title: Human pancreatic macrophages from donor SW037, ADT, HTO

city: NYC

first: Alexey

last: Koshkin

department: Department of Pathology and Cell Biology

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

description:
Library name: SW037_Pancreas_Macrophages_ADT_HTO
10x Genomics Feature Barcode library containing 137 antibody-derived tags (ADT) for protein detection and 10 hashtag oligonucleotides (HTO) for sample demultiplexing

data_processing:
Data Preprocessing Macrophages Raw sequencing data were processed using Cell Ranger, loaded as Seurat objects, and underwent quality control to remove cells with high mitochondrial genes. Each donor sample underwent independent processing with initial dimensionality reduction using buildUMAP and marker identification using findMarkers functions. Multiple rounds of cluster-based sequential selection (2-5 rounds per donor) were performed with comprehensive marker validation, including lineage contamination assessment. Clusters were excluded based on high expression of lymphocyte markers (CD2, CD7, CD8A, CD3E, CD19) and mast and epithelial cell markers (SPINK1, KRT8, TPSAB1). Macrophage confirmation utilized established macrophage markers (CD163, CD14, CD33). Multi-modal validation compared RNA-protein expression pairs (CD14/Hu.CD14-M5E2, CD163/Hu.CD163, CD33/Hu.CD33). Final macrophage populations were exported as donor-specific whitelists and saved as cleaned Seurat objects. T cells:   Raw sequencing data were processed with Cell Ranger (v6.0, 10x Genomics) and underwent quality control removing cells with high mitochondrial transcripts and low unique molecular identifiers (UMIs). Hashtag Oligonucleotide (HTO) Demultiplexing: For this multi-tissue CITE-seq study, T cells and macrophages from different tissue sites were labeled using TotalSeq-C hashtag oligonucleotides (BioLegend).  For demultiplexing, raw antibody capture counts were processed separately using Seurat in R.  HTO counts were normalized using the centered log-ratio (CLR) method, followed by  demultiplexing with the HTODemux function using a threshold at the 99th percentile to remove  doublets. Post-demultiplexing, the Seurat object was filtered to include only singlets and were  exported as CSV files for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: SW031_RNA_counts.csv (CSV): Raw RNA UMI count matrix (genes x cells) for donor SW031, SW031_ADT_counts.csv (CSV): Raw ADT count matrix (proteins x cells) for donor SW031, SW031_HTO_counts.csv (CSV): Raw HTO count matrix (hashtags x cells) for donor SW031, SW031_HTO_classification.csv (CSV): HTO demultiplexing results (cell barcodes with classifications) for donor SW031, SW031_cell_metadata.csv (CSV): Full cell-level metadata (QC metrics, features, clusters, and annotations) for donor SW031, SW031_gene_metadata.csv (CSV): Gene metadata (gene IDs and symbols) for donor SW031, SW031_genes.csv (CSV): Gene list (gene IDs) for donor SW031, SW031_obs.csv (CSV): Subset of cell metadata (QC metrics like nCount_RNA, nFeature_RNA, percent.mt, and clusters) for donor SW031, SW031_barcodes.tsv.gz (TSV.GZ): Filtered cell barcodes for donor SW031, SW031_features.tsv.gz (TSV.GZ): Filtered features (genes, ADTs, HTOs with types) for donor SW031, SW031_matrix.mtx.gz (MTX.GZ): Filtered count matrix (combined RNA/ADT/HTO) for donor SW031; SW032_RNA_counts.csv (CSV): Raw RNA UMI count matrix (genes x cells) for donor SW032, SW032_ADT_counts.csv (CSV): Raw ADT count matrix (proteins x cells) for donor SW032, SW032_HTO_counts.csv (CSV): Raw HTO count matrix (hashtags x cells) for donor SW032, SW032_HTO_classification.csv (CSV): HTO demultiplexing results (cell barcodes with classifications) for donor SW032, SW032_cell_metadata.csv (CSV): Full cell-level metadata (QC metrics, features, clusters, and annotations) for donor SW032, SW032_gene_metadata.csv (CSV): Gene metadata (gene IDs and symbols) for donor SW032, SW032_genes.csv (CSV): Gene list (gene IDs) for donor SW032, SW032_obs.csv (CSV): Subset of cell metadata (QC metrics like nCount_RNA, nFeature_RNA, percent.mt, and clusters) for donor SW032, SW032_barcodes.tsv.gz (TSV.GZ): Filtered cell barcodes for donor SW032, SW032_features.tsv.gz (TSV.GZ): Filtered features (genes, ADTs, HTOs with types) for donor SW032, SW032_matrix.mtx.gz (MTX.GZ): Filtered count matrix (combined RNA/ADT/HTO) for donor SW032; SW033_RNA_counts.csv (CSV): Raw RNA UMI count matrix (genes x cells) for donor SW033, SW033_ADT_counts.csv (CSV): Raw ADT count matrix (proteins x cells) for donor SW033, SW033_HTO_counts.csv (CSV): Raw HTO count matrix (hashtags x cells) for donor SW033, SW033_HTO_classification.csv (CSV): HTO demultiplexing results (cell barcodes with classifications) for donor SW033, SW033_cell_metadata.csv (CSV): Full cell-level metadata (QC metrics, features, clusters, and annotations) for donor SW033, SW033_gene_metadata.csv (CSV): Gene metadata (gene IDs and symbols) for donor SW033, SW033_genes.csv (CSV): Gene list (gene IDs) for donor SW033, SW033_obs.csv (CSV): Subset of cell metadata (QC metrics like nCount_RNA, nFeature_RNA, percent.mt, and clusters) for donor SW033, SW033_barcodes.tsv.gz (TSV.GZ): Filtered cell barcodes for donor SW033, SW033_features.tsv.gz (TSV.GZ): Filtered features (genes, ADTs, HTOs with types) for donor SW033, SW033_matrix.mtx.gz (MTX.GZ): Filtered count matrix (combined RNA/ADT/HTO) for donor SW033; SW034_RNA_counts.csv (CSV): Raw RNA UMI count matrix (genes x cells) for donor SW034, SW034_ADT_counts.csv (CSV): Raw ADT count matrix (proteins x cells) for donor SW034, SW034_HTO_counts.csv (CSV): Raw HTO count matrix (hashtags x cells) for donor SW034, SW034_HTO_classification.csv (CSV): HTO demultiplexing results (cell barcodes with classifications) for donor SW034, SW034_cell_metadata.csv (CSV): Full cell-level metadata (QC metrics, features, clusters, and annotations) for donor SW034, SW034_gene_metadata.csv (CSV): Gene metadata (gene IDs and symbols) for donor SW034, SW034_genes.csv (CSV): Gene list (gene IDs) for donor SW034, SW034_obs.csv (CSV): Subset of cell metadata (QC metrics like nCount_RNA, nFeature_RNA, percent.mt, and clusters) for donor SW034, SW034_barcodes.tsv.gz (TSV.GZ): Filtered cell barcodes for donor SW034, SW034_features.tsv.gz (TSV.GZ): Filtered features (genes, ADTs, HTOs with types) for donor SW034, SW034_matrix.mtx.gz (MTX.GZ): Filtered count matrix (combined RNA/ADT/HTO) for donor SW034; SW037_RNA_counts.csv (CSV): Raw RNA UMI count matrix (genes x cells) for donor SW037, SW037_ADT_counts.csv (CSV): Raw ADT count matrix (proteins x cells) for donor SW037, SW037_HTO_counts.csv (CSV): Raw HTO count matrix (hashtags x cells) for donor SW037, SW037_HTO_classification.csv (CSV): HTO demultiplexing results (cell barcodes with classifications) for donor SW037, SW037_cell_metadata.csv (CSV): Full cell-level metadata (QC metrics, features, clusters, and annotations) for donor SW037, SW037_gene_metadata.csv (CSV): Gene metadata (gene IDs and symbols) for donor SW037, SW037_genes.csv (CSV): Gene list (gene IDs) for donor SW037, SW037_obs.csv (CSV): Subset of cell metadata (QC metrics like nCount_RNA, nFeature_RNA, percent.mt, and clusters) for donor SW037, SW037_barcodes.tsv.gz (TSV.GZ): Filtered cell barcodes for donor SW037, SW037_features.tsv.gz (TSV.GZ): Filtered features (genes, ADTs, HTOs with types) for donor SW037, SW037_matrix.mtx.gz (MTX.GZ): Filtered count matrix (combined RNA/ADT/HTO) for donor SW037.
Library strategy: CITE-seq

molecule: protein

source_name: Pancreas

extract_protocol:
Human Tissue Samples Tissues were obtained from 68 deceased adult organ donors (Supplemental information 1) as part of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement with organ procurement organizations as described previously¹⁻⁶. All donors had no reported autoimmune diseases, or cancers, tested seronegative for hepatitis B, C, and HIV and did not have a history of chronic pancreatitis or evidence of acute pancreatitis (peak lipase < 3 times upper limit of normal, non-indurated). 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. Isolation and preparation of single cell suspensions from tissue samples After procurement in the operating room, tissue samples were maintained in cold saline or CoStorSol® (University of Wisconsin (UW) solution (Preservation Solutions, Elkhorn, WI, Cat# PS004) and transported to the laboratory within 2–4 hours. Pancreas and small intestine were carefully inspected for the presence of lymph nodes, and these were removed and processed separately. Spleen, PLN, and small intestine samples were processed using enzymatic and mechanical digestion, resulting in high yields of live leukocytes, as previously described ¹⁻⁶.  Human pancreatic tissue was processed by the Human Islet Core at Columbia University as described previously⁷. After taking tissue samples for paraffin embedding and image analysis, the body and tail portions of the pancreas were perfused through the pancreatic duct and digested with warmed and circulating enzyme solution in a Ricordi chamber (Biorep Technologies, Inc., Miami Lakes, FL, Cat# RC3–600-MUL) containing Premium Grade Collagenase (SERVA Electrophoresis GmbH, Heidelberg, Germany, Cat#17455.1) and Neutral Protease (SERVA Electrophoresis GmbH, Cat#30301.5) until the majority of the islets were separated from exocrine tissue as examined microscopically by Dithizone-staining (Sigma, Cat#D5130). The pancreas cell suspension, was diluted, washed, and collected using at least 8L of circulating RPMI (Mediatech, Cat# 99–595-CM). Islets were purified using an Optiprep gradient (densities 1.11–1.06) and COBE 2991 blood cell processor, further manually selected to achieve >90% purity by dithizone staining and dispersed using Accutase (Innovative Cell Technologies). Aliquots of the crude pancreas suspension and dispersed islets were immediately cryopreserved in a solution of 90% FBS and 10% dimethyl sulfoxide (DMSO) and stored in a temperature controlled liquid nitrogen freezer for subsequent immune cell recovery. Sorting Pancreas Immune Cells Cryopreserved tissue suspension aliquots were rapidly thawed at 37°C, washed in RPMI with 10% FBS and DNase I (Sigma, Cat# DN25–5G) (50–100 µg/ml). Dead cells were labeled using Zombie-NIR followed by surface staining with antibodies (Supplemental information 2). For the multi-tissue CITE-seq studies, each different tissue site was labeled with distinct TotalSeq barcoded hashtag antibodies (Biolegend). For sorting, samples were resuspended in PBS with 2% human AB serum and 4',6-diamidino-2-phenylindole (DAPI) for added sensitivity in detection of dead and dying cells. Sorting was performed using either the BD Influx or FACS Aria Cell Sorters. For multi-tissue CITE-seq, hash tagged cells were sorted from each tissue site at equal proportions.  Viable pancreas immune cells were detected as Zombie-NIR⁻ DAPI⁻ CD45⁺. Due to the low abundance of T cells relative to macrophages in pancreas⁷, for the multi-tissue T cell CITE-seq studies, the T cells were further selected as CD2⁺ CD19⁻. Cells were sorted into Hanks' Balanced Salt Solution (HBSS) with 5% human albumin and 10mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer. Post-sort viability was confirmed to be >90%. The sorted immune cells were then processed for CITE-seq, bulk RNA-seq and co-culture studies. CITE-seq of Pancreatic Immune Cells After sorting, the pancreas immune cells were pelleted, blocked using human TruStain FcX (Biolegend), and then incubated for 30 minutes at 4°C with the TotalSeq-B (10x Genomics Chromium Single Cell 3' sequencing) or TotalSeq-C (for 10x Genomics Chromium Single Cell 5' sequencing) Universal cocktail per the manufacturer’s instructions. Immediately after staining and washing 3 times, 8,000–10,000 cells were processed by the Columbia Genome Center Single Cell Analysis Core. Briefly, the cells were loaded into the 10X Genomics Chromium controller and cDNA synthesis, amplification, and sequencing libraries were prepared using Next GEM Single Cell 5’ or 3’ Kit (10X Genomics) and sequenced on a NovaSeq X (Illumina). 1. Carpenter, C.B. Safety considerations for working with animal models involving human health hazards. Animal Model Exp Med 1, 91-99 (2018). 2. Gordon, C.L., et al. Tissue reservoirs of antiviral T cell immunity in persistent human CMV infection. J Exp Med 214, 651-667 (2017). 3. Granot, T., et al. Dendritic Cells Display Subset and Tissue-Specific Maturation Dynamics  over Human Life. Immunity 46, 504-515 (2017). 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) 5. Miron, M., et al. Human Lymph Nodes Maintain TCF-1(hi) Memory T Cells with High Functional Potential and Clonal Diversity throughout Life. J Immunol 201, 2132-2140 (2018). 6. Senda, T., et al. Microanatomical dissection of human intestinal T-cell immunity reveals site specific changes in gut-associated lymphoid tissues over life. Mucosal Immunol 12, 378-389 (2019). 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)
library preparation and RNA-seq was performed by the Columbia Genome Center as previously described. In this study the HTO and ADT matrices come from the same fastq batch.

value: Pancreas

value: Macrophage

value: ADT & HTO

tag: library type

value: 137 antibodies

tag: adt

value: 10 hashtags


title: UPN827 cells, TN114 TrailNet Baseline T1D plasma

status: Public on Jun 01 2026

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

molecule: total RNA

organism: Homo sapiens

source_name: UPN827 cells stimulated with TN114 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: DO iPSC line 1302, untreated

type: SRA

city: Bar Harbor

first: Madison

last: Armstrong

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: Library name: DO_iPSC_1302_CTRL

library_source: transcriptomic

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 1302

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.

tag: cell line

value: DO iPSC 1302

tag: cell type

value: iPSC

tag: treatment

value: untreated

tag: Sex

value: female

tag: do generation

tag: batch

tag: run


title: UPN827 cells, TN113 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN113 TrailNet Baseline T1D plasma


title: MSS CRC tumor organoids + CA 2

city: Freiburg

first: Rebecca

last: Kesselring

address: Breisacher Straße 115

department: General and Visceral Surgery

country: Germany

institute: Medical Center University Freiburg

description:
Library name: Sample 5
read counts in CA2.txt

data_processing:
Read QC and trimming: cutadapt 3.7 (with Python 3.6.9) according to FastQC and MultiQC, meaning trimming of adapter sequences and overrepresented sequences in affected line(s) cutadapt -a  -A  --output --paired-output  --error-rate=0.1 --times=1 --overlap=3   --action=trim --minimum-length=20 --pair-filter=any   --quality-cutoff=28
Annotation file: gencode.v45.primary_assembly.annotation.gtf
Raw read counts == output of subread-2.0.6
featureCounts -a 'gencode.v45.primary_assembly.annotation.gtf' -F "GTF" -o -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap  1 --fracOverlap 0 --fracOverlapFeature 0 -p -C --countReadPairs --extraAttributes "gene_biotype"
Assembly: Reference genome: GRCh38.primary_assembly.genome.fa == GRCh38.p14
Supplementary files format and content: tab delimited txt file containing raw counts of the corresponding sample

source_name: primary tumor, MSS colorectal carcinoma

growth_protocol: human tumor organoids of a MSS colorectal carcinoma are cultured in human organoid culture medium

extract_protocol:
RNA was isolated with RNeasy Mini Kit (Qiagen).
bulk RNA sequencing was performed by Azenta, Leipzig according to their in-house SOPs with NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: Human tumor organoids were co-cultured for 24 hours with the primary bile acids (CA, TCA, GCA)

tag: tissue

value: primary tumor, MSS colorectal carcinoma

value: tumor organoids

value: tumor cell

tag: genotype

value: MSS CRC

value: CA


title: Human pancreatic macrophages from donor SW037, GEX

state: New York

description:
Library name: SW037_Pancreas_Macrophages_mRNA
Human pancreas macrophages isolated from donor SW037 using 10x Genomics CITE-seq protocol for mRNA modality (5' Gene Expression library).

molecule: polyA RNA

value: mRNA


title: DO iPSC line 1298, triphenyl phosphate treated

description: Library name: DO_iPSC_1298_TPHP

source_name: DO iPSC 1298

value: DO iPSC 1298

value: triphenyl phosphate


title: MSS CRC tumor organoids + CA 1

description:
Library name: Sample 4
read counts in CA1.txt


title: Human pancreatic macrophages from donor SW034, ADT

description:
Library name: SW034_Pancreas_Macrophages_ADT
10x Genomics Feature Barcode library containing 140 antibody-derived tags (ADT) for protein detection

library_source: other

value: Pancreas

value: Macrophage

value: ADT

value: 140 antibodies


title: UPN827 cells, TN112 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN112 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: MSS CRC tumor organoids + DMSO, Control 3

description:
Library name: Sample 3
read counts in DMSO3.txt

value: DMSO


title: DO iPSC line 1298, untreated

description: Library name: DO_iPSC_1298_CTRL

value: iPSC

value: untreated


title: Human pancreatic macrophages from donor SW034, GEX

description:
Library name: SW034_Pancreas_Macrophages_mRNA
Human pancreas macrophages isolated from donor SW034 using 10x Genomics CITE-seq protocol for mRNA modality (3' Gene Expression library).


title: DO iPSC line 1454, triphenyl phosphate treated

description: Library name: DO_iPSC_1454_TPHP

source_name: DO iPSC 1454

value: DO iPSC 1454

value: male


title: DO iPSC line 1290, triphenyl phosphate treated

description: Library name: DO_iPSC_1290_TPHP

source_name: DO iPSC 1290

value: DO iPSC 1290

value: female


title: UPN827 cells, TN111 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN111 TrailNet Baseline T1D plasma


title: MSS CRC tumor organoids + DMSO, Control 2

description:
Library name: Sample 2
read counts in DMSO2.txt

value: primary tumor, MSS colorectal carcinoma

value: tumor organoids

value: tumor cell

value: MSS CRC


title: Human pancreatic macrophages from donor SW033, ADT

description:
Library name: SW033_Pancreas_Macrophages_ADT
10x Genomics Feature Barcode library containing 140 antibody-derived tags (ADT) for protein detection

value: Pancreas


title: DO iPSC line 1290, untreated

description: Library name: DO_iPSC_1290_CTRL


title: MSS CRC tumor organoids + DMSO, Control 1

description:
Library name: Sample 1
read counts in DMSO1.txt


title: UPN827 cells, TN110 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN110 TrailNet Baseline T1D plasma


title: UPN827 cells, TN109 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN109 TrailNet Baseline T1D plasma


title: DO iPSC line 1286, triphenyl phosphate treated

description: Library name: DO_iPSC_1286_TPHP

source_name: DO iPSC 1286

value: DO iPSC 1286

value: triphenyl phosphate


title: Normal human dermal fibroblasts knockdown of  NAT10-3

city: Beijing

first: Xuan

last: Ma

address: No.33 Badachu Road,Shijingshan District

country: China

institute: Plastic Surgery Hospital,Chinese Academy of Medical Science and Peking Union Medical College

description: Library name: Hfb_siN10_3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38
Supplementary files format and content: expression matrix file

source_name: skin

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDropTechnologies). Only high-quality RNA sample [OD260/280=1.8~2.2,OD260/230≥2.0,RQN≥6.5,28S:18S≥1.0, >1μg]was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at ShanghaiMajorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego,CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300-400bp use magnetic beads followed by PCR amplified for 10-15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: skin

value: human dermal fibroblasts

value: knockdown of  NAT10


title: Human pancreatic macrophages from donor SW033, GEX

description:
Library name: SW033_Pancreas_Macrophages_mRNA
Human pancreas macrophages isolated from donor SW033 using 10x Genomics CITE-seq protocol for mRNA modality (3' Gene Expression library).

value: Macrophage

value: mRNA


title: UPN827 cells, TN158 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN158 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: Human pancreatic macrophages from donor SW032, ADT

description:
Library name: SW032_Pancreas_Macrophages_ADT
10x Genomics Feature Barcode library containing 140 antibody-derived tags (ADT) for protein detection

value: ADT

value: 140 antibodies


title: UPN827 cells, TN108 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN108 TrailNet Baseline T1D plasma


title: Donor_29_Non_neuron_Control

city: New York

first: Swadha

last: Singh

state: NY

address: 1470 Madison Ave

department: Psychiatry

institute: Icahn School of medicine, Mount sinai

description: Library name: Donor 29

data_processing:
• Adapter trimming using Trimmomatic v0.36
• Alignment to the human genome (GRCh38/hg38) with STAR v2.5.3a
• Gene and transcript quantification using GENCODE v27 annotations
• Quality control using QTLtools (mbv) and sex-marker validation
• Normalization and differential expression modeling using voom/limma-dream
Assembly: GRCh38 / hg38 (GENCODE v27 for gene annotation)
Supplementary files format and content: Processed data include normalized gene-level and transcript-level counts (CPM / log2CPM) and differential expression statistics. Files contain gene identifiers (GENCODE v27), expression values per sample, and model outputs.

source_name: Midbrain

growth_protocol: Postmortem human ventral midbrain (substantia nigra, A9/A10 region) tissue was obtained from established brain banks participating in the CommonMind Consortium. Donors provided informed consent for brain donation, and all tissue collection followed institutional ethical guidelines and the Declaration of Helsinki.

extract_protocol:
Nuclei were isolated from ventral midbrain tissue using Dounce homogenization in sucrose-based lysis buffer, followed by ultracentrifugation through a sucrose cushion to obtain purified nuclei. Immunotagging was performed using NeuN-Alexa488 and Nurr1-Alexa647 antibodies. Approximately 50,000 NeuN+/Nurr1+ (dopaminergic) and 50,000 NeuN-/Nurr1- nuclei were sorted on a BD FACSAria. RNA was extracted from sorted nuclei in TRIzol LS, followed by chloroform extraction and cleanup using the Zymo RNA Clean & Concentrator kit with extended DNase treatment.
RNA-seq libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara). cDNA synthesis, rRNA depletion, adapter ligation, and PCR amplification were performed following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq-6000 (100 bp paired-end).

treatment_protocol: No experimental treatments were applied. Tissue was collected postmortem and processed directly for nuclei isolation and downstream assays. Medication history (including antipsychotic exposure) was recorded by the brain banks but no treatments were administered as part of this study.

value: Midbrain

value: postmortem brain tissue

value: Non neuron

value: Control


title: Normal human dermal fibroblasts knockdown of  NAT10-2

description: Library name: Hfb_siN10_2


title: DO iPSC line 1286, untreated

description: Library name: DO_iPSC_1286_CTRL

value: iPSC

value: untreated

value: female


title: UPN827 cells, TN107 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN107 TrailNet Baseline T1D plasma


title: Human pancreatic macrophages from donor SW032, GEX

description:
Library name: SW032_Pancreas_Macrophages_mRNA
Human pancreas macrophages isolated from donor SW032 using 10x Genomics CITE-seq protocol for mRNA modality (3' Gene Expression library).

source_name: Pancreas

value: Pancreas


title: DO iPSC line 1282, triphenyl phosphate treated

description: Library name: DO_iPSC_1282_TPHP

source_name: DO iPSC 1282

value: DO iPSC 1282

value: triphenyl phosphate


title: Normal human dermal fibroblasts knockdown of  NAT10-1

description: Library name: Hfb_siN10_1

value: skin

value: human dermal fibroblasts

value: knockdown of  NAT10


title: DO iPSC line 1282, untreated

description: Library name: DO_iPSC_1282_CTRL


title: Human pancreatic macrophages from donor SW031, ADT

description:
Library name: SW031_Pancreas_Macrophages_ADT
10x Genomics Feature Barcode library containing 140 antibody-derived tags (ADT) for protein detection

value: Macrophage

value: ADT & HTO


title: UPN827 cells, TN105 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN105 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: hUCMSCs,Control-2

city: 江苏省

first: yajie

last: li

state: China

address: 江苏省徐州市铜山路209号

institute: 徐州医科大学

description:
Library name: Sample2
column name in gene.count.matrix.annotation.csv:D2

data_processing:
Raw sequencing data were filtered to remove adaptor sequences, low-quality reads (Phred score < 20), sequences with high N content, and short sequences using fastp with default parameters, generating high-quality clean reads.
Clean reads were aligned to the reference genome in orientation mode using HISAT2, and alignment metrics (e.g., gene coverage, read distribution across genomic regions/chromosomes) were analyzed.
Mapped reads of each sample were assembled by StringTie, and gene expression levels were quantified as Read Counts using RSEM ; normalized expression values (e.g., FPKM) were calculated for subsequent analysis.
Differential expression analysis was performed using DESeq2 (for samples with biological replicates) or DEGseq. Differentially expressed genes (DEGs) were defined with the threshold: adjusted P-value < 0.05 and log2 fold change> 1.
Functional annotation of DEGs (including GO and KEGG) was conducted using Diamond (https://github.com/bbuchfink/diamond), which assigned genes to biological processes, cellular components, molecular functions (GO), and metabolic pathways (KEGG).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw read counts for each gene across all samples (control & H2O2-treated hUCMSCs)
Supplementary files format and content: csv files include FPKM values for each gene across all samples

source_name: Umbilical Cord

growth_protocol: Human umbilical cord stem cells (hUCMSCs) were cultured in StemGro Mesenchymal Stem Cell Medium (BasaMedia) supplemented with fetal bovine serum, in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
RNA was harvested from hUCMSCs (control & H2O2-treated groups) using MJZol total RNA extraction kit (Shanghai Majorbio Biomedical Technology Co., Ltd., China). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing (low-input) (Clontech, USA), following the manufacturer’s protocols.

treatment_protocol: Oxidative stress model (designated as hUCMSCs,H2O2) was induced by adding 200 μM H2O2 to hUCMSCs at 2 days post-adhesion.

value: Umbilical Cord

value: Primary hUCMSCs

value: mesenchymal stem cells

value: WT

value: Control (0 μM H2O2)


title: Normal human dermal fibroblasts3

description: Library name: Hfb_NC3


title: DO iPSC line 1278, triphenyl phosphate treated

description: Library name: DO_iPSC_1278_TPHP

source_name: DO iPSC 1278

value: DO iPSC 1278

value: iPSC


title: Human pancreatic macrophages from donor SW031, GEX

description:
Library name: SW031_Pancreas_Macrophages_mRNA
Human pancreas macrophages isolated from donor SW031 using 10x Genomics CITE-seq protocol for mRNA modality (3' Gene Expression library).

value: Pancreas


title: Normal human dermal fibroblasts2

description: Library name: Hfb_NC2


title: DO iPSC line 1278, untreated

description: Library name: DO_iPSC_1278_CTRL

value: untreated

value: female


title: Normal human dermal fibroblasts1

description: Library name: Hfb_NC1

value: skin


title: VRC-COVAIL-10-06-2023-Pool2-GEX

city: Bethesda

first: Sarah

last: Andrews

address: 40 Convent Drive

institute: NIH

description: Library name: VRC-COVAIL-10-06-2023-Pool2-GEX

data_processing:
CellRanger v7.2.0
GEX and ADT libraries were run through CellRanger count together to produce one matrix file
Assembly: GRCh38 human reference genome 3.0.0
Supplementary files format and content: Sample_GEX_ADT_barcodes.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_features.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_matrix.mtx.gz
Supplementary files format and content: my_FeatureReferenceFile.csv

source_name: pbmc

extract_protocol:
Single-cells were encapsulated in Gel-beads-in-emulsion using the 10x Genomics Chromium Controller and a Single Cell Immune Profiling Next GEM v2 Chemistry Kit.
10x Genomics Single Cell Immune Profiling Next GEM v2 Chemistry Kit

value: pbmc

value: B Cell

value: Covid Vaccination


title: UPN827 cells, TN103 TrailNet Baseline T1D plasma

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

source_name: UPN827 cells stimulated with TN103 TrailNet Baseline T1D plasma


title: UPN827 cells, TN104 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN104 TrailNet Baseline T1D plasma


title: UPN827 cells, TN106 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN106 TrailNet Baseline T1D plasma


title: VRC-COVAIL-10-06-2023-Pool1-GEX

description: Library name: VRC-COVAIL-10-06-2023-Pool1-GEX


title: DO iPSC line 1274, triphenyl phosphate treated

description: Library name: DO_iPSC_1274_TPHP

source_name: DO iPSC 1274

value: DO iPSC 1274

value: triphenyl phosphate


title: VRC-COVAIL-10-05-2023-Pool1-GEX

description: Library name: VRC-COVAIL-10-05-2023-Pool1-GEX


title: Donor_21_Non_neuron_BP

description: Library name: Donor 21

value: Midbrain

value: postmortem brain tissue

value: Non neuron

value: BP


title: PDAC patient Nr 3 derived Tumour

city: Munich

first: Rouzanna

last: Istvánffy

address: Ismaningerstr. 22

department: Department of Surgery

institute: Klinikum rechts der Isar

description:
Library name: HSU3
Column_name_in_Human_FPKMs.xlsx_HSU3_fpkm

data_processing:
Data Quality Control: Raw reads were processed using fastp to remove adapter-containing reads, poly-N reads, and low-quality reads, resulting in clean reads. Q20, Q30, and GC content were calculated for the clean data.
Ribosomal RNA Removal: Ribosomal RNA sequences were removed by aligning reads to the Silva database using Bowtie2 v2.3.4.3.
Genome Alignment: Clean reads were aligned to the reference genome using HISAT2 v2.0.5 for accurate mapping. The reference genome used was GRCh38/hg38 ( (download link: Ensembl Release 94).
Assembly: Gene Expression Quantification: Gene expression levels were quantified using the featureCounts tool in the Subread package. Reads with mapping quality scores below 10, unpaired reads, and reads mapped to multiple genomic regions were filtered out. Final expression values were normalized to FPKM by accounting for sequencing depth and gene length.
Supplementary files format and content: tab-delimited text files including raw files for each sample

source_name: pancreas tumour

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were generated using the SMARTer mRNA-Seq Library Preparation Kit (Takara Bio), following the manufacturer's instructions (Eukaryotic 250~300 bp insert cDNA library)

value: pancreas tumour

value: Cancer cells

tag: subject status

value: PDAC patient


title: DO iPSC line 1274, untreated

description: Library name: DO_iPSC_1274_CTRL

value: iPSC


title: PDAC patient Nr 2 derived Tumour

description:
Library name: HSU2
Column_name_in_Human_FPKMs.xlsx_HSU2_fpkm


title: VRC-COVAIL-09-28-2023-Pool3-GEX

description: Library name: VRC-COVAIL-09-28-2023-Pool3-GEX


title: DO iPSC line 1270, triphenyl phosphate treated

description: Library name: DO_iPSC_1270_TPHP

source_name: DO iPSC 1270

value: DO iPSC 1270


title: PDAC patient Nr 1 derived Tumour

description:
Library name: HSU1
Column_name_in_Human_FPKMs.xlsx_HSU1_fpkm

value: untreated


title: UPN827 cells, TN100 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN100 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: UPN827 cells, TN99 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN99 TrailNet Baseline T1D plasma


title: UPN827 cells, TN101 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN101 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-28-2023-Pool2-GEX

description: Library name: VRC-COVAIL-09-28-2023-Pool2-GEX

value: pbmc


title: PDAC patient Nr 3 derived Ganglion

description:
Library name: HGang3
Column_name_in_Human_FPKMs.xlsx_HGang3_fpkm

source_name: Neural ganglia

value: Neural ganglia

value: Neural cells


title: DO iPSC line 1270, untreated

description: Library name: DO_iPSC_1270_CTRL

value: female


title: DO iPSC line 1262, triphenyl phosphate treated

description: Library name: DO_iPSC_1262_TPHP

source_name: DO iPSC 1262

value: DO iPSC 1262

value: triphenyl phosphate


title: UPN827 cells, TN98 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN98 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-28-2023-Pool1-GEX

description: Library name: VRC-COVAIL-09-28-2023-Pool1-GEX

value: B Cell

value: Covid Vaccination


title: PDAC patient Nr 2 derived Ganglion

description:
Library name: HGang2
Column_name_in_Human_FPKMs.xlsx_HGang2_fpkm


title: VRC-COVAIL-09-27-2023-Pool2-GEX

description: Library name: VRC-COVAIL-09-27-2023-Pool2-GEX


title: DO iPSC line 1418, untreated

description: Library name: DO_iPSC_1418_CTRL

source_name: DO iPSC 1418

value: DO iPSC 1418

value: male


title: VRC-COVAIL-09-27-2023-Pool1-GEX

description: Library name: VRC-COVAIL-09-27-2023-Pool1-GEX


title: DO iPSC line 1262, untreated

description: Library name: DO_iPSC_1262_CTRL


title: PDAC patient Nr 1 derived Ganglion

description:
Library name: HGang1
Column_name_in_Human_FPKMs.xlsx_HGang1_fpkm


title: UPN827 cells, TN97 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN97 TrailNet Baseline T1D plasma


title: UPN827 cells, TN96 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN96 TrailNet Baseline T1D plasma


title: DO iPSC line 542, triphenyl phosphate treated

description: Library name: DO_iPSC_542_TPHP

source_name: DO iPSC 542

value: DO iPSC 542


title: R2

city: wenzhou

first: Ziqiang

last: Xia

address: First Affiliated Hospital of Wenzhou Medical University

description: Library name: Sample4

data_processing:
The libraries were quality controlled with Agilent 2200 and sequenced by DNBSEQ-T7 on a 150 bp paired-end run.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to rat genome (Rnor6.0, Ensembl) using the Hisat2.HTseq was used to get gene counts and RPKM method was used to determine the gene expression.
Assembly: Rnor6.0_Ensembl
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction.
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

value: hepatic stellate cell line


title: VRC-COVAIL-09-26-2023-Pool2-GEX

description: Library name: VRC-COVAIL-09-26-2023-Pool2-GEX

source_name: pbmc


title: UPN827 cells, TN95 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN95 TrailNet Baseline T1D plasma


title: DO iPSC line 542, untreated

description: Library name: DO_iPSC_542_CTRL

value: iPSC


title: R1

institute: First Affiliated Hospital of Wenzhou Medical University

description: Library name: Sample3


title: VRC-COVAIL-09-26-2023-Pool1-GEX

description: Library name: VRC-COVAIL-09-26-2023-Pool1-GEX


title: DO iPSC line 539, triphenyl phosphate treated

description: Library name: DO_iPSC_539_TPHP

source_name: DO iPSC 539

value: DO iPSC 539


title: VRC-COVAIL-09-21-2023-Pool2-GEX

description: Library name: VRC-COVAIL-09-21-2023-Pool2-GEX


title: C2

description: Library name: Sample2


title: DO iPSC line 539, untreated

description: Library name: DO_iPSC_539_CTRL

value: untreated


title: UPN827 cells, TN94 TrailNet Baseline T1D plasma

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

source_name: UPN827 cells stimulated with TN94 TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN92 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN92 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: C1

description: Library name: Sample1


title: VRC-COVAIL-09-21-2023-Pool1-GEX

description: Library name: VRC-COVAIL-09-21-2023-Pool1-GEX

value: pbmc


title: UPN827 cells, TN93 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN93 TrailNet Baseline T1D plasma


title: DO iPSC line 535, triphenyl phosphate treated

description: Library name: DO_iPSC_535_TPHP

source_name: DO iPSC 535

value: DO iPSC 535


title: Root, inoculated, timepoint 5, post drought, replicate 3

city: East Lansing

first: Reid

last: Longley

state: MI

address: 612 Wilson Rd #106

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7
reads were trimmed to remove adapter sequences and low quality reads with trimmomatic; only reads of 30 bp or longer were kept
SortMeRNA was used to remove any residual rRNA reads
Transcripts quantified with Salmon, mapped to the Williams 82 transcriptome from JGI
Differential expression analysis performed using DESeq2
Assembly: JGI - Williams 82 Wm82.a4.v1
Supplementary files format and content: matrix of Normalized counts from DESeq2

organism: Glycine max

source_name: root

growth_protocol: Soybean seedlings were grown in greenhouses with 12 hour photoperiods, T1 occurred 14 dayas after planting and each timepoint was 6 days apart. T2-T4 represent low moisture stress

extract_protocol:
RNA was extracted from 50 mg of flash frozen (liquid N) soybean root tissue using RNeasy plant mini kit (Qiagen
ibraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit with IDT for Illumina DNA/RNA UD Indexes following manufacturer's recommendations

treatment_protocol: Inoculated samples were inoculated with clay beads colonized by microbes, control plants were created by placing the same set of beads as inoculated samples, but the beads had been dry heat sterilized at 200c.

value: root

value: William 82

value: inoculated


title: VRC-COVAIL-09-20-2023-Pool3-GEX

description: Library name: VRC-COVAIL-09-20-2023-Pool3-GEX


title: DO iPSC line 535, untreated

description: Library name: DO_iPSC_535_CTRL


title: Root, inoculated, timepoint 5, post drought, replicate 2


title: UPN827 cells, TN91 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN91 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-20-2023-Pool2-GEX

description: Library name: VRC-COVAIL-09-20-2023-Pool2-GEX


title: UPN827 cells, TN90 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN90 TrailNet Baseline T1D plasma


title: UPN827 cells, TN135 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN135 TrailNet Baseline T1D plasma


title: Root, inoculated, timepoint 5, post drought, replicate 1


title: DO iPSC line 533, triphenyl phosphate treated

description: Library name: DO_iPSC_533_TPHP

source_name: DO iPSC 533

value: DO iPSC 533

value: triphenyl phosphate


title: VRC-COVAIL-09-20-2023-Pool1-GEX

description: Library name: VRC-COVAIL-09-20-2023-Pool1-GEX

value: B Cell

value: Covid Vaccination


title: DO iPSC line 533, untreated

description: Library name: DO_iPSC_533_CTRL

value: male


title: Root, control, timepoint 5, post drought, replicate 3

value: control


title: VRC-COVAIL-09-19-2023-Pool3-GEX

description: Library name: VRC-COVAIL-09-19-2023-Pool3-GEX


title: UPN827 cells, TN89 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN89 TrailNet Baseline T1D plasma


title: DO iPSC line 527, triphenyl phosphate treated

description: Library name: DO_iPSC_527_TPHP

source_name: DO iPSC 527

value: DO iPSC 527


title: Root, control, timepoint 5, post drought, replicate 2


title: VRC-COVAIL-09-19-2023-Pool2-GEX

description: Library name: VRC-COVAIL-09-19-2023-Pool2-GEX


title: UPN827 cells, TN87 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN87 TrailNet Baseline T1D plasma


title: UPN827 cells, TN88 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN88 TrailNet Baseline T1D plasma


title: DO iPSC line 527, untreated

description: Library name: DO_iPSC_527_CTRL

value: iPSC


title: UPN827 cells, TN86 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN86 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-19-2023-Pool1-GEX

description: Library name: VRC-COVAIL-09-19-2023-Pool1-GEX

source_name: pbmc


title: Root, control, timepoint 5, post drought, replicate 1


title: DO iPSC line 524, triphenyl phosphate treated

description: Library name: DO_iPSC_524_TPHP

source_name: DO iPSC 524

value: DO iPSC 524


title: Root, inoculated, timepoint 4, late drought, replicate 3


title: VRC-COVAIL-10-06-2023-Pool2-CSO

description: Library name: VRC-COVAIL-10-06-2023-Pool2-CSO

data_processing:
CellRanger v7.2.0
GEX and ADT libraries were run through CellRanger count together to produce one matrix file
Assembly: GRCh38 human reference genome 3.0.0
Supplementary files format and content: Sample_GEX_ADT_barcodes.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_features.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_matrix.mtx.gz
Supplementary files format and content: my_FeatureReferenceFile.csv
Library strategy: CITE-seq


title: DO iPSC line 524, untreated

description: Library name: DO_iPSC_524_CTRL

value: untreated


title: Root, inoculated, timepoint 4, late drought, replicate 2


title: UPN827 cells, TN85 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN85 TrailNet Baseline T1D plasma

value: UPN827 cells


title: VRC-COVAIL-10-06-2023-Pool1-CSO

description: Library name: VRC-COVAIL-10-06-2023-Pool1-CSO


title: UPN827 cells, TN84 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN84 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: Root, inoculated, timepoint 4, late drought, replicate 1


title: DO iPSC line 520, triphenyl phosphate treated

description: Library name: DO_iPSC_520_TPHP

source_name: DO iPSC 520

value: DO iPSC 520


title: VRC-COVAIL-10-05-2023-Pool1-CSO

description: Library name: VRC-COVAIL-10-05-2023-Pool1-CSO

value: pbmc


title: UPN827 cells, TN83 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN83 TrailNet Baseline T1D plasma


title: DO iPSC line 520, untreated

description: Library name: DO_iPSC_520_CTRL


title: VRC-COVAIL-09-28-2023-Pool3-CSO

description: Library name: VRC-COVAIL-09-28-2023-Pool3-CSO


title: Root, control, timepoint 4, late drought, replicate 3

value: root


title: DO iPSC line 517, triphenyl phosphate treated

description: Library name: DO_iPSC_517_TPHP

source_name: DO iPSC 517

value: DO iPSC 517


title: Root, control, timepoint 4, late drought, replicate 2

source_name: root

value: William 82


title: DO iPSC line 517, untreated

description: Library name: DO_iPSC_517_CTRL


title: VRC-COVAIL-09-28-2023-Pool2-CSO

description: Library name: VRC-COVAIL-09-28-2023-Pool2-CSO


title: Root, control, timepoint 4, late drought, replicate 1


title: VRC-COVAIL-09-28-2023-Pool1-CSO

description: Library name: VRC-COVAIL-09-28-2023-Pool1-CSO


title: UPN827 cells, TN80 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN80 TrailNet Baseline T1D plasma


title: DO iPSC line 516, triphenyl phosphate treated

description: Library name: DO_iPSC_516_TPHP

source_name: DO iPSC 516

value: DO iPSC 516


title: UPN827 cells, TN79 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN79 TrailNet Baseline T1D plasma


title: Root, inoculated, timepoint 3, middle drought, replicate 3

value: inoculated


title: UPN827 cells, TN82 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN82 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-27-2023-Pool2-CSO

description: Library name: VRC-COVAIL-09-27-2023-Pool2-CSO

value: B Cell


title: DO iPSC line 516, untreated

description: Library name: DO_iPSC_516_CTRL


title: Root, inoculated, timepoint 3, middle drought, replicate 2


title: VRC-COVAIL-09-27-2023-Pool1-CSO

description: Library name: VRC-COVAIL-09-27-2023-Pool1-CSO

value: Covid Vaccination


title: DO iPSC line 512, triphenyl phosphate treated

description: Library name: DO_iPSC_512_TPHP

source_name: DO iPSC 512

value: DO iPSC 512

value: triphenyl phosphate

value: male


title: UPN827 cells, TN77RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN77RH2 TrailNet Baseline T1D plasma


title: UPN827 cells, TN78 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN78 TrailNet Baseline T1D plasma


title: Root, inoculated, timepoint 3, middle drought, replicate 1


title: DO iPSC line 512, untreated

description: Library name: DO_iPSC_512_CTRL

value: iPSC


title: VRC-COVAIL-09-26-2023-Pool2-CSO

description: Library name: VRC-COVAIL-09-26-2023-Pool2-CSO


title: UPN827 cells, TN76 TrailNet Baseline T1D plasma

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

source_name: UPN827 cells stimulated with TN76 TrailNet Baseline T1D plasma


title: Root, control, timepoint 3, middle drought, replicate 3

value: control


title: VRC-COVAIL-09-26-2023-Pool1-CSO

description: Library name: VRC-COVAIL-09-26-2023-Pool1-CSO


title: DO iPSC line 504, triphenyl phosphate treated

description: Library name: DO_iPSC_504_TPHP

source_name: DO iPSC 504

value: DO iPSC 504

value: female


title: Root, control, timepoint 3, middle drought, replicate 2


title: VRC-COVAIL-09-21-2023-Pool2-CSO

description: Library name: VRC-COVAIL-09-21-2023-Pool2-CSO

source_name: pbmc


title: DO iPSC line 504, untreated

description: Library name: DO_iPSC_504_CTRL

value: untreated


title: Root, control, timepoint 3, middle drought, replicate 1


title: VRC-COVAIL-09-21-2023-Pool1-CSO

description: Library name: VRC-COVAIL-09-21-2023-Pool1-CSO


title: UPN827 cells, TN75 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN75 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: UPN827 cells, TN74 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN74 TrailNet Baseline T1D plasma


title: UPN827 cells, TN73 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN73 TrailNet Baseline T1D plasma


title: Root, inoculated, timepoint 2, drought start, replicate 3

value: root


title: DO iPSC line 478, triphenyl phosphate treated

description: Library name: DO_iPSC_478_TPHP

source_name: DO iPSC 478

value: DO iPSC 478


title: VRC-COVAIL-09-20-2023-Pool3-CSO

description: Library name: VRC-COVAIL-09-20-2023-Pool3-CSO

value: pbmc


title: VRC-COVAIL-09-20-2023-Pool2-CSO

description: Library name: VRC-COVAIL-09-20-2023-Pool2-CSO


title: Root, inoculated, timepoint 2, drought start, replicate 2

value: William 82


title: DO iPSC line 478, untreated

description: Library name: DO_iPSC_478_CTRL


title: UPN827 cells, TN71 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN71 TrailNet Baseline T1D plasma


title: UPN827 cells, TN72 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN72 TrailNet Baseline T1D plasma


title: DO iPSC line 466, triphenyl phosphate treated

description: Library name: DO_iPSC_466_TPHP

source_name: DO iPSC 466

value: DO iPSC 466


title: UPN827 cells, TN70 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN70 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-20-2023-Pool1-CSO

description: Library name: VRC-COVAIL-09-20-2023-Pool1-CSO

value: B Cell


title: Root, inoculated, timepoint 2, drought start, replicate 1

source_name: root

value: inoculated


title: DO iPSC line 466, untreated

description: Library name: DO_iPSC_466_CTRL


title: Root, control, timepoint 2, drought start, replicate 3


title: DO iPSC line 452, triphenyl phosphate treated

description: Library name: DO_iPSC_452_TPHP

source_name: DO iPSC 452

value: DO iPSC 452


title: VRC-COVAIL-09-19-2023-Pool3-CSO

description: Library name: VRC-COVAIL-09-19-2023-Pool3-CSO

value: Covid Vaccination


title: Root, control, timepoint 2, drought start, replicate 2


title: VRC-COVAIL-09-19-2023-Pool2-CSO

description: Library name: VRC-COVAIL-09-19-2023-Pool2-CSO


title: DO iPSC line 452, untreated

description: Library name: DO_iPSC_452_CTRL


title: VRC-COVAIL-09-19-2023-Pool1-CSO

description: Library name: VRC-COVAIL-09-19-2023-Pool1-CSO


title: Root, control, timepoint 2, drought start, replicate 1


title: DO iPSC line 449, triphenyl phosphate treated

description: Library name: DO_iPSC_449_TPHP

source_name: DO iPSC 449

value: DO iPSC 449

value: triphenyl phosphate

value: male


title: Root, inoculated, timepoint 1, pre-drought, replicate 3


title: UPN827 cells, TN67 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN67 TrailNet Baseline T1D plasma


title: UPN827 cells, TN68 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN68 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-13-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-09-13-2023-VDJ-Pool1

data_processing:
CellRanger v7.2.0
GEX and ADT libraries were run through CellRanger count together to produce one matrix file
Assembly: GRCh38 human reference genome 3.0.0
Supplementary files format and content: Sample_GEX_ADT_barcodes.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_features.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_matrix.mtx.gz
Supplementary files format and content: my_FeatureReferenceFile.csv
Library strategy: BCR-Seq


title: DO iPSC line 449, untreated

description: Library name: DO_iPSC_449_CTRL

value: iPSC


title: UPN827 cells, TN66 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN66 TrailNet Baseline T1D plasma


title: Root, inoculated, timepoint 1, pre-drought, replicate 2


title: VRC-COVAIL-10-06-2023-VDJ-Pool2

description: Library name: VRC-COVAIL-10-06-2023-VDJ-Pool2


title: UPN827 cells, TN69 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN69 TrailNet Baseline T1D plasma


title: UPN827 cells, TN65 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN65 TrailNet Baseline T1D plasma


title: DO iPSC line 446, triphenyl phosphate treated

description: Library name: DO_iPSC_446_TPHP

source_name: DO iPSC 446

value: DO iPSC 446


title: UPN827 cells, TN64 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN64 TrailNet Baseline T1D plasma


title: Root, inoculated, timepoint 1, pre-drought, replicate 1


title: Root, control, timepoint 1, pre-drought, replicate 3

value: control


title: VRC-COVAIL-10-05-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-10-05-2023-VDJ-Pool1

source_name: pbmc


title: DO iPSC line 446, untreated

description: Library name: DO_iPSC_446_CTRL

value: untreated


title: VRC-COVAIL-10-06-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-10-06-2023-VDJ-Pool1


title: DO iPSC line 431, triphenyl phosphate treated

description: Library name: DO_iPSC_431_TPHP

source_name: DO iPSC 431

value: DO iPSC 431


title: Root, control, timepoint 1, pre-drought, replicate 2

value: root


title: VRC-COVAIL-09-28-2023-VDJ-Pool3

description: Library name: VRC-COVAIL-09-28-2023-VDJ-Pool3


title: UPN827 cells, TN62 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN62 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: UPN827 cells, TN63 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN63 TrailNet Baseline T1D plasma


title: Root, control, timepoint 1, pre-drought, replicate 1

value: William 82


title: DO iPSC line 431, untreated

description: Library name: DO_iPSC_431_CTRL


title: VRC-COVAIL-09-28-2023-VDJ-Pool2

description: Library name: VRC-COVAIL-09-28-2023-VDJ-Pool2

value: pbmc


title: DO iPSC line 428, triphenyl phosphate treated

description: Library name: DO_iPSC_428_TPHP

source_name: DO iPSC 428

value: DO iPSC 428


title: Primary NRCMs, Adeno-Yap1 shRNA, replicate 3

city: Guangzhou

first: Ning

last: Hou

address: Xinzao Street

institute: Guangzhou Medical University

description: Library name: Ad-Yap1 shRNA3

data_processing:
Data filtering: The raw sequencing data are called raw tags. We obtained clean tags using the SOAPnuke. The filtering rules were as follows: removed low quality tags; removed tags with 5’ primer contaminants; remove tags without 3’ primer; removed tags without insertion; removed tags with poly A; removed tags shorter than 15nt.
Small RNA Annotation and miRNA Identification: After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2. Particularly, cmsearch was performed for Rfam mapping. In the annotation information of different RNAs, to ensure that each small RNA was mapped to a unique category, we set the following rules: MiRbase(v22) > pirnabank(v1.0) > snoRNA(v1.2 human/plant ) > Rfam (v12.1)> other sRNA. The miRDeep-P2 or miRDeep2 package was used to identify potentially novel miRNAs. The potentially novel miRNAs and were named novel_mirXXX, in which XXX is a unique number specified for each novel miRNA candidate.
Target Gene Prediction: RNAhybrid, miRanda and TargetScan were used to predict target genes of miRNAs (Only for animal; TargetFinder  and TAPIR were used for plant).  miRNA quantificatio: The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. The expression formula is:  C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
Differential Expression Analysis  Differential expression analysis was performed using the DEGseq  (or DESeq2 or PoissonDis ) on Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com). Q value≤ 0.05 (or FDR value≤0.001) was used to judge the significance of expression difference.
Target Genes Annotation: To annotate gene functions, all target genes were aligned against the Kyoto Encyclopedia of Genes KEGG and Gene Ontology database. GO enrichment analysis and KEGG enrichment analysis of target genes were performed using phyper, a function of R on Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com). The P-value was corrected using the Bonferroni method [15], and a corrected P-value ≤ 0.05 was taken as a threshold. GO terms or KEGG terms fulfilling this condition were defined as significantly enriched terms.
Assembly: ftp://hgdownload.cse.ucsc.edu/goldenPath/rn6
Supplementary files format and content: gene_expression.xls
Supplementary files format and content: core_table.xls

source_name: Neonatal rat cardiomyocytes (NRCMs) are isolated from the hearts of newborn rats and cultured in vitro

growth_protocol: Primary NRCMs were isolated from 1–2-day-old neonatal SD rats. In brief, hearts collected from anesthetized neonatal rats were digested with pancreatic enzymes and type II collagenase. The dissociated cells were cultured at a density of 5×106 cells/mL in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum and 1% penicillin-streptomycin for 18-20 h in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted infected NRCMs using a Trizol reagent kit. The RNA quality was evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) and confirmed with agarose gel electrophoresis. The mRNA was enriched with Oligo (dT) beads, fragmented, and reversely transcribed into cDNA using a NEBNext Ultra RNA Library Prep Kit
Library preparation is performed using MGIEasy Small RNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA is ligated 3’ and 5’ adaptors sequentially in two reaction systems for adaptors ligation. After adaptor ligation, RNA is reverse transcribed into cDNA and PCR amplified. The library is fragment size selected by polyacrylamide gel electrophoresis and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and sequencing reads of SE50 bases length are generated on G400 platform (BGI-Shenzhen, China)

treatment_protocol: NRCMs were initially cultured in DMEM supplemented with10% fetal bovine serum and 1% penicillin-streptomycin. Yap expression in these cells was manipulated using adenovirus. The cells were categorized into the Ad-Yap shRNA or Ad-Yap WT group under adenovirus transfection. The group transfected with Ad-GFP served as the CON group.

value: Primary neonatal rat cardiomyocytes

value: cardiomyocytes

value: Yap1 knock down

value: Ad-Yap shRNA transfected 48 hours


title: VRC-COVAIL-09-28-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-09-28-2023-VDJ-Pool1

value: B Cell

value: Covid Vaccination


title: DO iPSC line 428, untreated

description: Library name: DO_iPSC_428_CTRL

value: iPSC

value: male


title: UPN827 cells, TN61 TrailNet Baseline T1D plasma

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

source_name: UPN827 cells stimulated with TN61 TrailNet Baseline T1D plasma


title: Primary NRCMs, Adeno-Yap1 shRNA, replicate 2

description: Library name: Ad-Yap1 shRNA2

value: Neonatal rat cardiomyocytes (NRCMs) are isolated from the hearts of newborn rats and cultured in vitro


title: DO iPSC line 423, triphenyl phosphate treated

description: Library name: DO_iPSC_423_TPHP

source_name: DO iPSC 423

value: DO iPSC 423

value: triphenyl phosphate

value: female


title: VRC-COVAIL-09-27-2023-VDJ-Pool2

description: Library name: VRC-COVAIL-09-27-2023-VDJ-Pool2


title: Primary NRCMs, Adeno-Yap1 shRNA, replicate 1

description: Library name: Ad-Yap1 shRNA1


title: UPN827 cells, TN59 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN59 TrailNet Baseline T1D plasma

value: UPN827 cells


title: VRC-COVAIL-09-27-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-09-27-2023-VDJ-Pool1


title: UPN827 cells, TN60RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN60RH2 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN58 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN58 TrailNet Baseline T1D plasma


title: DO iPSC line 423, untreated

description: Library name: DO_iPSC_423_CTRL

value: untreated


title: Primary NRCMs, Adeno-Yap1 WT, replicate 3

description: Library name: Ad-Yap1 WT3

value: Yap1 overexpression

value: Ad-Yap WT transfected 48 hours


title: VRC-COVAIL-09-26-2023-VDJ-Pool2

description: Library name: VRC-COVAIL-09-26-2023-VDJ-Pool2

value: pbmc


title: DO iPSC line 420, triphenyl phosphate treated

description: Library name: DO_iPSC_420_TPHP

source_name: DO iPSC 420

value: DO iPSC 420


title: VRC-COVAIL-09-26-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-09-26-2023-VDJ-Pool1


title: UPN827 cells, TN56 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN56 TrailNet Baseline T1D plasma


title: Primary NRCMs, Adeno-Yap1 WT, replicate 2

description: Library name: Ad-Yap1 WT2

value: Primary neonatal rat cardiomyocytes

value: cardiomyocytes


title: DO iPSC line 420, untreated

description: Library name: DO_iPSC_420_CTRL


title: UPN827 cells, TN57 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN57 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-21-2023-VDJ-Pool2

description: Library name: VRC-COVAIL-09-21-2023-VDJ-Pool2

value: B Cell


title: UPN827 cells, TN55 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN55 TrailNet Baseline T1D plasma


title: DO iPSC line 414, triphenyl phosphate treated

description: Library name: DO_iPSC_414_TPHP

source_name: DO iPSC 414

value: DO iPSC 414


title: Primary NRCMs, Adeno-GFP, replicate 3

description: Library name: Ad-GFP3

value: WT

value: Ad-GFP  transfected 48 hours


title: Primary NRCMs, Adeno-Yap1 WT, replicate 1

description: Library name: Ad-Yap1 WT1

value: Neonatal rat cardiomyocytes (NRCMs) are isolated from the hearts of newborn rats and cultured in vitro


title: VRC-COVAIL-09-21-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-09-21-2023-VDJ-Pool1

value: Covid Vaccination


title: UPN827 cells, TN54 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN54 TrailNet Baseline T1D plasma


title: DO iPSC line 414, untreated

description: Library name: DO_iPSC_414_CTRL

value: iPSC


title: Primary NRCMs, Adeno-GFP, replicate 2

description: Library name: Ad-GFP2


title: VRC-COVAIL-09-20-2023-VDJ-Pool3

description: Library name: VRC-COVAIL-09-20-2023-VDJ-Pool3

source_name: pbmc


title: DO iPSC line 411, triphenyl phosphate treated

description: Library name: DO_iPSC_411_TPHP

source_name: DO iPSC 411

value: DO iPSC 411

value: triphenyl phosphate

value: male


title: Primary NRCMs, Adeno-GFP, replicate 1

description: Library name: Ad-GFP1


title: UPN827 cells, TN53 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN53 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: VRC-COVAIL-09-20-2023-VDJ-Pool2

description: Library name: VRC-COVAIL-09-20-2023-VDJ-Pool2


title: DO iPSC line 411, untreated

description: Library name: DO_iPSC_411_CTRL

value: untreated


title: VRC-COVAIL-09-20-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-09-20-2023-VDJ-Pool1

value: pbmc


title: DO iPSC line 383, triphenyl phosphate treated

description: Library name: DO_iPSC_383_TPHP

source_name: DO iPSC 383

value: DO iPSC 383

value: female


title: VRC-COVAIL-09-19-2023-VDJ-Pool3

description: Library name: VRC-COVAIL-09-19-2023-VDJ-Pool3


title: RNA library from 12 weeks Natural cumulus cells 4

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
Library name: 92_5_GC
92_5_GC
summary_count_cumulus_cells_12week.txt

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package. Chord plots were done using complexheatmap, clusterprofiler and circlize packages in R. WGCNA was done using the WGCNA package for R.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: 12 week cumulus cells

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
For tissue: RNA was extracted using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries. For single oocytes and cumulus cells: a modified SMART-seq extraction protocol was used using TCL and BME for cell lysis
For tissue: RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols. For single oocytes and cumulus cells: Nextera Library prep and Nextera sequencing indexes (Illumina) were used.

treatment_protocol: E18.5 ovaries, 12 weeks ovaries, 39 weeks ovaries, 12 weeks single oocytes, 39 weeks single oocytes, 12 cumulus cells pools, 39 weeks cumulus cells pools, F2 12 weeks testis, F2 12 weeks male livers, F2 12 weeks ovaries, F2 weeks female livers awere collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

value: 12 week cumulus cells

value: Female

value: Natural


title: RNA library from 12 weeks Natural cumulus cells 5

description:
Library name: 126_2_GC
126_2_GC
summary_count_cumulus_cells_12week.txt


title: DO iPSC line 383, untreated

description: Library name: DO_iPSC_383_CTRL


title: UPN827 cells, TN52 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN52 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks Natural cumulus cells 3

description:
Library name: 35_3_GC
35_3_GC
summary_count_cumulus_cells_12week.txt


title: UPN827 cells, TN50 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN50 TrailNet Baseline T1D plasma


title: UPN827 cells, TN49 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN49 TrailNet Baseline T1D plasma


title: UPN827 cells, TN51 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN51 TrailNet Baseline T1D plasma


title: VRC-COVAIL-09-19-2023-VDJ-Pool2

description: Library name: VRC-COVAIL-09-19-2023-VDJ-Pool2

value: B Cell


title: DO iPSC line 213, triphenyl phosphate treated

description: Library name: DO_iPSC_213_TPHP

source_name: DO iPSC 213

value: DO iPSC 213


title: RNA library from 12 weeks Natural cumulus cells 2

description:
Library name: Natural_12wks_cumulus_cells_2
Natural_12wks_cumulus_cells_2
summary_count_cumulus_cells_12week.txt


title: VRC-COVAIL-09-19-2023-VDJ-Pool1

description: Library name: VRC-COVAIL-09-19-2023-VDJ-Pool1


title: UPN827 cells, TN48 TrailNet Baseline T1D plasma

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

source_name: UPN827 cells stimulated with TN48 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks Natural cumulus cells 1

description:
Library name: Natural_12wks_cumulus_cells_1
Natural_12wks_cumulus_cells_1
summary_count_cumulus_cells_12week.txt


title: NTM-infected, autoantibody-negative, scRNA seq of patient 4

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

description: Library name: S011_novelbio-A_A305-GEX_AHGCMWDSX3_S3_L002

library_source: transcriptomic single cell

data_processing:
The original sequencing data were analyzed by using FastQC software. 10X Chromium single cell transcriptome sequencing can be divided into three regions near the polyA and five regions near the transcriptional initiation site. Among them, 5-terminal transcript sequencing is usually performed together with T cell and B cell receptor gene TCR/BCR sequences for sequencing analysis. Different kits (including 3-terminal vs 5-terminal, and different versions) have slightly different library structures: For example, for a sample processed by a 10X single-cell 3-terminal V2 kit, Read 1 consists of a 16bp 10X Cell Barcode and a 10bp UMI sequence; The sample processed by the V3 kit, Read 1, consisted of 16 bp 10X Cell Barcode and 12 bp UMI sequence. In the analysis, 10X Cell Barcode in Read1 was used to separate individual cells, and UMI was used to remove PCR amplification bias and distinguish between transcripts. Read2 is a 151 bp cDNA sequence, and the first 91 bp is generally used for downstream analysis of Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Matrix table wuth raw gene counts for every gene and every cell

source_name: PBMC

extract_protocol:
For the inspection and counting of single-cell suspension, the survival rate of cells is generally required to be above 85%, and the qualified cells are prepared by washing and re-suspension into a suitable cell concentration of 700~1200 cells/µl
According to the expected number of target cells, Gel Bead in Emulsion was constructed for single cell separation. After the normal formation of GEMs, GEMs were collected for reverse transcription in PCR instrument to realize labeling. For GEMs oil breaking treatment, a strand of cDNA was purified and enriched with magnetic beads, then cDNA amplification and quality inspection were carried out. The qualified cDNA was constructed by the second generation sequencing library, and the quantitative quality of the library was finally tested through the experimental processes of fragmentation, connecting sequencing joints, and sample Index PCR.

value: PBMC

tag: group

value: autoantibody-negative

tag: infection

value: NTM-infected


title: DO iPSC line 213, untreated

description: Library name: DO_iPSC_213_CTRL

value: iPSC


title: DO iPSC line 209, triphenyl phosphate treated

description: Library name: DO_iPSC_209_TPHP

source_name: DO iPSC 209

value: DO iPSC 209

value: triphenyl phosphate


title: UPN827 cells, TN47 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN47 TrailNet Baseline T1D plasma

value: UPN827 cells


title: RNA library from 12 weeks IVF cumulus cells 5

description:
Library name: IVF_12wks_cumulus_cells_2
IVF_12wks_cumulus_cells_2
summary_count_cumulus_cells_12week.txt

value: IVF


title: NTM-infected, autoantibody-negative, scRNA seq of patient 3

description: Library name: S012_novelbio-A_A163-GEX_AHGCMWDSX3_S4_L002


title: RNA library from 12 weeks IVF cumulus cells 4

description:
Library name: IVF_12wks_cumulus_cells_1
IVF_12wks_cumulus_cells_1
summary_count_cumulus_cells_12week.txt


title: NTM-infected, autoantibody-positive, scRNA seq of patient 2

description: Library name: R22007502-A129-jiace-A129_combined

value: autoantibody-positive


title: DO iPSC line 209, untreated

description: Library name: DO_iPSC_209_CTRL

value: untreated

value: male


title: DO iPSC line 208, triphenyl phosphate treated

description: Library name: DO_iPSC_208_TPHP

source_name: DO iPSC 208

value: DO iPSC 208


title: RNA library from 12 weeks IVF cumulus cells 3

description:
Library name: 127_2_GC
127_2_GC
summary_count_cumulus_cells_12week.txt

value: 12 week cumulus cells


title: UPN827 cells, TN46 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN46 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: NTM-infected, autoantibody-positive, scRNA seq of patient 1

description: Library name: R22007489-A104-jiace-A104_combined


title: UPN827 cells, TN45 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN45 TrailNet Baseline T1D plasma


title: UPN827 cells, TN44 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN44 TrailNet Baseline T1D plasma


title: DO iPSC line 208, untreated

description: Library name: DO_iPSC_208_CTRL


title: RNA library from 12 weeks IVF cumulus cells 2

description:
Library name: 126_4_GC
126_4_GC
summary_count_cumulus_cells_12week.txt

value: Female


title: DO iPSC line 207, triphenyl phosphate treated

description: Library name: DO_iPSC_207_TPHP

source_name: DO iPSC 207

value: DO iPSC 207


title: Primary HUVECs, ACSS2 + PDK4 siRNA, 6 days, 1% O2 30h_3

city: HANGZHOU

first: Yunyun

last: Wang

address: Yuhangtang Road 866

institute: Zhejiang University

description: Library name: PS_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: MSU_V7.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Cells at passage 4

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Human Umbilical Vein

value: Primary HUVECs

value: ACSS2 + PDK4 knockdown

value: siRNA and hypoxia


title: Primary HUVECs, ACSS2 + PDK4 siRNA, 6 days, 1% O2 30h_2

description: Library name: PS_2


title: RNA library from 12 weeks IVF cumulus cells 1

description:
Library name: 126_3_GC
126_3_GC
summary_count_cumulus_cells_12week.txt


title: UPN827 cells, TN42 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN42 TrailNet Baseline T1D plasma


title: UPN827 cells, TN43RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN43RH2 TrailNet Baseline T1D plasma


title: DO iPSC line 207, untreated

description: Library name: DO_iPSC_207_CTRL

value: iPSC


title: UPN827 cells, TN41 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN41 TrailNet Baseline T1D plasma


title: Primary HUVECs, ACSS2 + PDK4 siRNA, 6 days, 1% O2 30h_1

description: Library name: PS_1


title: DO iPSC line 204, triphenyl phosphate treated

description: Library name: DO_iPSC_204_TPHP

source_name: DO iPSC 204

value: DO iPSC 204


title: RNA library from 12 weeks IVF single oocyte 39

description:
Library name: 127_3_7
127_3_7
summary_count_12weeks_single_oocytes.txt

source_name: 12 week single oocyte

value: 12 week single oocyte


title: RNA library from 12 weeks IVF single oocyte 40

description:
Library name: 127_3_8
127_3_8
summary_count_12weeks_single_oocytes.txt


title: Primary HUVECs, ACSS2 siRNA, 6 days, 1% O2 30h_3

description: Library name: ACSS2_3

value: ACSS2 knockdown


title: UPN827 cells, TN40 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN40 TrailNet Baseline T1D plasma

value: UPN827 cells


title: RNA library from 12 weeks IVF single oocyte 38

description:
Library name: 127_3_6
127_3_6
summary_count_12weeks_single_oocytes.txt

value: IVF


title: DO iPSC line 204, untreated

description: Library name: DO_iPSC_204_CTRL

value: untreated


title: Primary HUVECs, ACSS2 siRNA, 6 days, 1% O2 30h_2

description: Library name: ACSS2_2


title: DO iPSC line 193, triphenyl phosphate treated

description: Library name: DO_iPSC_193_TPHP

source_name: DO iPSC 193

value: DO iPSC 193

value: triphenyl phosphate

value: male


title: RNA library from 12 weeks IVF single oocyte 37

description:
Library name: 127_3_5
127_3_5
summary_count_12weeks_single_oocytes.txt


title: Primary HUVECs, ACSS2 siRNA, 6 days, 1% O2 30h_1

description: Library name: ACSS2_1


title: UPN827 cells, TN39 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN39 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 193, untreated

description: Library name: DO_iPSC_193_CTRL


title: RNA library from 12 weeks IVF single oocyte 36

description:
Library name: 127_3_4
127_3_4
summary_count_12weeks_single_oocytes.txt

value: Female


title: Primary HUVECs, Scramble siRNA, 6 days, 1% O2 30h_3

description: Library name: Scra_3

value: Scramble


title: UPN827 cells, TN38 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN38 TrailNet Baseline T1D plasma


title: DO iPSC line 192, triphenyl phosphate treated

description: Library name: DO_iPSC_192_TPHP

source_name: DO iPSC 192

value: DO iPSC 192


title: UPN827 cells, TN37 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN37 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks IVF single oocyte 35

description:
Library name: 127_3_3
127_3_3
summary_count_12weeks_single_oocytes.txt


title: UPN827 cells, TN36 TrailNet Baseline T1D plasma

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

source_name: UPN827 cells stimulated with TN36 TrailNet Baseline T1D plasma


title: DO iPSC line 192, untreated

description: Library name: DO_iPSC_192_CTRL


title: Primary HUVECs, Scramble siRNA, 6 days, 1% O2 30h_2

description: Library name: Scra_2

value: Human Umbilical Vein

value: Primary HUVECs


title: Primary HUVECs, Scramble siRNA, 6 days, 1% O2 30h_1

description: Library name: Scra_1

value: siRNA and hypoxia


title: RNA library from 12 weeks IVF single oocyte 34

description:
Library name: 127_3_2
127_3_2
summary_count_12weeks_single_oocytes.txt


title: DO iPSC line 190, triphenyl phosphate treated

description: Library name: DO_iPSC_190_TPHP

source_name: DO iPSC 190

value: DO iPSC 190

value: iPSC


title: UPN827 cells, TN35 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN35 TrailNet Baseline T1D plasma


title: DO iPSC line 190, untreated

description: Library name: DO_iPSC_190_CTRL


title: RNA library from 12 weeks IVF single oocyte 33

description:
Library name: 127_3_1
127_3_1
summary_count_12weeks_single_oocytes.txt

value: 12 week single oocyte


title: DNAseq_ChIPseq_control_repB

city: Los Angeles

first: Aram

last: Modrek

state: Ca

address: 1441 EastLake Ave

institute: USC

description: Library name: DNAseq_ChIPseq_control_B

library_source: genomic

data_processing:
To assess the frequency and distribution of small insertions and deletions (indels) and large structural variants (SVs) arising from CRISPR–Cas9-induced DNA double-strand breaks, we used separate, tailored analysis pipelines based on the sequencing assay. In both analysis pipelines, we constricted the analysis to verified cut sites and the pulled down regions that achieved coverage levels exceeding 100X. ENCODE defined blacklisted regions were filtered out. For small indel analysis, we applied the crispr-DART (Downstream Analysis and Reporting Tool) pipeline (9). Paired-end Illumina reads were subjected to quality control using FastQC (version 0.11.7) and trimmed with Trim Galore, followed by alignment to the human reference genome (hg38) using BBMap. To enhance detection sensitivity, reads overlapping putative indels were realigned using the Genome Analysis Toolkit GATK (version 3.8.0) for local realignment around indels and base quality score recalibration. Indel frequency profiles were visualized using IGV (version 2.18) and aggregated into heatmaps with deeptools (v3.5.1) using BigWig files output by crispr-DART.
For large SV analysis, we followed a parallel preprocessing workflow. Raw paired-end reads underwent quality control using FastQC (version 0.11.7) and adapter trimming via Trimmomatic (version 0.36). Reads were aligned to hg38 with BWA-MEM (version 0.7.17), and duplicates were removed using sambamba (version 0.6.8). BAM files were processed with GATK (v3.8.0) for local realignment around indels and base quality score recalibration. These realigned and recalibrated BAMs were used for structural variant calling with DELLY (version 0.8.1). DELLY identified deletions, duplications, inversions, and translocations using split-read and paired-end evidence from tumor-versus-control BAM comparisons. Output .bcf files were converted to .vcf using bcftools, and high-confidence SVs were annotated and visualized using Circos and other genome plotting tools.
Assembly: GRCh38/hg38
Supplementary files format and content: Small indels are represented in .bigwig files as scores (deletions, insertions and indels). Large structural variants are represented in .vcf files, wherin the control acts as the control baseline comparison.

molecule: genomic DNA

source_name: Brain tumor

growth_protocol: Patient derived glioma stem-like cultures (GSCs) were cultured in serum free media, as detailed in a publication from (Bhat et al. Cancer Cell 2013).

extract_protocol:
genomic DNA was extracted using the AllPrep genomic DNA/RNA extraction kit (Qiagen)
Two custom biotin-tagged capture panels (xGen DNA panels, Integrated DNA Technologies) were designed to enrich specific DNA regions, each featuring 120 bp probes with one to four probes flanking each targeted cut site, see Supplemental Table S5-6. One panel contained 402 probes (mtg142) and another contained 979 probes (mtg483). The degeneracy of genomic sequences around cut sites prevented the design of probes with high enough specificity to target all sites, therefore only probe/site combinations which could be targeted without significant overlap were included in the panel. Following library construction, the prepared libraries were hybridized with the panels according to the manufacturer’s guidelines, subjected to stringent washes to remove nonspecific fragments, and subsequently PCR-amplified. The enriched libraries were purified and assessed for quality with a tapestation prior to sequencing. Sequencing was multiplexed and performed on a MiSeq 2000 with 10% PhiX spike-in.

treatment_protocol: Treated with 10 ng/uL doxycycline for 3 hours to induce CRISPR-Cas9 guide RNA expression.

value: Brain tumor

value: human glioblastmoma (patient derived)

value: control


title: UPN827 cells, TN34 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 TN34 TrailNet Baseline T1D plasma

value: UPN827 cells


title: RNA library from 12 weeks IVF single oocyte 32

description:
Library name: 127_2_8
127_2_8
summary_count_12weeks_single_oocytes.txt

value: IVF


title: DNAseq_ChIPseq_control_repA

description: Library name: DNAseq_ChIPseq_control_A


title: DO iPSC line 177, triphenyl phosphate treated

description: Library name: DO_iPSC_177_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 177

value: DO iPSC 177

value: triphenyl phosphate


title: RNA library from 12 weeks IVF single oocyte 31

description:
Library name: 127_2_7
127_2_7
summary_count_12weeks_single_oocytes.txt


title: DNAseq_ChIPseq_c483_2wk_repB

description: Library name: DNAseq_ChIPseq_c483_2wk_B

value: mtgRNA


title: UPN827 cells, TN33 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN33 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN32 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN32 TrailNet Baseline T1D plasma


title: DO iPSC line 177, untreated

description: Library name: DO_iPSC_177_CTRL

value: untreated

value: male


title: RNA library from 12 weeks IVF single oocyte 30

description:
Library name: 127_2_6
127_2_6
summary_count_12weeks_single_oocytes.txt

value: Female


title: DNAseq_ChIPseq_c483_2wk_repA

description: Library name: DNAseq_ChIPseq_c483_2wk_A


title: UPN827 cells, TN31 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN31 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks IVF single oocyte 29

description:
Library name: 127_2_5
127_2_5
summary_count_12weeks_single_oocytes.txt


title: DO iPSC line 174, triphenyl phosphate treated

description: Library name: DO_iPSC_174_TPHP

source_name: DO iPSC 174

value: DO iPSC 174

value: female


title: DNAseq_ChIPseq_c483_3hr_repB

description: Library name: DNAseq_ChIPseq_c483_3hr_B


title: DO iPSC line 174, untreated

description: Library name: DO_iPSC_174_CTRL


title: RNA library from 12 weeks IVF single oocyte 28

description:
Library name: 127_2_4
127_2_4
summary_count_12weeks_single_oocytes.txt

source_name: 12 week single oocyte


title: DNAseq_ChIPseq_c483_3hr_repA

description: Library name: DNAseq_ChIPseq_c483_3hr_A


title: DO iPSC line 173, triphenyl phosphate treated

description: Library name: DO_iPSC_173_TPHP

source_name: DO iPSC 173

value: DO iPSC 173


title: RNA library from 12 weeks IVF single oocyte 27

description:
Library name: 127_2_3
127_2_3
summary_count_12weeks_single_oocytes.txt


title: UPN827 cells, TN30 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN30 TrailNet Baseline T1D plasma


title: UPN827 cells, TN29 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN29 TrailNet Baseline T1D plasma


title: DNAseq_ChIPseq_c142_2wk_repB

description: Library name: DNAseq_ChIPseq_c142_2wk_B


title: DO iPSC line 173, untreated

description: Library name: DO_iPSC_173_CTRL

value: iPSC


title: RNA library from 12 weeks IVF single oocyte 26

description:
Library name: 127_2_2
127_2_2
summary_count_12weeks_single_oocytes.txt

value: 12 week single oocyte


title: DO iPSC line 171, triphenyl phosphate treated

description: Library name: DO_iPSC_171_TPHP

source_name: DO iPSC 171

value: DO iPSC 171


title: UPN827 cells, TN28 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN28 TrailNet Baseline T1D plasma


title: DNAseq_ChIPseq_c142_2wk_repA

description: Library name: DNAseq_ChIPseq_c142_2wk_A

value: Brain tumor

value: human glioblastmoma (patient derived)


title: DNAseq_ChIPseq_c142_3hr_repB

description: Library name: DNAseq_ChIPseq_c142_3hr_B


title: UPN827 cells, TN27 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN27 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 171, untreated

description: Library name: DO_iPSC_171_CTRL


title: DO iPSC line 170, triphenyl phosphate treated

description: Library name: DO_iPSC_170_TPHP

source_name: DO iPSC 170

value: DO iPSC 170


title: UPN827 cells, TN26 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN26 TrailNet Baseline T1D plasma


title: UPN827 cells, TN24 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN24 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks IVF single oocyte 23

description:
Library name: 126_4_7
126_4_7
summary_count_12weeks_single_oocytes.txt

value: IVF


title: UPN827 cells, TN25 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN25 TrailNet Baseline T1D plasma


title: DO iPSC line 170, untreated

description: Library name: DO_iPSC_170_CTRL