeads. Purified cells were then activated on these plates in RPMI-1640 complete medium supplemented with 50 μmol/L β-mercaptoethanol, 1% L-glutamine, 0.5 μg/mL anti-CD28, and 100 U/mL IL-2, and cultured for 3 days.

extract_protocol:
Total RNA was isolated via PureLink RNA Mini Kit (Invitrogen).
RNA-seq libraries were generated from Poly(A) RNA capture using the Illumina TruSeq RNA Sample preparation kit v2. ATAC-seq libraries were prepared from approximately 100,000 T cells via Tn5 transposition with digitonin at 37 °C for 30 minutes, followed by DNA purification and 8–10 cycles of PCR amplification.

treatment_protocol: For treatment the CD8 T cells were supplemented with either lactate (20 mM), sodium pyruvate (20mM), or sodium chloride (20mM) from day 2 to day 3 post activation.

value: CD8 T cells

value: Na Lactate+Oxyrase treatment


title: LINC00857_1_C_LP2

description: Library name: RNA017409


title: LINC00857_1_B_LP2

description: Library name: RNA017408


title: DO iPSC line 5418, triphenyl phosphate treated

last: Armstrong

address: 600 Main St

description: Library name: DO_iPSC_5418_TPHP

source_name: DO iPSC 5418

value: DO iPSC 5418


title: CD8 cells, Na Lactate and Oxyrase treatment, mRNA replicate 2

description: Library name: 4-2


title: LINC00857_1_A_LP2

description: Library name: RNA017407


title: UPN827 cells, TN423 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN423 TrailNet Baseline T1D plasma


title: CD8 cells, Na Lactate and Oxyrase treatment, mRNA replicate 1

description: Library name: 4-1


title: UPN827 cells, TN422 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN422 TrailNet Baseline T1D plasma


title: GS1-124K5.4_1_D_LP2

description: Library name: RNA017406


title: DO iPSC line 5418, untreated

description: Library name: DO_iPSC_5418_CTRL


title: DO iPSC line 5393, triphenyl phosphate treated

description: Library name: DO_iPSC_5393_TPHP

source_name: DO iPSC 5393

value: DO iPSC 5393


title: UPN827 cells, TN421 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN421 TrailNet Baseline T1D plasma


title: UPN827 cells, TN420 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN420 TrailNet Baseline T1D plasma


title: CD8 cells, Na Lactate treatment, mRNA replicate 3

description: Library name: 3-3

value: Na Lactate treatment


title: GS1-124K5.4_1_C_LP2

description: Library name: RNA017405


title: DO iPSC line 5393, untreated

description: Library name: DO_iPSC_5393_CTRL


title: CD8 cells, Na Lactate treatment, mRNA replicate 2

description: Library name: 3-2


title: GS1-124K5.4_1_B_LP2

description: Library name: RNA017404


title: CD8 cells, Na Lactate treatment, mRNA replicate 1

description: Library name: 3-1


title: GS1-124K5.4_1_A_LP2

description: Library name: RNA017403


title: UPN827 cells, TN418 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN418 TrailNet Baseline T1D plasma


title: DO iPSC line 5391, triphenyl phosphate treated

description: Library name: DO_iPSC_5391_TPHP

source_name: DO iPSC 5391

value: DO iPSC 5391

value: triphenyl phosphate


title: UPN827 cells, TN419 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN419 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 5391, untreated

description: Library name: DO_iPSC_5391_CTRL


title: CD8 cells, Na Pyruvate treatment, mRNA replicate 3

description: Library name: 2-3

value: Na Pyruvate treatment


title: LINC00665_1_D_LP2

description: Library name: RNA017402

value: embryonic kidney cell


title: DO iPSC line 5387, triphenyl phosphate treated

description: Library name: DO_iPSC_5387_TPHP

source_name: DO iPSC 5387

value: DO iPSC 5387


title: LINC00665_1_C_LP2

description: Library name: RNA017401


title: CD8 cells, Na Pyruvate treatment, mRNA replicate 2

description: Library name: 2-2


title: UPN827 cells, TN416 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN416 TrailNet Baseline T1D plasma


title: LINC00665_1_B_LP2

description: Library name: RNA017400


title: UPN827 cells, TN415 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN415 TrailNet Baseline T1D plasma


title: CD8 cells, Na Pyruvate treatment, mRNA replicate 1

description: Library name: 2-1


title: DO iPSC line 5387, untreated

description: Library name: DO_iPSC_5387_CTRL


title: UPN827 cells, TN417 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN417 TrailNet Baseline T1D plasma


title: DO iPSC line 5386, triphenyl phosphate treated

description: Library name: DO_iPSC_5386_TPHP

source_name: DO iPSC 5386

value: DO iPSC 5386


title: CD8 cells, NaCl treatment, mRNA replicate 3

description: Library name: 1-3

value: NaCl treatment


title: UPN827 cells, TN414 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN414 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 5386, untreated

description: Library name: DO_iPSC_5386_CTRL

value: untreated


title: CD8 cells, NaCl treatment, mRNA replicate 2

description: Library name: 1-2


title: LINC00665_1_A_LP2

description: Library name: RNA017399


title: GS1-124K5.3_1_D_LP2

description: Library name: RNA017398


title: CD8 cells, NaCl treatment, mRNA replicate 1

description: Library name: 1-1


title: DO iPSC line 5332, triphenyl phosphate treated

description: Library name: DO_iPSC_5332_TPHP

source_name: DO iPSC 5332

value: DO iPSC 5332

value: iPSC

value: male


title: GS1-124K5.3_1_C_LP2

description: Library name: RNA017397


title: DO iPSC line 5332, untreated

description: Library name: DO_iPSC_5332_CTRL


title: MAY25N sorted GFP+ Foxl1+ telocytes

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description:
Library name: MAY25N
10X Genomics

data_processing:
The NextSeq output was converted to raw fastq files with cellranger v3.0.2, using the 'mkfastq' command. Raw fastq files were processed with cellranger v3.0.2, using the 'count' command, with parameter --expect-cells=5000 and a custom genome that included both the mouse GRCm38 genome with Ensembl release 95 gene annotations and the external EGFP gene.
Assembly: GRCm38
Supplementary files format and content: counts per gene in h5 format

source_name: Jejunum

extract_protocol:
Isolation of FOXL1+ cells using FACS was performed using Foxl1-cre;Rosa26- mTmG mice. Jejunums were dissected and washed thoroughly with Hank’s balanced salt solution (HBSS) and were incubated in 5 mM EDTA in HBSS for 10 min at 4 °C. Intestinal villi were scraped off using a coverslip and the remaining tissue was cut into small pieces and incubated in 5 mM EDTA and HBSS on ice for 10 min while pipetting to completely remove the remaining epithelium. After vigorous washes, the remaining mesenchymal fraction was incubated with 6 mg/ml Dispase II/0.05% trypsin solution (Sigma-Aldrich, 04942078001) supplemented with 1 U/ml DNaseI (Invitrogen) at 37 °C, until the solution became cloudy and the mesenchyme was dissociated (15 min). Supernatant was filtered through a 70-μm strainer, centrifuged and resuspended with anti CD45–APC and anti EPCAM–APC antibodies (1:300, Biosciences, and 1:100, BioLegend, respectively) in 10%FBS/5 mM EDTA/HBSS for 45 min at room temperature to exclude immune and epithelial cells from sorting. A single-cell suspension was obtained by filtering the supernatant through a 40-μm strainer and washing with 5 mM EDTA in HBSS, before cell sorting.
Cells were loaded onto a Chromium single-cell 3′ v2 chip (10x Genomics) or Chromium GEM-X Single Cell Gene Expression v4 (3’) (10x Genomics) and libraries were prepared according to the manufacturer’s protocol.

value: Jejunum

value: Telocytes

tag: age

value: 8 weeks old


title: UPN827 cells, TN412 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN412 TrailNet Baseline T1D plasma


title: UPN827 cells, TN413 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN413 TrailNet Baseline T1D plasma


title: GS1-124K5.3_1_B_LP2

description: Library name: RNA017396


title: DO iPSC line 5312, triphenyl phosphate treated

description: Library name: DO_iPSC_5312_TPHP

source_name: DO iPSC 5312

value: DO iPSC 5312

value: female


title: MAY25M sorted GFP+ Foxl1+ telocytes

description:
Library name: MAY25M
10X Genomics


title: GS1-124K5.3_1_A_LP2

description: Library name: RNA017395


title: UPN827 cells, TN411 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN411 TrailNet Baseline T1D plasma


title: DO iPSC line 5312, untreated

description: Library name: DO_iPSC_5312_CTRL


title: UPN827 cells, TN410 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN410 TrailNet Baseline T1D plasma


title: GFPF24 sorted GFP+ Foxl1+ telocytes

description:
Library name: GFPF24
10X Genomics


title: LINC00630_1_D_LP2

description: Library name: RNA017394


title: DO iPSC line 5298, triphenyl phosphate treated

description: Library name: DO_iPSC_5298_TPHP

source_name: DO iPSC 5298

value: DO iPSC 5298

value: triphenyl phosphate


title: RP11-498C9.15_A_LP5

description: Library name: RNA017547


title: GFPF10 sorted GFP+ Foxl1+ telocytes

description:
Library name: GFPF10
10X Genomics


title: UPN827 cells, TN409 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN409 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 5298, untreated

description: Library name: DO_iPSC_5298_CTRL


title: LINC00630_1_C_LP2

description: Library name: RNA017393

value: embryonic kidney cell


title: N1 sorted GFP+ Foxl1+ telocytes

description:
Library name: N1
10X Genomics


title: UPN827 cells, TN408 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN408 TrailNet Baseline T1D plasma


title: LINC00630_1_B_LP2

description: Library name: RNA017392


title: DO iPSC line 5285, triphenyl phosphate treated

description: Library name: DO_iPSC_5285_TPHP

source_name: DO iPSC 5285

value: DO iPSC 5285


title: LINC00630_1_A_LP2

description: Library name: RNA017391


title: DO iPSC line 5285, untreated

description: Library name: DO_iPSC_5285_CTRL


title: M1 sorted GFP+ Foxl1+ telocytes

description:
Library name: M1
10X Genomics


title: UPN827 cells, TN407 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN407 TrailNet Baseline T1D plasma


title: FTX_1_D_LP2

description: Library name: RNA017390


title: UPN827 cells, TN406 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN406 TrailNet Baseline T1D plasma


title: GFP sorted GFP+ Foxl1+ telocytes

description:
Library name: GFP
10X Genomics


title: DO iPSC line 5282, triphenyl phosphate treated

description: Library name: DO_iPSC_5282_TPHP

source_name: DO iPSC 5282

value: DO iPSC 5282


title: Mouse Mononuclear cells, DZNep, 14 weeks

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

description:
scRNA_mouse_DZNep
10x Genomics

data_processing:
Combining human GRCh38 and mouse mm10 reference genomes using "cellranger mkref".
After obtaining the expression matrix through the Cellranger software, low-quality cells were filtered, and PCA was applied for dimensionality reduction of the highly variable gene expression matrix. Using a graph-based clustering algorithm, the clustering results were also visualized with UMAP in two dimensions. We extracted human-derived cells for re-clustering based on UMAP. Cell annotation was followed using the R package SingleR version 2.5.0 (https://bioconductor.org/packages/devel/bioc/html/SingleR.html). Cells of interest were selected for subset analysis.
Assembly: GRCh38_mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
To verify whether DZNep-treated erythroid cells are capable of lineage reconstruction in vivo,we intravenously injected 2.5 × 105 erythroid cells from day 11 of erythroid differentiation treated with 0.2 μM DZNep into the tail vein of NCG-c-kit-Cas9-TM 8- to 10-week-old mice. At week 12, mouse bone marrow cells were collected, and mouse-derived and erythroid cells were filtered out with mouse CD45 microbeads and microbeads labeled with biotin-labeled Ter119 antibody, followed by scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone marrow

value: Mononuclear cells

value: DZNep 0.2μM


title: FTX_1_C_LP2

description: Library name: RNA017389


title: UPN827 cells, TN404 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN404 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN405 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN405 TrailNet Baseline T1D plasma


title: p53 R172H: Hom mBanana, biological replicate 2, scRNAseq

city: Oxford, Oxfordshire

last: Lu

address: Roosevelt Drive

country: United Kingdom

institute: Ludwig Institute for Cancer Research, University of Oxford

description: 10x Genomics

data_processing:
Pre-processing of scRNA-seq data was conducted using Cell Ranger (version 3.1.0). Briefly, FASTQ files were demultiplexed from raw BCL format using cellranger mkfastq. A custom Cell Ranger reference was then prepared (cellranger mkref) using a concatenation of the default Cell Ranger mouse genome sequence and annotation files (mm10-2020-A: GENCODE vM23/Ensembl 98) and custom sequence and annotation files for the fluorescent markers used in this study. Alignment to this custom reference, identification of true cells, and tabulation of Unique Molecular Identifier (UMI) counts for each sample was performed using cellranger count. The UMI counts for each sample were then combined into a single matrix using cellranger aggr without normalization.
Initial downstream processing was conducted using Seurat (v3.9.9.9038). As an initial filter for low-quality cells, cellular barcodes with less than 2000 genes detected or more than 10% mitochondrial reads were removed. Normalization, variance-stabilizing transformation (VST), and scaling were conducted on the remaining cells using Seurat’s implementation of sctransform (v0.3.2.9002), and the scaled VST counts for the 3000 most variable features were extracted from the Seurat object (scale.data slot). Principal Component Analysis (PCA) was performed on these scaled variance-stabilized counts, followed by Uniform Manifold Approximation and Projection (UMAP, umap-learn v0.5.0) for final dimensionality reduction. Clusters were identified using the FindClusters method within Seurat (Louvain algorithm). Marker genes were identified for each cluster/genotype using FindAllMarkers with a Wilcoxon signed-rank test performed for statistical analysis.
Assembly: mm10-2020-A: GENCODE vM23/Ensembl 98 (concatenated with transcriptome sequences/annotations for fluorescent markers)
Supplementary files format and content: filtered feature-barcode matrices (h5 format, read into R using Read10X_h5 from Seurat)

extract_protocol:
Organoids were individually seeded in a 384-well plate and cultured for 7 days before processing. On day 7, the organoids were retrieved from the matrigel using ice-cold PBS, centrifuged at 300 g for 5min and incubated in TrypLE for 15min. The dissociated organoids were then passed through a 35 µm cell strainer and the flow through centrifuged at 300 g for 5min. The pellet was resuspended in 1mL Cell Recovery Solution (Sigma Aldrich, DLW354253) and incubated for 2h at 4°C under constant rotation. Samples were then centrifuged at 300 g for 5min and the pellet resuspended in 1 mL 0.04% BSA (in PBS). The pellet was resuspended in 100 µl 0.04% BSA and dissociated organoids were passed through a 35 µm cell strainer. Filtered cell suspensions were then counted using an automated cell counter, diluted to a concentration of 1 million total cells / mL in 0.04% BSA and kept on ice until encapsulation.
scRNA-seq was conducted using a 5’ scRNA-seq gene expression workflow (Chromium Single Cell Immune Profiling, Solution v1.1, 10x Genomics). Following encapsulation of cells using the Chromium Controller, GEM-RT, cDNA amplification, and construction of final libraries was conducted following manufacturer’s instructions. Size profile and concentration of final libraries were assessed by the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit, Agilent, 5067-4626) and Qubit (BR DNA Assay, ThermoFisher, Q32853), respectively. Sequencing of final libraries was conducted on the Illumina NextSeq 550 10x Genomics recommendations (26 cycles read 1, 8 cycles i7 index, 98 cycles read 2, targeting a minimum depth of 20,000 reads/cell).

tag: strain

value: 6-10 weeks

value: Female

tag: disease state

value: Healthy

tag: mus musculus_genotype

value: p53 LSL-R172H:Hom

tag: in vivo_treatment

tag: tissue isolated

value: Proximal colon

tag: cell type_cultured

value: Colon organoid

tag: in vitro_colon_organoid_treatment

value: Infected with adevovirus expressing Cre recombinase, transduced with lentivirus expressing mBanana

tag: colon organoid_final_genotype

value: p53 R172H:Hom mBanana


title: DO iPSC line 5282, untreated

description: Library name: DO_iPSC_5282_CTRL

tag: cell line

tag: cell type

value: iPSC

tag: treatment

value: untreated

value: female

tag: batch


title: DO iPSC line 5277, triphenyl phosphate treated

description: Library name: DO_iPSC_5277_TPHP

source_name: DO iPSC 5277

value: DO iPSC 5277

value: triphenyl phosphate

tag: Sex


title: p53 R172H: Hom mBanana, biological replicate 1, scRNAseq

description: 10x Genomics


title: UPN827 cells, TN403 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN403 TrailNet Baseline T1D plasma

tag: responder cells

value: UPN827 cells

tag: sample timepoint


title: UPN827 cells, TN402 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN402 TrailNet Baseline T1D plasma


title: p53 Null mBanana, scRNA-seq

description: 10x Genomics

value: Transduced with lentivirus expressing mBanana

value: p53 Null mBanana


title: LINC00467_1_D_LP2

description: Library name: RNA017386

value: embryonic kidney cell

tag: genotype


title: DO iPSC line 5273, triphenyl phosphate treated

description: Library name: DO_iPSC_5273_TPHP

source_name: DO iPSC 5273

value: DO iPSC 5273

tag: do generation

tag: run


title: LINC00467_1_C_LP2

description: Library name: RNA017385


title: KRAS LSL-G12D/+ EYFP p53 Null, scRNA-seq

description: 10x Genomics

tag: strain

tag: age

value: 6-10 weeks

value: Female

tag: disease state

value: KRAS LSL-G12D/+ Villin-CreERT2-EYFP p53 Null

value: Tamoxifen

value: KRAS LSL-G12D/+ EYFP p53 Null


title: UPN827 cells, TN401 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN401 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 5273, untreated

description: Library name: DO_iPSC_5273_CTRL


title: KRAS G12D/+ EYFP, scRNA-seq

description: 10x Genomics

value: Male

value: Healthy

tag: mus musculus_genotype

value: KRAS LSL-G12D/+ Villin-CreERT2-EYFP

tag: in vivo_treatment

tag: tissue isolated

value: Proximal colon

value: Colon organoid

value: Infected with adevovirus expressing Cre recombinase

value: KRAS LSL-G12D/+ EYFP


title: UPN827 cells, TN400 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN400 TrailNet Baseline T1D plasma

value: UPN827 cells


title: APCmin/+ mCherry, biological replicate 2, scRNAseq

description: 10x Genomics

value: APCmin/+

tag: cell type_cultured

tag: in vitro_colon_organoid_treatment

value: Transduced with lentivirus expressing mCherry

tag: colon organoid_final_genotype

value: APCmin/+ mCherry


title: UPN827 cells, TN399 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN399 TrailNet Baseline T1D plasma


title: LINC00467_1_A_LP2

description: Library name: RNA017383

tag: cell line

tag: cell type

value: embryonic kidney cell

tag: treatment


title: DO iPSC line 5258, untreated

description: Library name: DO_iPSC_5258_CTRL

source_name: DO iPSC 5258

value: DO iPSC 5258

value: iPSC

value: untreated

tag: Sex

value: male

tag: batch


title: UPN827 cells, TN398 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN398 TrailNet Baseline T1D plasma

tag: responder cells

tag: sample timepoint

value: TrailNet Baseline


title: APCmin/+ mCherry, biological replicate 1, scRNAseq

description: 10x Genomics

value: 6-10 weeks

value: Female


title: EPB41L4A-AS1_1_D_LP2

description: Library name: RNA017382

tag: genotype


title: Wild Type, biological replicate 2, scRNAseq

description: 10x Genomics

tag: strain

value: Healthy

value: Wild Type


title: EPB41L4A-AS1_1_C_LP2

description: Library name: RNA017381


title: DO iPSC line 5243, untreated

description: Library name: DO_iPSC_5243_CTRL

source_name: DO iPSC 5243

value: DO iPSC 5243

value: female

tag: do generation

tag: run


title: EPB41L4A-AS1_1_B_LP2

description: Library name: RNA017380


title: Wild Type, biological replicate 1, scRNAseq

description: 10x Genomics

tag: age

tag: disease state

tag: mus musculus_genotype

value: Proximal colon

value: Colon organoid


title: UPN827 cells, TN397 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN397 TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN395 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN395 TrailNet Baseline T1D plasma