title: 3_4_19_TWM1_C_GCTCGA_R1

description:
Library name: 12685_5751_144693_HW3JMBGXJ_NSF023_D04_3_4_19_TWM1_C_GCTCGA_R1
Total RNA single illumina

extract_protocol:
Total RNA was extracted from grapevine bud tissue using a modified CTAB protocol or standard commercial RNA isolation kit optimized for woody plant tissues. RNA quality and quantity were assessed using an Agilent Bioanalyzer or NanoDrop spectrophotometer to ensure high-quality material prior to library preparation.
Sequencing libraries were constructed using the Illumina TruSeq RNA Library Prep Kit following the manufacturer's standard protocols. Poly-A selected mRNA was fragmented, converted to cDNA, ligated with TruSeq adapters, and PCR amplified to generate single-end sequencing libraries.

value: Controlled Chilling


title: MSR scaffold from mice vaccinated with EZM2302 vaccine, bio rep4s

status: Public on Jun 30 2026

type: SRA

city: Boston

first: Xixi

last: Zhang

state: Massachusetts

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

description: Library name: EZM2302-4s

library_source: transcriptomic

data_processing:
Paired-end sequence reads were aligned to mouse mm10 using STAR.  Quality metrics were assessed using Samtools.Transcript counts from aligned reads were quantified using Salmon3, then summarized to the gene level using the R package Tximport4.Sequencing depth was normalized between samples using the median of ratios method in R package DESeq2.
Assembly: Mouse mm10
Supplementary files format and content: Raw count matrix
Supplementary files format and content: Normalized counts for each indicated samples

molecule: total RNA

organism: Mus musculus

source_name: vaccination site

extract_protocol:
RNA was extracted by Trizol following manufacturer's protocol; 500ng of total RNA was used for construction of sequencing libraries.
RNA library preparation and sequencing were conducted at Azenta Life Sciences (South Plainfield, NJ, USA).

tag: tissue

value: vaccination site


title: ex_vivo_expanded_cKITenriched_cells_mouse2_L2_HTO

city: Warsaw

first: Vladyslava

last: Liudkovska

address: Flisa 6

country: Poland

institute: IMol Polish Academy of Sciences

description:
Library name: mouse_2_HTO_L2
10x Genomics
CITE-seq hashing (HTO) – sample demultiplexing only

library_source: other

data_processing:
For single cell profiling, FASTQ files were processed using Cell Ranger (v7.2.0), with gene expression counts quantified through the cellranger count function. The resulting h5 object was analyzed in R (v4.2.2) using Seurat (v4.4.0). Sample demultiplexing was performed with MULTIseqDemux from Seurat (https://satijalab.org/seurat/reference/multiseqdemux), and normalization was applied using the Centered Log Ratio (CLR) method.
Assembly: GRCm39
Supplementary files format and content: the .h5 file stores the gene expression count matrix and associated metadata for single-cell RNA-seq experiment
Library strategy: CITE-seq

molecule: protein

source_name: bone marrow

growth_protocol: Bone marrow cells were enriched for the cKit-positive fraction using MACS separation (Miltenyi Biotec) and plated at 100,000 cells per well in a fibronectin-coated (100 ng/mL, Sigma-Aldrich) 96-well plate in hematopoietic stem cell (HSC) expansion medium. HSC expansion medium consisted of Ham’s F-12 Nutrient Mix (Gibco) supplemented with 1% Insulin-Transferrin-Selenium-Ethanolamine (ITS-X, Gibco), 1% penicillin/streptomycin/glutamine (Gibco), 1% HEPES (Gibco), 1 mg/mL polyvinyl alcohol (PVA, Sigma-Aldrich), 10 ng/mL animal-free recombinant stem cell factor (SCF, Peprotech), and 100 ng/mL thrombopoietin (TPO, Peprotech). All cells were cultured at 37°C in 5% CO₂ and routinely tested for mycoplasma contamination using PCR.

extract_protocol:
For CITE-seq, cell suspensions containing 2.5 × 10⁶ cells per sample were pooled and centrifuged at 300 × g at 4°C for 10 minutes. Each pool included a sample from each tested condition, with replicates separated across different pools to control for batch effects. Next, cells were resuspended in 100 µL PBS and filtered through 40 µm Flowmi™ cell strainers (Scienceware). Cell density and viability were assessed using an EVE™ Automatic Cell Counter (NanoEnTek Inc., USA). If necessary, the cell suspension was diluted to a final density of 2,000 – 10,000 cells/µL. Sample pools were processed in quadruplicates, with each replicate loaded onto a separate chip well (Chip G, 10x Genomics).
Cell encapsulation and library preparation were performed using the Chromium Controller (10x Genomics) and the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 with Feature Barcoding technology for Cell Surface Protein (10x Genomics), following the manufacturer's user guide (CG000206 Rev D). Library quality and quantity were assessed using a High-Sensitivity DNA Kit (Agilent Technologies, USA) on a 2100 Bioanalyzer (Agilent Technologies, USA). Samples were sequenced on a NovaSeq 6000 in paired-end mode (Read 1: 28 cycles, i7 index read: 8 cycles, i5 index read: 0 cycles, Read 2: 91 cycles). The sequencing depth was targeted at 4 × 10⁴ mRNA reads and 7 × 10³ Ab-oligo reads per cell.

treatment_protocol: For CRISPR/Cas9 editing of the Sf1 5′ UTR we designed a gRNA oligonucleotide  with the CRISPR-Cas9 gRNA Design Checker and UCSC Genome Browser (Integrated DNA Technologies). Functional CRISPR-Cas9 complexes were assembled with the Alt-R® CRISPR-Cas9 Guide RNA Kit (Integrated DNA Technologies and cells were nucleofected using the P3 Primary Cell 4D X Kit (Lonza) with the DS-130 program. Single cell RNA sequencing with CITE-seq tagging was performed after 21 days of ex vivo expansion.

value: bone marrow

tag: cell line

value: primary

tag: cell type

value: hematopoietic stem and progenitor cells

tag: genotype

value: wild type C57Bl6

tag: treatment

value: pooled samples (CTRL, Sf1 del(51–100), Sf1 del(251–300)); CITE-seq hashed

tag: mouse


title: Genome-wide BRIE screen day 5 chronic stimulation Prdm1-low bin

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street, Room 6032

department: Cell Circuits Program / Center for Cell Circuits

institute: Broad Institute

description:
Library name: D5_cont_prdm1_low
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells were maintained on anti-CD3/CD28-coated plates for chronic stimulation, collected on day 5, stained for Prdm1, and sorted into the Prdm1-low bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_cont_prdm1_low in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

library_source: genomic

data_processing:
Guide sequencing reads were processed with PoolQ using sample-barcode or condition tables and the corresponding guide sequence sets.
Supplementary files format and content: Tab-delimited guide-by-sample count matrices. Rows are sgRNAs with guide sequence, guide identifier, and target-gene fields where available; columns contain complete sgRNA counts for the submitted samples or conditions.
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: spleen and lymph node

growth_protocol: Primary Cas9-expressing mouse CD8 T cells were isolated from spleen and lymph node and transduced with pooled sgRNA lentiviral libraries on RetroNectin-coated plates in complete T cell medium containing IL-7, IL-15, and LentiBOOST. Cells were maintained without TCR activation through day 5 post-transduction before Thy1.1 enrichment or screen-specific culture. For in vivo Tcf7 sort screens, transduced Cas9 x OT-I CD8 T cells were transferred into congenic recipient mice, and recipients were implanted bilaterally with B16-OVA tumors 1 day after T cell transfer.

extract_protocol:
Genomic DNA was isolated from sorted cell populations, input cell populations, tumor-infiltrating T cell samples, draining-lymph-node samples, or plasmid-library controls for guide-count sequencing. Standard cell pellets were processed using QIAamp DNA Mini Kit or QIAamp Mini spin-column workflows. Fixed or low-input sorted material was recovered using SPRI-based DNA cleanup where appropriate. Tumor-infiltrating T cell guide-count samples were prepared from tumor digests enriched over Lympholyte-M and/or with CD8 TIL MicroBeads before pelleting or freezing for genomic DNA isolation. The extracted genomic DNA or plasmid DNA was used as input for integrated sgRNA cassette amplification.
Integrated sgRNA cassettes were amplified from genomic DNA using indexed Illumina-compatible primers following Broad/GPP pooled-screen PCR workflows. Standard pXPR guide-count PCR used up to 10 ug genomic DNA per 100 uL reaction with Titanium Taq DNA polymerase, DMSO, a staggered P5 primer mix, and a unique indexed P7 primer. Primer sets were selected for the vector backbone, including pXPR_045-compatible and pXPR_206 or pRDA_206-derived vectors. For lower-input or nested tissue workflows, PCR cycle number was selected by qPCR using Q5 Hot Start high-fidelity polymerase, and available genomic DNA was split across multiple reactions to limit PCR jackpotting. No-template controls and test gels were used to check contamination and expected amplicon size. PCR products were pooled by sample and purified by AMPure XP cleanup, double-sided AMPure XP size selection at 0.6x/1.2x, or gel extraction depending on amplicon workflow and input complexity. Purified amplicons were quantified by Qubit and Bioanalyzer or TapeStation, pooled, and sequenced on Illumina MiSeq or NextSeq instruments using custom sequencing primers where required.

treatment_protocol: In vitro screen samples included unsorted input and plasmid-library controls and sorted Tcf7-, Prdm1-, Eomes-, or Tox-high and -low populations. Acute stimulation used overnight culture on plates coated with anti-CD3 clone 145-2C11 and anti-CD28 clone 37.51 at 5 ug/mL each, followed by culture off stimulation plates in cytokine-containing T cell medium. Chronic stimulation kept cells on anti-CD3/CD28-coated plates throughout the experiment, and hypoxia screens were cultured under 1% oxygen. Tcf7, Prdm1, Eomes, and Tox screens used intracellular transcription-factor staining to identify high- and low-expressing cells except where Tcf7-GFP reporter sorting was used; some Tcf7 sorts were divided into four bins to separate highest and lower-high populations from lowest and higher-low populations. In vivo Tcf7 sort screens recovered input cells, draining-lymph-node samples, tumor-infiltrating Tcf7-high and Tcf7-low fractions, and plasmid-library controls, typically 14 days after tumor implantation; male and female samples were processed separately where indicated.

value: spleen and lymph node

value: CD8 T cells

value: BRIE genome-wide sgRNA library; chronic anti-CD3/CD28 stimulation; day 5 Prdm1-low sort


title: 2_12_19_TWM1_C_TTTATG_R1

city: Brookings

first: Anne

last: Fennell

state: SD

address: Raven Precision Ag Building Box 2100A

department: Agronomy, Horticulture & Plant Science

institute: South Dakota State University

description:
Library name: 12685_5751_144690_HW3JMBGXJ_NSF023_A04_2_12_19_TWM1_C_TTTATG_R1
Total RNA single illumina

data_processing:
1. Quality Control of Raw Reads- Raw RNA-seq reads were assessed for quality using FastQC, and summary reports across all samples were generated using MultiQC.
2. Adapter Trimming and Filtering- Adapter sequences and low-quality bases were removed using Trimmomatic. Since the data consisted of single-end reads, the TruSeq2 single-end adapter file was used during trimming.
3. Reference Genome Preparation- The Vitis vinifera 12Xv2 reference genome assembly and V2.20 GFF3 annotation file were downloaded and prepared for downstream analysis.
4. Genome Index Generation - Genome indices were generated using STAR to facilitate efficient alignment of RNA-seq reads.
5. Read Alignment - Trimmed reads were aligned to the Vitis vinifera reference genome using STAR, producing BAM alignment files for each sample.
Assembly: 6. Gene Expression Quantification- Gene-level read counts were generated using featureCounts  with the V2.20 GFF3 annotation file, retaining gene IDs for downstream expression analysis.
Supplementary files format and content: The processed data file consists of a tab-delimited text matrix file generated by featureCounts. The matrix contains raw, un-normalized digital gene-level counts, where rows correspond to specific unique Gene IDs derived from the Vitis vinifera 12Xv2 (V2.20 GFF3) reference annotation, and columns represent the individual biological samples (replicates) mapped using single-end RNA-seq reads. No normalized values (such as FPKM or TPM) are included in this specific file.

organism: Vitis hybrid cultivar

source_name: Bud

growth_protocol: Standard commercial vineyard management, Tuckers Walk, Garretson SD.

treatment_protocol: Controled chilling (4ºC) in dark.  Field natural chilling temperatures.

value: Bud

value: total RNA

value: single


title: 11_20_18_TWM1_F_CAGCGT_R1

description:
Library name: 12685_5751_144666_HW3JMBGXJ_NSF023_A01_11_20_18_TWM1_F_CAGCGT_R1
Total RNA single illumina

value: Field Chilling


title: 2_12_19_TWM2_C_AACGCC_R1

description:
Library name: 12685_5751_144691_HW3JMBGXJ_NSF023_B04_2_12_19_TWM2_C_AACGCC_R1
Total RNA single illumina


title: Genome-wide BRIE screen day 5 chronic stimulation normoxic input

description:
Library name: D5lib_2_12_cont_normoxic
Unsorted sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells were maintained on anti-CD3/CD28-coated plates for chronic stimulation under standard oxygen conditions and collected on day 5 before transcription-factor sorting to measure input sgRNA representation. Processed guide-count matrix column is D5lib_2_12_cont_normoxic in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; chronic anti-CD3/CD28 stimulation under standard oxygen; day 5 pre-sort input


title: MSR scaffold from mice vaccinated with EZM2302 vaccine, bio rep1s

description: Library name: EZM2302-1s


title: Genome-wide BRIE screen day 5 hypoxic stimulation Tox-low bin

description:
Library name: D5_hyp_tox_low
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells were stimulated with anti-CD3/CD28 and cultured under hypoxic 1% oxygen conditions, collected on day 5, stained for Tox, and sorted into the Tox-low bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_hyp_tox_low in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; anti-CD3/CD28 stimulation under 1% oxygen; day 5 Tox-low sort


title: Genome-wide BRIE screen day 5 hypoxic stimulation Tox-high bin

description:
Library name: D5_hyp_tox_high
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells were stimulated with anti-CD3/CD28 and cultured under hypoxic 1% oxygen conditions, collected on day 5, stained for Tox, and sorted into the Tox-high bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_hyp_tox_high in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; anti-CD3/CD28 stimulation under 1% oxygen; day 5 Tox-high sort


title: ex_vivo_expanded_cKITenriched_cells_mouse2_L1_HTO

description:
Library name: mouse_2_HTO_L1
10x Genomics
CITE-seq hashing (HTO) – sample demultiplexing only


title: EA.hy926 cells, PFOA 100uM, 48h, biological replicate 3

city: Novi Sad

first: Katarina

middle: Dragiša

last: Borković

address: Trg Dositeja Obradovića 3

department: Department for biology and ecology

country: Serbia

institute: University of Novi Sad, Faculty of Sciences

description: Library name: PA_48h_100_3

data_processing:
Raw sequencing reads were subjected to quality control filtering. Reads containing more than 5% ambiguous bases (N), adapter contamination, or more than 20% bases with quality scores below Q15 were removed to generate clean reads.
Sequencing was performed on the DNBSEQ™ platform using paired-end 150 bp reads (PE150).
HISAT was used to align the clean reads to the reference genome (species: Homo sapiens; source: NCBI; reference genome version: GRCh38.p14, https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/, accessed 18 October 2024), while Bowtie2 was used to align the clean reads to reference genes. The average alignment ratio of the sample comparison genome was 98.74%, whereas the average alignment of the gene set was 85.92%; a total of 18048 genes were detected. The analysis of differentially expressed genes (DEGs) was performed by BGI using the DESeq2 method.
Gene expression quantification and differential expression analysis were performed using DESeq2. Differentially expressed genes were identified using thresholds of FDR < 0.05 and |log2 fold change| ≥ 1.
The reference genome used for alignment was Homo sapiens GRCh38.p14 (NCBI).
Assembly: GRCh38.p14
Supplementary files format and content: CSV files contain normalized read count (NRC) values for all detected genes across biological replicates. Separate files correspond to the 48 h, 6-week, and 12-week exposure experiments.
Supplementary files format and content: Processed data files are CSV tables containing normalized read count (NRC) values for all detected genes across biological replicates from each experimental time point (48 h, 6 weeks, and 12 weeks). Columns correspond to GEO library names and rows correspond to annotated human genes.

organism: Homo sapiens

growth_protocol: The human macrovascular endothelial cell line EA.hy926 was maintained as a monolayer culture at 37 °C in a humidified atmosphere containing 5% CO2. The complete culture medium consisted of Dulbecco's Modified Eagle's Medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin solution, 1.5 g/L NaHCO3, 0.11 g/L sodium pyruvate, 10 mM HEPES buffer, and 4% HAT supplement (5 mM sodium hypoxanthine, 20 µM aminopterin, 0.8 mM thymidine). The medium was refreshed every three to four days, with subculturing performed when the cells reached ~90% confluency. Cells were washed twice with phosphate-buffered saline (PBS) and then trypsinized using 0.25% trypsin-ethylenediaminetetraacetic acid solution for 4 min. Following this, complete culture medium was added, and the cells were centrifuged at 400 × g for 5 min. The resulting suspension was mixed with Trypan blue solution and counted using an automated cell counter. Following counting, cells were seeded in appropriate flasks or assay plates.

extract_protocol:
EA.hy926 cells were exposed either to vehicle control (0.05% DMSO) or to PFOA under short-term (1, 10 and 100 µM) and long-term (1, 10 and 100 nM) exposure conditions. Cells were harvested and lysed directly in TRIzol™ Reagent (Invitrogen). Following treatment, cells were washed with PBS and lysed directly in TRIzol™ Reagent (Invitrogen). Total RNA was isolated according to the TRIzol™ manufacturer's protocol using chloroform extraction and isopropanol precipitation. RNA pellets were washed with 75% ethanol, air-dried, and resuspended in DEPC-treated water. RNA concentration and purity were determined using a BioSpec-Nano spectrophotometer (Shimadzu). RNA quality was further assessed by BGI Europe using an Agilent 4150 Bioanalyzer. All samples exhibited high RNA integrity (RIN > 9) and were considered suitable for RNA sequencing.
High-quality total RNA samples were submitted to BGI Europe (Warsaw, Poland) for library preparation and sequencing. RNA quantity and integrity were evaluated using an Agilent 4150 Bioanalyzer prior to library construction. Sequencing libraries were prepared according to the standard BGI mRNA-seq workflow and sequenced on the DNBSEQ™ platform using paired-end 150 bp reads (PE150).

treatment_protocol: For short-term exposure, EA.hy926 cells were plated in 35-mm dishes (0.6 × 10^6 cells per dish; Nunc™, Thermo Scientific) and exposed to either vehicle (0.05% DMSO; 0 µM PFOA – control group) or three micromolar concentrations of PFOA (1 µM, 10 µM, and 100 µM PFOA – treatment groups) the following day. After 48 h of exposure, the cells were rinsed with PBS, collected in 0.5 mL of TRIzol, and the RNA was extracted afterward. In long-term exposure experiments, EA.hy926 cells originating from each flask after 6 and 12 weeks of continuous exposure to either vehicle (0.05% DMSO; 0 nM PFOA – control group) or three nanomolar concentrations of PFOA (1 nM, 10 nM, and 100 nM PFOA – treatment groups) were collected directly during subculturing on Fridays into clean RNase-, DNase-, and pyrogen-free 1.5 mL microcentrifuge tubes (~1 × 10^6 cells per tube). Cells were centrifuged at 400 × g for 5 min, rinsed with PBS, centrifuged again, and stored in 0.5 mL of TRIzol at –80 °C for subsequent RNA isolation.

value: endothelial cells

value: WT

value: 100 uM PFOA

tag: time


title: Genome-wide BRIE screen day 7 chronic stimulation Tcf7-high bin

description:
Library name: D7_cont_tcf7_high
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells were maintained on anti-CD3/CD28-coated plates for chronic stimulation, collected on day 7, stained for Tcf7, and sorted into the Tcf7-high bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D7_cont_tcf7_high in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; chronic anti-CD3/CD28 stimulation; day 7 Tcf7-high sort


title: Genome-wide BRIE screen day 7 chronic stimulation Tcf7-low bin

description:
Library name: D7_cont_tcf7_low
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells were maintained on anti-CD3/CD28-coated plates for chronic stimulation, collected on day 7, stained for Tcf7, and sorted into the Tcf7-low bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D7_cont_tcf7_low in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; chronic anti-CD3/CD28 stimulation; day 7 Tcf7-low sort


title: EA.hy926 cells, PFOA 100uM, 48h, biological replicate 2

description: Library name: PA_48h_100_2


title: ex_vivo_expanded_cKITenriched_cells_mouse2_L2_GEX

description:
Library name: mouse_2_GEX_L2
10x Genomics
scRNA-seq (GEX) – used for gene expression profiling

library_source: transcriptomic single cell

data_processing:
For single cell profiling, FASTQ files were processed using Cell Ranger (v7.2.0), with gene expression counts quantified through the cellranger count function. The resulting h5 object was analyzed in R (v4.2.2) using Seurat (v4.4.0). Sample demultiplexing was performed with MULTIseqDemux from Seurat (https://satijalab.org/seurat/reference/multiseqdemux), and normalization was applied using the Centered Log Ratio (CLR) method.
Assembly: GRCm39
Supplementary files format and content: the .h5 file stores the gene expression count matrix and associated metadata for single-cell RNA-seq experiment

value: bone marrow

value: primary

value: hematopoietic stem and progenitor cells

value: wild type C57Bl6


title: ex_vivo_expanded_cKITenriched_cells_mouse2_L1_GEX

description:
Library name: mouse_2_GEX_L1
10x Genomics
scRNA-seq (GEX) – used for gene expression profiling

value: pooled samples (CTRL, Sf1 del(51–100), Sf1 del(251–300)); CITE-seq hashed


title: Genome-wide BRIE screen day 7 acute stimulation Tcf7-low bin

description:
Library name: D7_std_tcf7_low
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in the standard acute anti-CD3/CD28 stimulation arm were collected on day 7, stained for Tcf7, and sorted into the Tcf7-low bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D7_std_tcf7_low in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: spleen and lymph node

value: CD8 T cells

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation; day 7 Tcf7-low sort


title: Genome-wide BRIE screen day 7 acute stimulation input

description:
Library name: D7lib_std
Unsorted sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells from the standard acute anti-CD3/CD28 stimulation arm were collected on day 7 before transcription-factor sorting to measure input sgRNA representation. Processed guide-count matrix column is D7lib_std in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation; day 7 pre-sort input


title: EA.hy926 cells, PFOA 100uM, 48h, biological replicate 1

description: Library name: PA_48h_100_1


title: Genome-wide BRIE screen day 7 acute stimulation Tcf7-high bin

description:
Library name: D7_std_tcf7_high
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in the standard acute anti-CD3/CD28 stimulation arm were collected on day 7, stained for Tcf7, and sorted into the Tcf7-high bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D7_std_tcf7_high in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation; day 7 Tcf7-high sort


title: MSR scaffold from mice vaccinated with EZM2302 vaccine, bio rep4

description: Library name: EZM2302-4

value: vaccination site


title: MSR scaffold from mice vaccinated with EZM2302 vaccine, bio rep2

description: Library name: EZM2302-2


title: Genome-wide BRIE screen day 5 acute stimulation replicate 2 Tcf7-high bin

description:
Library name: D5_std2_tcf7_high
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in standard acute anti-CD3/CD28 stimulation replicate 2 were collected on day 5, stained for Tcf7, and sorted into the Tcf7-high bin, the highest of four Tcf7-expression bins. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_std2_tcf7_high in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 2; day 5 Tcf7-high sort


title: ex_vivo_expanded_cKITenriched_cells_mouse1_L2_HTO

description:
Library name: mouse_1_HTO_L2
10x Genomics
CITE-seq hashing (HTO) – sample demultiplexing only


title: Genome-wide BRIE screen day 5 acute stimulation replicate 2 Tcf7 high-middle bin

description:
Library name: D5_std2_tcf7_HM
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in standard acute anti-CD3/CD28 stimulation replicate 2 were collected on day 5, stained for Tcf7, and sorted into the Tcf7 high-middle bin, the second-highest of four Tcf7-expression bins. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_std2_tcf7_HM in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 2; day 5 Tcf7 high-middle sort


title: MSR scaffold from mice vaccinated with control vaccine, bio rep6

description: Library name: Ctrl-6


title: Genome-wide BRIE screen day 5 acute stimulation replicate 2 Tcf7 low-middle bin

description:
Library name: D5_std2_tcf7_LM
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in standard acute anti-CD3/CD28 stimulation replicate 2 were collected on day 5, stained for Tcf7, and sorted into the Tcf7 low-middle bin, the second-lowest of four Tcf7-expression bins. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_std2_tcf7_LM in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 2; day 5 Tcf7 low-middle sort


title: EA.hy926 cells, PFOA 10uM, 48h, biological replicate 3

description: Library name: PA_48h_10_3

value: endothelial cells

value: WT

value: 10 uM PFOA


title: ex_vivo_expanded_cKITenriched_cells_mouse1_L1_HTO

description:
Library name: mouse_1_HTO_L1
10x Genomics
CITE-seq hashing (HTO) – sample demultiplexing only

value: bone marrow


title: Genome-wide BRIE screen day 5 acute stimulation replicate 2 Tcf7-low bin

description:
Library name: D5_std2_tcf7_low
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in standard acute anti-CD3/CD28 stimulation replicate 2 were collected on day 5, stained for Tcf7, and sorted into the Tcf7-low bin, the lowest of four Tcf7-expression bins. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_std2_tcf7_low in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 2; day 5 Tcf7-low sort


title: EA.hy926 cells, PFOA 10uM, 48h, biological replicate 2

description: Library name: PA_48h_10_2


title: Genome-wide BRIE screen day 5 acute stimulation replicate 1 Tcf7-high bin

description:
Library name: D5_std1_tcf7_high
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in standard acute anti-CD3/CD28 stimulation replicate 1 were collected on day 5, stained for Tcf7, and sorted into the Tcf7-high bin, the highest of four Tcf7-expression bins. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_std1_tcf7_high in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 1; day 5 Tcf7-high sort


title: ex_vivo_expanded_cKITenriched_cells_mouse1_L2_GEX

description:
Library name: mouse_1_GEX_L2
10x Genomics
scRNA-seq (GEX) – used for gene expression profiling

value: primary

value: hematopoietic stem and progenitor cells

value: wild type C57Bl6


title: Genome-wide BRIE screen day 5 acute stimulation replicate 2 input

description:
Library name: D5lib_std2
Unsorted sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells from replicate 2 of the day-5 standard acute anti-CD3/CD28 stimulation arm were collected before Tcf7-expression bin sorting to measure input sgRNA representation. Processed guide-count matrix column is D5lib_std2 in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: spleen and lymph node

value: CD8 T cells

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 2; day 5 pre-sort input


title: EA.hy926 cells, PFOA 10uM, 48h, biological replicate 1

description: Library name: PA_48h_10_1


title: ex_vivo_expanded_cKITenriched_cells_mouse1_L1_GEX

description:
Library name: mouse_1_GEX_L1
10x Genomics
scRNA-seq (GEX) – used for gene expression profiling

value: pooled samples (CTRL, Sf1 del(51–100), Sf1 del(251–300)); CITE-seq hashed


title: Genome-wide BRIE screen day 5 acute stimulation replicate 1 Tcf7 high-middle bin

description:
Library name: D5_std1_tcf7_HM
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in standard acute anti-CD3/CD28 stimulation replicate 1 were collected on day 5, stained for Tcf7, and sorted into the Tcf7 high-middle bin, the second-highest of four Tcf7-expression bins. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_std1_tcf7_HM in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 1; day 5 Tcf7 high-middle sort


title: Genome-wide BRIE screen day 5 acute stimulation replicate 1 Tcf7 low-middle bin

description:
Library name: D5_std1_tcf7_LM
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in standard acute anti-CD3/CD28 stimulation replicate 1 were collected on day 5, stained for Tcf7, and sorted into the Tcf7 low-middle bin, the second-lowest of four Tcf7-expression bins. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_std1_tcf7_LM in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 1; day 5 Tcf7 low-middle sort


title: EA.hy926 cells, PFOA 1uM, 48h, biological replicate 3

description: Library name: PA_48h_1_3

value: 1 uM PFOA


title: Sf1_5UTR_del_rep4

description: Library name: Sf1_5UTR_del51_100nt_replicate4

data_processing:
Demultiplexing of sequencing reads was performed with Illumina bcl2fastq (version 2.20). Adapters were trimmed using Skewer (version 0.2.2) (9). Quality trimming of the reads was not performed. Sequencing reads were demultiplexed with Illumina bcl2fastq (version 2.20). Adapters were trimmed using Skewer (version 0.2.2) (53). The quality of the FASTQ files was assessed using FastQC (version 0.11.5-cegat) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). RNA-seq datasets were aligned to the GRCm39 (Ensembl release 111) mouse genome using STAR v2.5.2b. Read counts were assigned to genes using featureCounts from the Subread package (2.0.1) with options -p -s 2 -g gene_id -t exon and respective annotation file (GENCODE vM34). Multimappers and reads overlapping multiple features were not counted. Differential gene expression was analyzed using the Bioconductor package DESeq2 (version 1.42.1), with batch correction.
Assembly: GRCm39
Supplementary files format and content: gene counts in .txt format

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MicroPrep (Zymo Research) according to the manufacturer’s protocol, including in-column DNase treatment. RNA quality and quantity were assessed using the RNA 6000 Nano LabChip Bioanalyzer (Agilent Technologies).
Libraries were constructed from 100 ng of total RNA using the KAPA RNA HyperPrep with RiboErase (HMR) and KAPA Globin Depletion Hybridization Oligos (Roche). Library quality was verified using the Bioanalyzer High Sensitivity DNA kit (Agilent Technologies), and sequencing was performed on the NovaSeq 6000 platform (2 × 101 cycles, Illumina).

treatment_protocol: For CRISPR/Cas9 editing of the Sf1 5′ UTR we designed a gRNA oligonucleotide  with the CRISPR-Cas9 gRNA Design Checker and UCSC Genome Browser (Integrated DNA Technologies). Functional CRISPR-Cas9 complexes were assembled with the Alt-R® CRISPR-Cas9 Guide RNA Kit (Integrated DNA Technologies and cells were nucleofected using the P3 Primary Cell 4D X Kit (Lonza) with the DS-130 program.  Bulk RNA sequencing was performed after 21 days of ex vivo expansion.

value: hematopoietic stem and progenitor cells, expanded for 21 days

value: deletion in 5' UTR Sf1 position 51-100 nt


title: Genome-wide BRIE screen day 5 acute stimulation replicate 1 input

description:
Library name: D5lib_std1
Unsorted sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells from replicate 1 of the day-5 standard acute anti-CD3/CD28 stimulation arm were collected before Tcf7-expression bin sorting to measure input sgRNA representation. Processed guide-count matrix column is D5lib_std1 in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 1; day 5 pre-sort input


title: Genome-wide BRIE screen day 5 acute stimulation replicate 1 Tcf7-low bin

description:
Library name: D5_std1_tcf7_low
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in standard acute anti-CD3/CD28 stimulation replicate 1 were collected on day 5, stained for Tcf7, and sorted into the Tcf7-low bin, the lowest of four Tcf7-expression bins. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_std1_tcf7_low in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation replicate 1; day 5 Tcf7-low sort


title: EA.hy926 cells, PFOA 1uM, 48h, biological replicate 2

description: Library name: PA_48h_1_2

value: endothelial cells

value: WT


title: Control_rep4

description: Library name: Control_replicate4

value: bone marrow

value: non-targeting control


title: LCMV D7 post-transduction with stimulation Thy1.1 negative rep 13

description:
Library name: LCMV_D7_lenti_stim_Thy1neg_rep_13
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_13_Thy1neg

data_processing:
Salmon NumReads were summed to gene-level counts, rounded, filtered to nonzero-count genes, normalized with DESeq2.
Assembly: GRCm38/mm10 mouse reference; GENCODE vM25 annotation for transcript-to-gene assignment.
Supplementary files format and content: naive_lenti_activated_normalized_counts.tsv: tab-delimited gene-by-sample matrix containing complete DESeq2-normalized expression values for the 27 CD8 T cell state bulk RNA-seq libraries. Rows are genes; columns are submitted sample/library identifiers.
Supplementary files format and content: day30_mem_normalized_counts.tsv: tab-delimited gene-by-sample matrix containing complete DESeq2-normalized expression values for the 59 day-30 memory P14 CD8 T cell bulk RNA-seq libraries. Rows are genes; columns are submitted sample/library identifiers.

source_name: spleen

growth_protocol: P14 CD8 T cells were isolated from mouse spleen and lymph node. For the lenti naive condition, naive P14 CD8 T cells were transduced using the naive-state-preserving lentiviral workflow and maintained without TCR stimulation before transfer. For the lenti-activated condition, P14 CD8 T cells were transduced and activated with anti-CD3/CD28 before transfer. Experimental donor populations were mixed with freshly isolated congenically marked naive P14 CD45.1+CD45.2+ CD8 T cells as cotransferred controls, and recipient mice were infected with LCMV Armstrong after transfer.

extract_protocol:
T cell populations were sorted on a Sony cell sorter into 96-well plates at 1,000 cells per well in lysis buffer consisting of TCL buffer supplemented with 1% 2-mercaptoethanol, then frozen before RNA capture and cDNA synthesis. RNA was isolated using SPRI beads and eluted directly into oligo-dT/dNTP-containing reverse-transcription mix.
Full-length cDNA was generated using the Smart-seq2 protocol with SuperScript II reverse transcriptase, a template-switching oligonucleotide, and RNase inhibitor. cDNA was amplified by whole-transcriptome amplification using KAPA HiFi HotStart ReadyMix, purified with SPRI beads, quantified, and assessed by Bioanalyzer or TapeStation. Sequencing libraries were prepared from amplified cDNA using Nextera XT tagmentation with indexed adapters, pooled, and sequenced on Illumina NextSeq platforms at the Broad Institute Genomics Platform.

value: spleen

value: day 7 post infection post-transduction with stimulation; Thy1.1 negative


title: LCMV D7 post-transduction with stimulation Thy1.1 positive rep 13

description:
Library name: LCMV_D7_lenti_stim_Thy1pos_rep_13
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_13_Thy1pos

value: day 7 post infection post-transduction with stimulation; Thy1.1 positive


title: Sf1_5UTR_del_rep3

description: Library name: Sf1_5UTR_del51_100nt_replicate3

value: primary

value: wild type C57Bl6


title: LCMV D7 post-transduction with stimulation Thy1.1 positive rep 12

description:
Library name: LCMV_D7_lenti_stim_Thy1pos_rep_12
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_12_Thy1pos

value: CD8 T cells


title: LCMV D7 post-transduction with stimulation Thy1.1 negative rep 12

description:
Library name: LCMV_D7_lenti_stim_Thy1neg_rep_12
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_12_Thy1neg


title: LCMV D7 post-transduction with stimulation Thy1.1 positive rep 11

description:
Library name: LCMV_D7_lenti_stim_Thy1pos_rep_11
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_11_Thy1pos


title: ID_441

city: New York City

first: Ragavi

last: Vijayakumar

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: Sloan Kettering Institute

description:
Library name: Sample 54
Ribodepleted bulk RNA_seq

data_processing:
The fastq files were processed using salmon to generate the "quant" files
The "quant" files were used as input for Rstudio (deseq2 package)
Assembly: mm10
Supplementary files format and content: Salmon-outputs

source_name: Diversity Outbred

extract_protocol:
Frozen cells were lysed in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro or Mini Kit (Qiagen catalog # 217084/217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 20-35 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 71-500 ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 or S4 NovaSeq Reagent Kit (200 or 300 Cycles) (Illumina).  An average of 69 million paired reads was generated per sample. Ribosomal reads represented 0.1-1.7% of the total reads generated and the percent of mRNA bases averaged 91%.

value: Diversity Outbred

value: Neural Progenitor Cells


title: EA.hy926 cells, PFOA Control, 48h, biological replicate 3

description: Library name: PA_48h_C_3

value: Control


title: EA.hy926 cells, PFOA Control, 48h, biological replicate 2

description: Library name: PA_48h_C_2


title: LCMV D7 post-transduction with stimulation Thy1.1 negative rep 11

description:
Library name: LCMV_D7_lenti_stim_Thy1neg_rep_11
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_11_Thy1neg


title: Sf1_5UTR_del_rep2

description: Library name: Sf1_5UTR_del51_100nt_replicate2

value: hematopoietic stem and progenitor cells, expanded for 21 days


title: LCMV D7 post-transduction no stimulation Thy1.1 positive rep 9

description:
Library name: LCMV_D7_lenti_no_stim_Thy1pos_rep_9
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_9_Thy1pos

value: day 7 post infection post-transduction with no stimulation; Thy1.1 positive


title: EA.hy926 cells, PFOA Control, 48h, biological replicate 1

description: Library name: PA_48h_C_1


title: LCMV D7 post-transduction no stimulation Thy1.1 negative rep 9

description:
Library name: LCMV_D7_lenti_no_stim_Thy1neg_rep_9
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_9_Thy1neg

value: day 7 post infection post-transduction with no stimulation; Thy1.1 negative


title: Control_rep2

description: Library name: Control_replicate2


title: LCMV D7 post-transduction no stimulation Thy1.1 positive rep 8

description:
Library name: LCMV_D7_lenti_no_stim_Thy1pos_rep_8
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_8_Thy1pos


title: EA.hy926 cells, PFOA 100nM, 12 weeks, biological replicate 3

description: Library name: PA_12w_100_3

value: 100 nM PFOA

value: 12 weeks


title: LCMV D7 post-transduction no stimulation Thy1.1 negative rep 8

description:
Library name: LCMV_D7_lenti_no_stim_Thy1neg_rep_8
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_8_Thy1neg


title: Sf1_5UTR_del_rep1

description: Library name: Sf1_5UTR_del51_100nt_replicate1

value: deletion in 5' UTR Sf1 position 51-100 nt


title: LCMV D7 post-transduction no stimulation Thy1.1 positive rep 7

description:
Library name: LCMV_D7_lenti_no_stim_Thy1pos_rep_7
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_7_Thy1pos


title: Control_rep1

description: Library name: Control_replicate1

value: bone marrow


title: LCMV D7 post-transduction no stimulation Thy1.1 negative rep 7

description:
Library name: LCMV_D7_lenti_no_stim_Thy1neg_rep_7
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_7_Thy1neg


title: LCMV D7 untransduced cotransfer control rep 9

description:
Library name: LCMV_D7_untransduced_cotransfer_control_rep_9
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_9_DP

value: day 7 post infection baseline; untransduced cotransfer control; Thy1.1 negative


title: EA.hy926 cells, PFOA 100nM, 12 weeks, biological replicate 1

description: Library name: PA_12w_100_1

value: endothelial cells

value: WT


title: LCMV D7 untransduced cotransfer control rep 13

description:
Library name: LCMV_D7_untransduced_cotransfer_control_rep_13
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_13_DP

value: spleen


title: Post-stimulation rep 4

description:
Library name: stimulated_rep_4
Column name in naive_lenti_activated_normalized_counts.tsv: Tcellsstim_4

value: spleen and lymph node

value: post-stimulation; Thy1.1 not applicable


title: EA.hy926 cells, PFOA 10nM, 12 weeks, biological replicate 3

description: Library name: PA_12w_10_3

value: 10 nM PFOA


title: LCMV D7 untransduced cotransfer control rep 11

description:
Library name: LCMV_D7_untransduced_cotransfer_control_rep_11
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_11_DP

value: CD8 T cells


title: EA.hy926 cells, PFOA 10nM, 12 weeks, biological replicate 2

description: Library name: PA_12w_10_2


title: Post-stimulation rep 3

description:
Library name: stimulated_rep_3
Column name in naive_lenti_activated_normalized_counts.tsv: Tcellsstim_3


title: stomach, day35, Arid1a mutant, ChIP, Esrrg, rep1

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description: Library name: 6ChIPseq_Esrrg_day35_KO_rep1

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using TrimGalore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the bowtie2 aligner (http://bowtie-bio.sourceforge.net/).
bigWig files were generated using Galaxy (usegalaxy.org)
Assembly: mm10
Supplementary files format and content: BIGWIG (wiggle type files using the program wigToBigWig)

source_name: Stomach

growth_protocol: Arid1a mice were grwon and stomachs glands were isolated after 0, 7 or 35 days after the treatment.

extract_protocol:
Tissue and cells were lysed and chromatin pellets were isolated, and then solubilized and fragmented by sonication. Fragmented chromatin was then subject to immunoprecipitation using antibodies against the protein of interest.
ChIP-seq libraries were prepared according to the standard Illumina protocols. Briefly, DNA was end-repaired and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: Arid1a mice were treated with 5mg/20g tamoxifen for 3 consecutive days.

value: Stomach

value: Arid1a mutant

tag: antibody

value: Esrrg (R&D Systems, PP-H6812-00)

value: Tamoxifen - 35 days after treatment


title: stomach, day35, wt, ChIP, Esrrg, rep2

description: Library name: 5ChIPseq_Esrrg_day35_wt_rep2

value: wt

value: Esrrg (Proteintech, 14017-1-AP)


title: Post-stimulation rep 2

description:
Library name: stimulated_rep_2
Column name in naive_lenti_activated_normalized_counts.tsv: Tcellsstim_2


title: EA.hy926 cells, PFOA 10nM, 12 weeks, biological replicate 1

description: Library name: PA_12w_10_1

value: 12 weeks


title: Post-stimulation rep 1

description:
Library name: stimulated_rep_1
Column name in naive_lenti_activated_normalized_counts.tsv: Tcellsstim_1


title: EA.hy926 cells, PFOA 1nM, 12 weeks, biological replicate 3

description: Library name: PA_12w_1_3

value: 1 nM PFOA


title: Post-transduction no stimulation Thy1.1 positive rep 2

description:
Library name: lenti_no_stim_Thy1pos_rep_2
Column name in naive_lenti_activated_normalized_counts.tsv: Lenti_Thy1Pos_2

value: post-transduction with no stimulation; Thy1.1 positive


title: Post-transduction no stimulation Thy1.1 positive rep 3

description:
Library name: lenti_no_stim_Thy1pos_rep_3
Column name in naive_lenti_activated_normalized_counts.tsv: Lenti_Thy1Pos_3


title: stomach, day35, Arid1a mutant, ChIP, Mist1, rep1

description: Library name: 3ChIPseq_Mist1_day35_KO_rep1

value: Mist1 (D7N4B) (Cell Signaling, 14896)


title: Post-transduction no stimulation Thy1.1 positive rep 1

description:
Library name: lenti_no_stim_Thy1pos_rep_1
Column name in naive_lenti_activated_normalized_counts.tsv: Lenti_Thy1Pos_1


title: stomach, day35, wt, ChIP, Mist1, rep2

description: Library name: 2ChIPseq_Mist1_day35_wt_rep2


title: Post-transduction no stimulation Thy1.1 negative

description:
Library name: lenti_no_stim_Thy1neg
Column name in naive_lenti_activated_normalized_counts.tsv: Lenti_Thy1Neg

value: post-transduction with no stimulation; Thy1.1 negative


title: Baseline naive rep 3

description:
Library name: naive_rep_3
Column name in naive_lenti_activated_normalized_counts.tsv: NaiveCD8_3

value: baseline; Thy1.1 not applicable


title: Baseline naive rep 2

description:
Library name: naive_rep_2
Column name in naive_lenti_activated_normalized_counts.tsv: NaiveCD8_2


title: stomach, day35, wt, ChIP, Mist1, rep1

description: Library name: 1ChIPseq_Mist1_day35_wt_rep1


title: Baseline naive rep 1

description:
Library name: naive_rep_1
Column name in naive_lenti_activated_normalized_counts.tsv: NaiveCD8_1


title: EA.hy926 cells, PFOA Control, 12 weeks, biological replicate 3

description: Library name: PA_12w_C_3

value: endothelial cells

value: WT

value: Control


title: mSIorg_108h

city: Basel

first: Prisca

last: Liberali

address: Klingelbergstrasse 48

department: D-BSSE

country: Switzerland

institute: ETHZ

description: Library name: mSIorg_108h

data_processing:
Raw sequencing reads were processed using the Alevin module of Salmon (v1.2.0) (Patro et al., 2017; Srivastava et al., 2019). Reads were quantified in paired-end mode (-l ISR) using the 10x Genomics Chromium v3 protocol specification (--chromiumV3). Multiple sequencing lanes per sample were combined at the FASTQ level prior to quantification. Quantification was performed against a spliced–unspliced “gentrome” reference derived from GENCODE mouse release M24 (GRCm38), enabling simultaneous estimation of spliced and intronic counts for RNA velocity–compatible analyses. Gene-level quantification was obtained using a transcript-to-gene mapping file (--tgMap), and feature-level output (spliced/unspliced) was generated using the --dumpFeatures option. Cell barcode whitelisting and UMI deduplication were handled internally by Alevin. Quantification uncertainty was estimated using 50 bootstrap replicates (--numCellBootstraps 50). All runs were executed using 32 threads per sample. Quantification outputs were imported into R using tximeta (v1.12.4) (Love et al., 2020), with inferential replicates discarded (dropInfReps = TRUE). Spliced and unspliced counts were separated using splitSE, and spliced counts were used as the primary assay for downstream analyses. Cell barcodes were prefixed with sample identifiers, sample metadata were appended, and samples were merged into a single SingleCellExperiment object (v1.16.0) containing 54,446 features across 43,684 cells.
Gene annotations were added from GENCODE release M24, including gene biotype, gene symbol, Entrez ID and chromosome. Mitochondrial genes were annotated based on chromosome “chrM” and MitoCarta3.0, and ribosomal protein genes were annotated using GO:0003735 with org.Mm.eg.db (v3.14.0) (Rath et al., 2021). Genes were retained if annotated as protein-coding, immunoglobulin, T cell receptor, mitochondrial rRNA or mitochondrial tRNA genes; all other gene biotypes were removed before downstream analysis. Per-cell and per-feature quality control metrics were calculated using scater (v1.22.0) (McCarthy et al., 2017). Cells were retained if they contained >1,200 detected genes and <22% mitochondrial counts. Library-size normalization was performed using scran (v1.22.1) (Lun et al., 2016). Cells were first grouped into coarse clusters using quickCluster, and deconvolution size factors were estimated with computeSumFactors using min.mean = 0.5. Cells with size factors <0.1 were excluded. Log-normalized expression values were computed with logNormCounts and used for downstream analyses.
To preserve transcriptional heterogeneity and ensure representation of rare cell populations, cells were subsampled using geometric sketching as previously applied in large-scale single-cell analyses (Oost, Kahnwald et al., bioRxiv, 2023). In brief, we used sketchR (v0.1.4), an R interface to the geometric sketching strategy described by Hie et al. (2019). PCA was first computed on log-normalized expression values using 100 components, and representative cells were selected with geosketch using a target sketch size corresponding to approximately 10% of cells, with a minimum of 2,000 cells and capped at the total number of cells. Highly variable genes were identified using modelGeneVar in scran with an FDR threshold of 0.05. Variable genes were identified globally and within each experimental condition, and the union of condition-wise variable genes was used for dimensionality reduction. PCA was computed using 30 components. t-SNE embeddings were generated with snifter/FIt-SNE, and UMAP embeddings were generated using uwot (Linderman et al., 2019; McInnes et al., 2018).
Cell type identities were assigned using marker gene set scoring, graph-based clustering and manual annotation. Curated intestinal marker gene sets were scored separately within culture conditions using swissknife::normGenesetExpression, with non-variable genes used as the background set. Sketched cells were converted to a Seurat object (v4.1.0), and a shared nearest-neighbor graph was constructed in the sketch PCA space using FindNeighbors with k = 20 and 30 principal components (Hao et al., 2021). Cells were clustered using FindClusters across resolutions 0.4–4.0, and resolution 3.5 was used for annotation. Clusters were annotated based on marker gene expression, marker gene set scores and timepoint distribution. One mixed enterocyte cluster was split by timepoint, with 24–48 hour cells annotated as enterocyte reprogramming cells and 60–108 hour cells annotated as mature enterocytes. Cluster labels from sketched cells were transferred to the full dataset by 1-nearest-neighbor classification in sketch PCA space. Final annotations were collapsed into intestinal epithelial cell states, including reprogramming, regenerative, stem/progenitor, secretory and enterocyte-lineage populations.
Assembly: GRCm38/mm10
Supplementary files format and content: barcodes.tsv.gz: gzipped, tab-separated text file with column annotation of the (sparse) alignment count table (genes versus cells). The columns correspond to cell_id (cell identifier), culture medium (intesticult/enr), timepoint (0h, 24h, 36h, 48h, 60h, 72h, 84h, 108h), cell_type (annotated celltype label), TSNE1 (first coordinate for TSNE embedding), TSNE2 (second coordinate for TSNE embedding), UMAP1 (first coordinate for UMAP embedding), UMAP2 (second coordinate for UMAP embedding).
Supplementary files format and content: features.tsv.gz: gzipped, tab-separated text file with row annotation of the (sparse) alignment count table (genes versus cells). The columns correspond to gene symbol, gene_id (ensembl_id), is_variable (logical specifying variable genes used).
Supplementary files format and content: matrix.mtx.gz: gzipped, tab-separated text file with the number of mRNA counts per gene (row) and cell (column), as a sparse matrix in MatrixMarket format.
Supplementary files format and content: matrix_logcounts.mtx.gz: gzipped, tab-separated text file with the log-transformed and normalized expression per gene (row) and cell (column), as a sparse matrix in MatrixMarket format.

source_name: mouse small intestinal organoids

growth_protocol: Small intestinal organoids were derived from the duodenum of a 10-week-old male C57BL/6 wild-type mouse as described in Sato et al, Nature 2009. For amplification and maintenance, organoids were cultured in IntestiCult Organoid Growth Medium (STEMCELL Technologies) with 100 μg/ml Penicillin-Streptomycin. Organoid timecourses were started by performing a single-cell dissociation of the maintenance cultures. Specifically, organoids were collected 6 days after passaging and digested with TripLE (Invitrogen) with 10 μM Y-27632 (ROCK inhibitor; STEMCELL Technologies) for 20 min at 37 °C. Dissociated cells were passed through a cell strainer with a pore size of 30 µm and stained with DRAQ7 dye (Invitrogen). Single cells were isolated by fluorescence-activated cell sorting (FACS; SONY MA900 Cell Sorter) by gating for live (DRAQ7-negative) single cells. Cells were seeded into Matrigel (Corining) droplets (1:1 ratio Matrigel:ENR medium) at a density of 600 cell/ul, marking the start of the organoid timecourse. ENR medium consisted of Advanced DMEM/F-12 with 15 mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin and Streptomycin, 1x Glutamax (Thermo Fisher Scientific), 1x B27 (Thermo Fisher Scientific), 1x N2 (Thermo Fisher Scientific), 1 mM N-acetylcysteine (Sigma), 500 ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (R&D Systems). For the first 24 hr of the timecourse, ENR was supplemented with 25% Wnt3a-conditioned medium (Wnt3a-CM), 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies) and 3 µM of CHIR99021 (STEMCELL Technologies). From 24 to 72 hr, ENR was supplemented with 25% Wnt3a-CM and 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies). From 72 to 108 hr, only ENR was added to the organoids. Wnt3a-CM was produced in-house by Wnt3a L-cells (kind gift from Novartis).

extract_protocol:
Organoids were collected at baseline (0h) and at 12-hour intervals throughout the regeneration timecourse (24-108h) for single cell RNA sequencing. For each timepoint, organoids were collected and digested to a single-cell suspension and FACS sorted as described above. For single-cell RNA sequencing library preparation, 13k cells were sorted per collection vial per timepoint.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s protocol. Gel bead-in-emulsion (GEM) generation, reverse transcription, cDNA amplification, and library construction were performed following standard procedures. Libraries were sequenced on an Illumina NextSeq 500 platform using a 75-cycle kit with paired-end configuration (Read 1: 26 bp; Read 2: 56 bp; single index: 8 bp). Base calling was performed using Illumina RTA (v2.4.11), and FASTQ files were generated using bcl2fastq2 (v2.17).

value: mouse small intestinal organoids

tag: strain

value: intestinal epithelial cells

value: wildtype


title: Floxed control FP28

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

description:
Library name: FP28
10X Genomics

data_processing:
Illumina NovaSeq Control Software (NCS) 1.8.1 was used for the data acquisition on the sequencing instrument and on-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to FASTQ file conversion and demultiplexing was performed with Illumina bcl2fastq2 (2.20).
Short read alignment, counting and cell calling was performed via 10X Genomics Cell Ranger (7.0.0).
Assembly: 10X Genomics refdata-gex-mm10-2020-A, Based on UCSC Genome Browser mm10, based on GRCm38
Supplementary files format and content: 10X Genomics Cell Ranger-filtered count matrices in Hierarchical Data Format 5 (HDF5)

molecule: polyA RNA

source_name: heart

growth_protocol: All animals were kept in sterile conditions in the mouse vivarium in individually ventilated cages (IVCs) with controlled humidity and temperature before and during the treatments.

extract_protocol:
Whole hearts were minced and placed in a digestion solution composed of HBSS (with Ca/Mg), 5% FBS, 2mM EDTA, Collagenase D (450 UI/mL), DNase I (60 UI/mL),and Hyaluronidase (60 UI/mL). The tissue was digested for 45 min at 37°C in a thermomixer. Thereafter, the digested hearts were filtered through a 70µm cell strainer and pelleted by centrifugation (400g, 5 min at 4°C) in HBSS supplemented with 2% FBS + 0.2% BSA. Red blood cell lysis was done using RBC Lysis buffer (Biolegend) and resuspended in PBS containing 2% FBS and 2mM EDTA. Afterwards, samples were labeled with fluorescently tagged CD45 antibodies and cell sorted on a Cell Sorter (Sony MA900).
Cell counting, gel beads-in-emulsion (GEMs) generation, reverse transcritpion and library preparation was performed according to the 10X Genomics Single Cell 3' v3 protocol.

treatment_protocol: Mice were treated via oral gavage with either Linvemastat or vehicle (PBS + DMSO).

value: heart

value: CD45+, some CD45-

value: TSC2 fl/fl

value: Floxed control

tag: Sex

value: Female

tag: age

tag: phenotype


title: EA.hy926 cells, PFOA Control, 12 weeks, biological replicate 2

description: Library name: PA_12w_C_2

value: 12 weeks


title: mSIorg_84h

description: Library name: mSIorg_84h


title: Vehicle-treated FP27

description:
Library name: FP27
10X Genomics

value: TSC2 fl/fl CD11c Cre+

value: Vehicle-treated

value: Male

value: Sarcoidosis


title: mSIorg_72h

description: Library name: mSIorg_72h


title: mSIorg_60h

description: Library name: mSIorg_60h


title: MMP12-inhibitor treated FP26

description:
Library name: FP26
10X Genomics

value: MMP12-inhibitor treated


title: Floxed control FP25

description:
Library name: FP25
10X Genomics


title: EA.hy926 cells, PFOA 100nM, 6 weeks, biological replicate 3

description: Library name: PA_6w_100_3

value: endothelial cells

value: 100 nM PFOA

value: 6 weeks


title: mSIorg_36h_2

description: Library name: mSIorg_36h_2

value: mouse small intestinal organoids


title: EA.hy926 cells, PFOA 100nM, 6 weeks, biological replicate 2

description: Library name: PA_6w_100_2

value: WT


title: Vehicle-treated FP24

description:
Library name: FP24
10X Genomics


title: mSIorg_0h

description: Library name: mSIorg_0h

value: intestinal epithelial cells

value: wildtype


title: EA.hy926 cells, PFOA 100nM, 6 weeks, biological replicate 1

description: Library name: PA_6w_100_1


title: mSIorg_24h

description: Library name: mSIorg_24h


title: mice treated with CCl₄，smf-5

city: Xi'an

first: Xuan

last: Han

state: ShaanXi

address: Medical department of Xi'an JiaoTong University

country: China

institute: Xi'an Jiaotong University

description:
Library name: Sample8
10x Genomics

data_processing:
The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme N411-01), analyzed by Qubit (Thermo Fisher Scientific Qubit 4 Fluorometer) and Bio-Fragment Analyzer (Bioptic Qsep400). The libraries were then sequenced on DNBSEQ-T7 platform with PE150 read length.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
After harvested, tissues were washed in ice-cold PBS (Hyclone SH30256.01) and dissociated using SeekMate Tissue Dissociation Reagent Kit A Pro (SeekGene K01801-30) from SeekGene as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using Fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 (Gibco 11875119) and then resuspended at 1×106 cells per ml in RPMI1640 and 2% FBS (Gibco 10100147C).
Single-cell RNA-Seq libraries were prepared using SeekOne® DD Single Cell 3’ library preparation kit (SeekGene Catalog No.K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation reverse transcription were performed at 42℃for 90 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index.

value: liver

value: treated with CCl₄


title: mice treated with CCl₄，smf-4

description:
Library name: Sample7
10x Genomics


title: EA.hy926 cells, PFOA 10nM, 6 weeks, biological replicate 3

description: Library name: PA_6w_10_3

value: 10 nM PFOA


title: mice treated with CCl₄, smf-2

description:
Library name: Sample5
10x Genomics


title: MMP12-inhibitor treated FP23

description:
Library name: FP23
10X Genomics

value: heart

value: CD45+, some CD45-

value: Female


title: mice treated with CCl₄, smf-3

description:
Library name: Sample6
10x Genomics


title: Genome-wide BRIE screen day 3 input

description:
Library name: D3lib
Unsorted sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. Cas9-expressing CD8 T cells were transduced using the naive state-preserving workflow and collected on day 3 before transcription-factor sorting to measure input sgRNA representation. Processed guide-count matrix column is D3lib in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: spleen and lymph node

value: CD8 T cells

value: BRIE genome-wide sgRNA library; day 3 pre-sort input


title: Vehicle-treated FP21

description:
Library name: FP21
10X Genomics

value: TSC2 fl/fl CD11c Cre+

value: Vehicle-treated

value: Sarcoidosis


title: mice treated with CCl₄, smf-1

description:
Library name: Sample4
10x Genomics


title: EA.hy926 cells, PFOA 1uM, 48h, biological replicate 1

description: Library name: PA_48h_1_1

value: endothelial cells

value: 1 uM PFOA


title: Control_rep3

description: Library name: Control_replicate3

value: bone marrow

value: primary

value: hematopoietic stem and progenitor cells, expanded for 21 days

value: wild type C57Bl6

value: non-targeting control


title: MMP12-inhibitor treated FP20

description:
Library name: FP20
10X Genomics

value: MMP12-inhibitor treated


title: EA.hy926 cells, PFOA 10nM, 6 weeks, biological replicate 2

description: Library name: PA_6w_10_2

value: WT

value: 10 nM PFOA

value: 6 weeks


title: EA.hy926 cells, PFOA 10nM, 6 weeks, biological replicate 1

description: Library name: PA_6w_10_1


title: mice treated with CCl₄, control-3

description:
Library name: Sample3
10x Genomics

value: liver

value: treated with CCl₄


title: mice treated with CCl₄, control-2

description:
Library name: Sample2
10x Genomics


title: Floxed control FP19

description:
Library name: FP19
10X Genomics

value: heart

value: CD45+, some CD45-

value: TSC2 fl/fl

value: Floxed control

value: Female

value: Control


title: mice treated with CCl₄, control-1

description:
Library name: Sample1
10x Genomics


title: EA.hy926 cells, PFOA 1nM, 6 weeks, biological replicate 3

description: Library name: PA_6w_1_3

value: endothelial cells

value: 1 nM PFOA


title: EA.hy926 cells, PFOA 100nM, 12 weeks, biological replicate 2

description: Library name: PA_12w_100_2

value: 100 nM PFOA

value: 12 weeks


title: stomach, day35, Arid1a mutant, ChIP, Esrrg, rep2

description: Library name: 7ChIPseq_Esrrg_day35_KO_rep2

value: Stomach

value: Arid1a mutant

value: Esrrg (Proteintech, 14017-1-AP)

value: Tamoxifen - 35 days after treatment


title: LCMV D7 untransduced cotransfer control rep 12

description:
Library name: LCMV_D7_untransduced_cotransfer_control_rep_12
Column name in naive_lenti_activated_normalized_counts.tsv: LCMV_D7_12_DP

value: spleen

value: CD8 T cells

value: day 7 post infection baseline; untransduced cotransfer control; Thy1.1 negative


title: 80 weeks kidney Pdgfb-knockout

city: Aachen

first: Barbara

middle: Mara

last: Klinkhammer

address: Pauwelsstrasse 30

department: Pathology

country: Germany

institute: RWTH Aachen University

description: Library name: KO kidneys Aging

data_processing:
processed with the publicly available nf-core/RNA-seq pipeline version 3.517 implemented in Nextflow 21.10.6 using Docker 20.10.12 with the minimal command.
Lane-level reads were trimmed using Trim Galore 0.6.7
Aligned to the mouse genome (GRCm39) using STAR 2.7.9a
Assembly: Gene-level and transcript-level quantification was done by Salmon v1.5.2. All analysis was performed using custom scripts in R version 4.1.1 using the DESeq2 v.1.32.0 framework.
Supplementary files format and content: tab-delmited text file with raw count of each sample

source_name: kidney cortex

growth_protocol: Transgenic mice were generated by crossbreeding of Pdgfbflox/flox mice (B6.129P2-Pdgfbtm2Cbet/J; Jackson laboratories strain 017622) with Pax8-Cre mice (B6.129P2(Cg)-Pax8tm1.1(cre)Mbu/J; Jackson laboratories strain 028196). Housing conditions and tissue harvest was performed as described in the original manuscript.

extract_protocol:
Total RNA was isolated from kidney cortex using the RNeasy Mini Kit (Qiagen, Hilden, Germany).
Total RNA sequencing libraries were prepared using NEBNext Ultra II Directional Total RNA Library Prep Kit for Illumina with Unique Dual Indices (UDIs) following the manufacturer's protocol. Libraries were denatured, diluted, and loaded onto a NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles) flow cell. The PhiX control library was spiked in by 1% to improve base calling accuracy. Paired-end sequencing was performed with 100 cycles on the Illumina NovaSeq 6000 platform according to the manufacturer's instructions.

treatment_protocol: Transgenic cell-specific knockout mice (Pax8-Cre positive) were compared to (Pax8-Cre negative) littermates.

value: kidney cortex

value: Aged


title: stomach, day0, ChIP, Brg1, rep2

description: Library name: 12ChIPseq_Brg1_day0_rep2

value: Tamoxifen - No treatment

tag: chip antibody


title: 80 weeks kidney controls

description: Library name: CTRL kidneys Aging


title: EA.hy926 cells, PFOA 1nM, 6 weeks, biological replicate 2

description: Library name: PA_6w_1_2

value: WT

value: 6 weeks


title: UUOd5 kidney Pdgfb-knockout

description: Library name: KO kidneys UUO

treatment_protocol: Transgenic cell-specific knockout mice (Pax8-Cre positive) were compared to (Pax8-Cre negative) littermates after 5 days of UUO.

value: unilateral ureteral obstruction (UUO)


title: stomach, day0, ChIP, Brg1, rep1

description: Library name: 11ChIPseq_Brg1_day0_rep1


title: UUOd5 kidney controls

description: Library name: CTRL kidneys UUO


title: EA.hy926 cells, PFOA 1nM, 6 weeks, biological replicate 1

description: Library name: PA_6w_1_1

value: endothelial cells


title: stomach, day35, wt, ChIP, Esrrg, rep1

description: Library name: 4ChIPseq_Esrrg_day35_wt_rep1

value: wt

value: Esrrg (R&D Systems, PP-H6812-00)


title: stomach, day0, ChIP, Arid1a, rep2

description: Library name: 10ChIPseq_Arid1a_day0_rep2

value: Arid1a (D2A8U) (Cell Signaling, 12354; lot# 4)


title: Myct1 KO tumor CD45+ cells

city: St. Louis

first: Yoojung

last: Kwon

state: Missouri

address: 660 S Euclid Ave, BJCIH 8th floor, room 8302

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Library name: KO_HC

data_processing:
FASTQ files were aligned using cellranger v8.0.1. Filtered 10x output were processed and analyzed using Seurat v5.1.0  in R version 4.5.0.
Assembly: GRCm39-2024-A
Supplementary files format and content: Compressed archive containing raw and filtered feature.tsv, barcode.tsv, and count matrices (10x output).

source_name: tumor

extract_protocol:
Tumor were harvested from 4 individual mice and pulled together to digest and process for signle cell suspension with a cocktail of Collagenase-II, Dispase-II, and Deoxyribonuclease I. CD45+ immune cells were FACS sorted using BD FACSAria II (BD Bioscience).
Single-cell RNA-seq libraries were prepared using version 1 Chromium Single-cell 3′ Library, Gel Bead & Mutiplex Kit (10X Genomics) following to manufacturer's protocol. Sequencing was performed on Illumina NextSeq2500.

value: tumor

value: immune cells

value: Cdh5-Cre; Myct1-flox


title: Wildtype tumor CD45+ cells

description: Library name: WT_HC

value: wildtype


title: EA.hy926 cells, PFOA Control, 6 weeks, biological replicate 3

description: Library name: PA_6w_C_3

value: Control


title: TDLN_Treg cells_Foxp3EGFP mice_Rep_3

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

description:
Library name: LT3
LT3
raw_counts_table_LTvT_quant-seq.txt

data_processing:
For full-length mRNA-seq, Raw sequence data were quality-controlled using FastQC version 0.12.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapter sequences and poor-quality bases were removed with Cutadapt version 1.1656. Paired-end reads were aligned to the mouse genome GRCm38 using Rsubread version 2.12.3. Alignments were performed using default parameters. Reads associated with annotated genes were counted using the Rsubread function ‘featureCount’. Differentially expressed genes were identified using an FDR cut-off below 0.05 after normalization in EdgeR version 3.40.2 (PMID: 19910308)
Quant-seq: The quality of the FASTQ files was assessed with the FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse (mm10) genome  with the Hisat2 aligner (hisat2 -p32 -x $REFERENCE_GENOME -q fastq/$FILE_ID.fastq -S $FILE_ID.sam --score-min L,0,-0.5 -k 2). Htseq-counts was utilized to summarize reads at the gene level (htseq-count -f bam -s yes-igene_idbam/$FILE_ID.bamdata/refs/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf>$COUNTS_DIR/NGS$FILE_ID). Differential expression analysis (DEA) was conducted by running EdgeR via SARTools 1.5.0. For each comparison, DEGs were defined by applying the following thresholds adj. p-value <0.05, which was considered statistically significant.
Read quality was assessed using FastQC version 0.12.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapters and poor-quality bases were trimmed using fastp version 0.23.4 (PMID: 30423086). Samples were aligned to the mouse reference genome GRCm38 using default parameters in Rsubread version 2.12.3 (PMID: 30783653).  Mitochondrial reads were removed using SAMtools version 1.18. PCR duplicates were removed using the ‘MarkDuplicates’ function in Picard Tools version 17.0.13 (Java) (http://broadinstitute.github.io/picard/). Open chromatin was detected using MACS2 version 2.2.9.1 with an FDR < 0.05. The number of reads in each peak was determined using featureCounts embedded in Rsubread version 2.12.3. Differentially accessible peaks were identified using an FDR cut-off below 0.05 after normalization in DESeq2 version 1.38.3 (PMID: 25516281). Peaks were annotated using the ‘annotatePeak’ function using ChIPseeker version 1.34.1.  The bamCoverage function from deepTools version 3.5.6 was used to generate coverage track (BigWig) files. Trackplot version 1.6.0 was utilized to create IGV-style track plots (also known as locus plots) from BigWig files. Pheatmap version 1.0.12 was used to generate the heatmap of differentially accessible regions (DARs).
Assembly: mm10
Supplementary files format and content: Quant-seq: raw_counts_table_LTvT_quant-seq.txt, This matrix includes  counts of reads in ESMUSG Ensemble genes id  for 3 biological replicates (sample LT1,LT2,LT3 - TDLN_Treg cells_Foxp3EGFP mice; sample T1, T2, T345 - tumor_Treg cells_Foxp3EGFP mice)
Supplementary files format and content: ATAC-seq count matrix (Rbpj_ATACseq_counts_table.csv: This matrix excludes blacklisted regions, mitochondrial reads, and peaks detected in only one sample  (WT1, WT2, WT3:  biological Replicates of Tregs from Foxp3YFPcre;   KO1, KO2, KO3: biological Replicates of Tregs from Foxp3YFPcre RbpjΔFoxp3)
Supplementary files format and content: full length mRNA-seq raw count data (Rbpj_RNAseq_countdata.csv): Row names correspond to gene IDs, and column names represent the samples: (WT1, WT2, WT3:  biological Replicates of Tregs from Foxp3YFPcre;   KO2 KO3, KO4: biological Replicates of Tregs from Foxp3YFPcre RbpjΔFoxp3)

source_name: tumor-draining lymph nodes (TDLNs)

growth_protocol: murine B16.F10 melanoma, were cultured at 37°C under 5% CO2 in complete medium [RPMI-1640 medium (GlutaMAXTM, Gibco, #61870) supplemented with 10% foetal bovine serum (FBS, Gibco, #10270), 0.1% β-mercaptoethanol (Gibco, #31350) and 1% of a mix of Penicillin/Streptomycin (P/S, Gibco, #15140)]. B16.F10 melanoma and MB49 urothelial cancer cells were split at 90%–100% confluence.

extract_protocol:
For Full length strand-specific mRNA-seq, Treg cells (CD45+CD4+ Foxp3YFP+) were FACS-sorted from melanoma tumors of Foxp3YFPcre or RbpjΔFoxp3and RNA was extracted using the ArcturusTM PicoPure TM RNA isolation kit (Thermo Fisher, #12204-01) according to the manufacturer’s protocol. For Quant-seq (T1-345, LT1-3), total RNA was extracted from FACS-sorted Tregs cells derived TDLNs or tumors of Foxp3EGFP melanoma-bearing mice, using NucleoSpin RNA XS (Macherey-Nagel; cat. #740955.50) as per the manufacturer’s protocol. The quantity and quality of RNA samples were analyzed using Agilent RNA 6000 Nano kit with the bioanalyzer from Agilent.
For Full length strand-specific mRNA-seq, RNA-seq libraries were prepared using NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module according to manufacturer’s instructions and starting with three replicates per group and 50-120 ng of pure total RNA extracted from 18-28.000 sorted cells. Libraries were prepared using sample specific combinations of i5 and i7 indexed adapters, amplified for 16-18 cycles according to qPCR estimates and were size selected for sizes around 400 bp. Paired-end reads (2*111) were sequenced on an Illumina NextSeq 2000 at Genecore EMBL, DE. For Quant-seq (T1-345, LT1-3,) RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions. Amplification was controlled for obtaining optimal unbiased libraries across samples by assessing the number of cycles (ranging from 19-20 cycles) required by qPCR. DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent). Libraries were multiplexed and sequenced on an Illumina Nextseq 500 at the genomics facility of IMBB FORTH, GR. according to the manufacturer’s instructions.
The ATAC-seq protocol was performed as previously described57,58. In brief, 2-5 x 104 Treg cells were FACS-sorted (CD45+CD4+Foxp3YFP+) from melanoma tumors of Foxp3YFPcre or RbpjΔFoxp3, washed with ice-cold PBS and resuspended in lysis buffer [0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin in Resuspension Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2)]. Cell nuclei were washed (0.1% Tween-20 in Resuspension Buffer) and the transposition reaction was performed by using Tn5 Transposase in tagmentation buffer (Illumina Tagment DNA enzyme and Buffer, #20034210), 10%Tween-20, 1%Digitonin and incubating for 30min at 37oC. DNA was purified with the the MinElute Cleanup Kit (Qiagen, #28204) and amplified using the NEBNext High-Fidelity PCR Master Mix (New England BioLabs) and Nextera PCR primers with sample specific combinations of i5 and i7 indexes. Library were size selected for sizes between 200 and 500 bp using AMPure XP beads (Beckman Coulter). Paired-end reads (2*111) were sequenced on an Illumina NextSeq 2000 at Genecore EMBL, Heidelberg.

treatment_protocol: melanoma tumors growth in Foxp3YFPcre, RbpjΔFoxp3 and  Foxp3EGFP mice was monitored after implanting subcutaneously on the back 3 x 10^5 B16.F10 melanoma cells in each tested mouse.

value: tumor-draining lymph nodes (TDLNs)

value: Treg

value: Foxp3EGFP mice

value: subcutaneous implantation 3 x 10^5 B16.F10 melanoma cells

tag: batch


title: stomach, day0, ChIP, Arid1a, rep1

description: Library name: 9ChIPseq_Arid1a_day0_rep1

value: Stomach

value: Tamoxifen - No treatment


title: TDLN_Treg cells_Foxp3EGFP mice_Rep_2

description:
Library name: LT2
LT2
raw_counts_table_LTvT_quant-seq.txt


title: EA.hy926 cells, PFOA Control, 6 weeks, biological replicate 2

description: Library name: PA_6w_C_2

value: WT

value: 6 weeks


title: EA.hy926 cells, PFOA 1nM, 12 weeks, biological replicate 2

description: Library name: PA_12w_1_2

value: endothelial cells

value: 1 nM PFOA

value: 12 weeks


title: TDLN_Treg cells_Foxp3EGFP mice_Rep_1

description:
Library name: LT1
LT1
raw_counts_table_LTvT_quant-seq.txt


title: stomach, day 35, Arid1a mutant, ChIP, H3K27ac, rep2

description: Library name: 8ChIPseq_H3K27ac_mut_rep2

value: Tamoxifen - 35 days after treatment


title: EA.hy926 cells, PFOA 1nM, 12 weeks, biological replicate 1

description: Library name: PA_12w_1_1


title: tumor_Treg cells_Foxp3EGFP mice_Rep_3

description:
Library name: T345
T345
raw_counts_table_LTvT_quant-seq.txt

source_name: tumor melanoma

value: tumor melanoma


title: tumor_Treg cells_Foxp3EGFP mice_Rep_2

description:
Library name: T2
T2
raw_counts_table_LTvT_quant-seq.txt


title: EA.hy926 cells, PFOA Control, 6 weeks, biological replicate 1

description: Library name: PA_6w_C_1


title: stomach, day 35, Arid1a mutant, ChIP, H3K27ac, rep1

description: Library name: 7ChIPseq_H3K27ac_mut_rep1


title: Human, TMCi, Veh6h_3

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

country: Japan

institute: Kyushu University

description: Library name: HTMCi_Veh6h_3

data_processing:
FASTQ files were received from the sequencing provider.
Quality control, mapping, and differential gene expression analysis were performed using RaNAseq and BioJupies.
Differentially expressed genes were identified by comparing NE- or DEX-treated samples with vehicle-treated control samples at the corresponding exposure time points.
Assembly: To be confirmed based on the reference genome used for mapping in RaNAseq/BioJupies.
Supplementary files format and content: Processed data files contain gene-level expression values and differential expression analysis results generated from the RNA-seq data.

source_name: Immortalized Trabecular meshwork cell line

growth_protocol: Immortalized human primary trabecular meshwork cells (abm; T0371)  were plated in Type I collagen-coated 6-well plates and cultured until they reached 80–90% confluence. The medium was then replaced with serum-free trabecular meshwork cell medium (TMCM; ScienCell; #6591), and cells were incubated for 24 hours before treatment.

extract_protocol:
At the indicated time points, culture medium was aspirated, and cells were gently washed with 1 mL of ice-cold PBS. Cells were lysed by adding 0.2 mL of lysis reagent from the NucleoSpin RNA/Protein kit (Takara Bio) and detached using a cell scraper. RNA was extracted according to the manufacturer's protocol and quantified using a NanoDrop One spectrophotometer.
RNA sequencing library preparation and sequencing were performed by an external service provider using the submitted RNA samples.

treatment_protocol: After 24 hours in serum-free TMCM, cells were treated with norepinephrine (NE; final concentration, 1 µM) or dexamethasone (DEX; final concentration, 0.1 µM). Vehicle-treated control cells received DMSO. Cells were harvested 6 hours after treatment.

value: Trabecular meshwork

value: Immortalized Trabecular meshwork cell type


title: Xbp1_S2

city: Palo Alto

first: Kevin

last: Brulois

state: CA

address: 3801 Miranda Ave

institute: Stanford University

description:
Library name: Xbp1_S2
10x Genomics, chromium controller

data_processing:
Cell Ranger (v6.1, 10x Genomics) was used to align reads to the mm10 reference genome and perform quality control.
Assembly: mm10
Supplementary files format and content: tab-separated values  and .mtx files

source_name: perpheral lymph nodes (HT4 and HT6) and mesenteric lymph nodes (HT5 and HT7)

extract_protocol:
Endothelial cells (ECs) were isolated following the procedure outlined in the online protocol6. Briefly, PLNs were pooled in HBSS buffer and minced with scissors. The minced tissue was washed 2–3 times with HBSS, then resuspended in HBSS containing 0.2 mg/ml collagenase P, 0.8 mg/ml Dispase II, and 0.01 mg/ml DNase. The tissue was incubated at 37 °C for 10 minutes, followed by gentle disruption through repeated pipetting with P1000 pipette tips of successively smaller bore sizes. The tissue fragments were allowed to settle, and cells released by digestion were transferred to ice-cold FBS (final concentration: 30%). Fresh digestion buffer was added to the remaining tissue fragments for another round of digestion. Digested cells were filtered, and hematolymphoid cells were depleted using anti-CD45 MicroBeads (Miltenyi).
Endothelial cells were sorted and processed for scRNAseq using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10x Genomics) according to manufacturer guidelines.

value: WT (HT4 and HT5) and Xbp1-KO (HT6 and HT7)

value: tamoxifen


title: tumor_Treg cells_Foxp3EGFP mice_Rep_1

description:
Library name: T1
T1
raw_counts_table_LTvT_quant-seq.txt


title: stomach, day35, ChIP, H3K27ac, rep2

description: Library name: 6ChIPseq_H3K27ac_day35_rep2


title: Xbp1_S1

description:
Library name: Xbp1_S1
10x Genomics, chromium controller

value: perpheral lymph nodes (HT4 and HT6) and mesenteric lymph nodes (HT5 and HT7)

value: endothelial  cells


title: Human, TMCi, Veh6h_2

description: Library name: HTMCi_Veh6h_2


title: stomach, day35, ChIP, H3K27ac, rep1

description: Library name: 5ChIPseq_H3K27ac_day35_rep1


title: Macrophage treated with 100ng/ml lipopolysaccharide (LPS)-3

city: Saint Louis

first: Gabriel

last: Mbalaviele

address: 425 S. Euclid Ave., Steven & Susan Lipstein BJCIH, Floor: 11, Room 11203

institute: WashU School of Medicine

description: Library name: MA_LPS_3

data_processing:
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using the PE Cluster Kit cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform, and paired-end reads were generated
Raw FASTQ reads were processed with fastp to remove adapters, poly-N sequences, and low-quality reads. Clean paired-end reads were aligned to the reference genome (downloaded from NCBI/UCSC/Ensembl) using STAR.
FeatureCounts was used to quantify gene-level expression, and RPKM values were calculated.
Differential expression analysis (three biological replicates per group) was performed using DESeq2, with p-values adjusted by the Benjamini-Hochberg method. Genes with adjusted p < 0.05 were considered differentially expressed.
Assembly: mm10
Supplementary files format and content: tab delimited text file containing fpkm for all samples

source_name: Bone marrow derived macrophages

growth_protocol: The femurs and tibiae were harvested from WT mice and used to expand BMDMs in vitro. Bone marrow cells were flushed from the bones as previously described by Wang et al., 2024. Cells were cultured in 10 cm Petri dishes in the presence of CMG (a source of macrophage colony-stimulating factor, M-CSF) for 4–5 days. Expanded BMDMs were trypsinized and seeded into appropriate well plates at a density of 3 × 10⁴ cells per well in 24-well plates and 0.4 × 10⁶ cells per well in 6-well plates. OC differentiation was induced by the addition of receptor activator of nuclear factor kappa-B ligand (RANKL, 50–100 ng/mL) for 5–6 days.

extract_protocol:
RNA was isolated using the PureLink RNA Mini Kit, and on-column DNase I treatment (Ambion) was performed to eliminate any DNA contamination. RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
One microgram (1 μg) of RNA per sample was used as input material for RNA library preparation. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer’s instructions. Library quality was assessed using the Agilent Bioanalyzer 2100 system.

treatment_protocol: BMDMs were cultured for 5–6 days in 2% CMG, with or without RANKL, to induce mature osteoclasts. On day 5, both cell types were treated with or without LPS (100 ng/mL) for 3 hours.

value: D5, no RANKL, LPS treated

value: Bone marrow derived macrophages


title: Endometriosis 18

type: RNA

city: São Paulo

first: Helena

last: Malvezzi

state: São Paulo

address: Av. Morumbi

department: Research

country: Brazil

institute: Hospital Israelita Albert Einstein

data_processing: The calculations of the relative gene expression of the samples were made using the ΔΔCt method with the housekeeping gene 18S, ACTB and GAPDH as normalizer. The normalizer was determined based on the coefficient of variation (CV) obtained in similar datasets.

label: Taqman

source_name: Endometriosis 18.eds

label_protocol: cDNA synthesis and Real-Time Polymerase Chain Reaction (RT-PCR in Real time)  Reverse transcription of RNA samples was performed using the SuperScript VILO MasterMix (Invitrogen, ThermoFisher Scientific, Waltham, MA, USA) with oligo-dT primers. The final reaction volume was 14μL per sample. The samples were placed in a thermocycler (Master Cycler – Nexus, Eppendorf Sigma Aldrich, MERK SA, Darmstadt, Germany) at 50ºC for 50 minutes. The sequences of genes analysed and synthesized by Invitrogen Brazil were: Gene Name: 18S; ACTB; AIM2; BCL2; BIRC2; BIRC3; BLC2L1; CARD18; CARD6; CASP1; CASP4; CASP5; CASP8; CCL2; CCL5; CCL7; CD40LG; CFLAR; CHUK; CIITA; CTSB;CXCL1; CXCL2; FADD; GAPDH; GSDMD; HSP90AA1; HSP90AB1; HSP90B1; IFNB1; IFNG; IKBKB; IKBKG; IL10; IL12A; IL12B; IL17A; IL18; IL1B; IL33; IL4; IL6; IRAK1; IRF1; IRF2; LDHB; MAP3K7; MAPK1; MAPK11; MAPK12; MAPK13; MAPK3; MAPK8; MAPK9; MEFV; MOK; MYD88; NAIP; NFKB1; NFKBIA; NFKBIB; NLRC4; NLRC5; NLRP1; NLRP12; NLRP3;NLRP4; NLRP5; NLRP6; NLRP9; NLRX1; NOD2; P2RX7; PANX1; PEA15; PSTPIP1; PTGS2; PYCARD; PYDC1; RELA; RIPK2; SUGT1; TAB1; TAB2; TIRAP; TLR2; TLR3; TLR4; TLR9; TNF; TNFFS4; TNFSF11; TNFSF14; TRAF6; TXNIP; XIAP  Real-time amplification was performed according to the Taqman Array assay protocol (Thermo Fisher Scientific, Waltham, MA, USA). Briefly, 1.5μL of cDNA was added to 13.5μL of the mix, totalling the final volume of 15μL of reaction per well of the plate.

extract_protocol: RNA extraction   The PicoPure RNA Isolation Kit (Life Technologies, MERK SA, Darmstadt, Germany) was used to extract RNA from whole biopsy samples. The extracted total RNA was quantified by spectrophotometry using a NanoDrop One Microvolume UV-Vis Spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA) at an absorbance of 260nm and frozen at -80ºC.

tag: sample group

value: Case

tag: subject status

value: Endometriosis

value: Peritoneal Fluid


title: Endometriosis 17

source_name: Endometriosis 17.eds


title: stomach, day7, ChIP, H3K27ac, rep2

description: Library name: 4ChIPseq_H3K27ac_day7_rep2

value: Stomach

value: Tamoxifen - 7 days after treatment


title: Endometriosis 16

source_name: Endometriosis 16.eds


title: Human, TMCi, NE6h_3

description: Library name: HTMCi_NE6h_3


title: stomach, day7, ChIP, H3K27ac, rep1

description: Library name: 3ChIPseq_H3K27ac_day7_rep1


title: Human, TMCi, NE6h_2

description: Library name: HTMCi_NE6h_2


title: Endometriosis 13

source_name: Endometriosis 13.eds


title: Endometriosis 12

source_name: Endometriosis 12.eds


title: stomach, day0, ChIP, H3K27ac, rep2

description: Library name: 2ChIPseq_H3K27ac_day0_rep2

value: Tamoxifen - No treatment


title: Human, TMCi, NE6h_1

description: Library name: HTMCi_NE6h_1


title: stomach, day0, ChIP, H3K27ac, rep1

description: Library name: 1ChIPseq_H3K27ac_day0_rep1


title: Control 9

source_name: Control 9.eds

value: Control

value: Non-endometriosis


title: Human, TMCi, DEX6h_3

description: Library name: HTMCi_DEX6h_3


title: Slide-051-PreMalignant-07-10-2023-Immune-003

city: Kansas City

first: Harsh

last: Pathak

state: KS

address: 3901 Rainbow Blvd

institute: KUMC

description: Library name: DSP-1001660015531-A-A11

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Library strategy: Spatial Transcriptomics

source_name: OED

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 cycles) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

value: Immune

value: OED

tag: transformed status

value: Yes


title: Control 8

source_name: Control 8.eds

tag: tissue


title: Res3, with ketamine

city: Cleveland

first: Wanpeng

last: Cui

state: OH

address: Room E765, Robbins Building,, 10900 Euclid Ave, Department of Neurosciences,

department: Neurosciences

institute: Case Western Reserve University

description: Library name: sample6

data_processing:
Data quanlity control, alignment
Gene expression level analysis
differential gene expression analysis
Assembly: mm10
Supplementary files format and content: xlsx, DEGlist of downregulated genes
Supplementary files format and content: downregulated genes

source_name: Brain (PFC)

growth_protocol: C57bl/6j male mice were siblings, and group house, 3 mice/cage

extract_protocol:
Total RNA were extracted from the prefrontal cortex of each mice.
RNA library was constructed according to SMARTER RNA libarary prep kit

treatment_protocol: ketamine, i.p., 10 mg/kg, 24 hours before sacrifice

value: Brain (PFC)

tag: cell line

value: brian cells

value: all kind of brain cells

value: Res, responders to ketamine

value: 24 hours after ketamine

value: C57bl/6j male


title: Human, TMCi, DEX6h_2

description: Library name: HTMCi_DEX6h_2

value: Trabecular meshwork

tag: cell type

value: Immortalized Trabecular meshwork cell type


title: Control 7

source_name: Control 7.eds

value: Peritoneal Fluid


title: Res2, with ketamine

description: Library name: sample5

tag: genotype


title: Control 6

source_name: Control 6.eds


title: Control 5

source_name: Control 5.eds


title: Human, TMCi, DEX6h_1

description: Library name: HTMCi_DEX6h_1


title: Res1, with ketamine

description: Library name: sample4

tag: treatment


title: Control 4

source_name: Control 4.eds


title: NR3, with ketamine

description: Library name: sample3

value: NR, nonresponders to ketamine