title: Wild-type clone 15 biol rep 1

description: Library name: C15-1


title: splenic CD11c+MHCII+ Dendritic cells from 3-week and 6-week-old mice. GEX.

status: Public on Jul 24 2026

type: SRA

city: Planegg

first: Barbara

last: Schraml

address: Großhaderner Strasse 9

country: Germany

institute: LMU Munich

description: Library name: scRNAseq_DC_across_age_spleen_3+6

library_source: transcriptomic

data_processing:
Aligned to mm10 via 10x cellranger count pipeline
DC across age aggregated with correction for sequencing depth via cellranger aggregate pipeline. Processed data file contains aggregated data.
Assembly: mm10
Supplementary files format and content: Downstream processing using Seurat v4.0 through v5.3
Library strategy: CITE-seq

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Dissection of spleen, isolation from splenocytes via enzymatic digestion, sort purification of target cells via FACS
10X sequencing Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) according to the manufacturer's instructions.

tag: tissue

value: Spleen

tag: cell type

value: Dendritic cells

tag: genotype

value: Clec9a-cre Rosa26-TOM


title: pho4(B) strain T=15 min (pH 8.0), replicate C

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

description: Library name: B_T15_C

data_processing:
Raw reads (fastq format) were transformed into clean reads through fastp  (Chen et al., 2018, PMID: 30423086). The HISAT2 (v2.2.1) was used to align paired-end clean reads to the K. phaffii GS115 reference genome (assembly GCA_000027005.1) to generate BAM files.
Differential gene expression analysis was carried out with the BAM files using DESeq2 (Love et al., 2014, PMID:25516281) and stablishing a |log2(FoldChange)| >= 1 and a p-value <= 0.01, unless otherwise stated.
Assembly: GCA_000027005.1
Supplementary files format and content: File "All_data_FPKM.xlsx" excel file with "Fragment per kilobase Million" data for each sample.
Supplementary files format and content: File "LowvsHigh Pi.xlsx", excel file with diverse comparisons for the low vs high phosphate experiments
Supplementary files format and content: File "Alkali_stress.xlsx", Excel file with diverse comparisons of the pH 5.5 to pH 8.0 time-course experiments

organism: Komagataella phaffii GS115

source_name: whole cell

growth_protocol: For evaluation of the transcriptional response of K. phaffii to alkalinization of the medium cells were grown overnight on YPGly medium. Cultures were then diluted in 100 ml of fresh medium at OD600=0.2 (~ 107 cells/ml) and grown until an OD600 around 0.6. At this point, two 50 ml-aliquots were centrifuged (5 min at 1000xg). For assessment of the effects of phosphate starvation, cells were grown for ~40 h on 20 ml of synthetic medium prepared with Formedium premade mix (ref. CYN0803, Yeast Nitrogen Base without Amino Acids and Phosphate) supplemented with 15 mM KCl, 2% glycerol and 7.35 mM KH2PO4, and adjusted to pH 5.8.

extract_protocol:
Total RNA extraction was carried out as described in (Albacar et al., 2023, PMID: 37013612 ) from three independent cultures of wild-type, pho4(A) (strain PJA-004), pho4(B) (strain PJA-021) and pho4(A) pho4(B) (PJA-026) cells. RNA concentration was assessed by Qubit assay (ThermoFisher) and its integrity with an Agilent 5400 Fragment Analyzer System.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, synthesis of the first strand cDNA was achieved by means of random hexamer primers, followed by the second strand cDNA synthesis using dTTP. After end repair, A-tailing, and adapter ligation, fragments were size selected, PCR amplified, and purified. Libraries were then pooled and subjected to sequencing in a NovaSeq X Plus equipment (Illumina) by Novogene Co., Ltd.

treatment_protocol: For alkalinization experiments, two 50 ml-aliquots were centrifuged (5 min at 1000xg). One aliquot was resuspended in the same volume of fresh YPGly medium plus 50 mM TAPS pH 5.5 (control cells) or in YPGly supplemented with 50 mM TAPS adjusted to pH 8.0 (stressed cells). Samples (15 ml) were taken immediately after resuspension in medium at pH 5.5 (T=0) and, for each stressed culture, after 15, 30 and 60 min, placed on ice and immediately centrifuged (5 min at 1000 xg) at 4 °C. Then one ml of cold H2O was added, and cells were transferred to pre-cooled 1.5 ml screw cap tubes and centrifuged (2 min at 1000 xg) at 4 °C. Finally, the supernatant was removed, and samples were frozen with liquid N2 and stored at -80 ºC. For cultures to be subjected to Pi starvation (low Pi), cells (10 OD600) were centrifuged and washed twice with medium without KH2PO4, whereas for control cultures (high Pi) 2.5 OD600 were taken and washed twice with medium containing 7.35 mM KH2PO4. In all cases, cells were resuspended in 50 ml the appropriate medium and growth resumed for 24 h.  Then, ~5 OD600 of each culture was collected and processed as described above.

value: whole cell

tag: cell line


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB882WTU)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR316GRL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR316GRL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB882WTU

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: 40 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS956MWF at ENCODE; https://www.encodeproject.org/ENCBS956MWF/


title: SCAF3015t_24919_TCR

city: Bethesda

first: Huaitian

last: Liu

state: MD

address: Building 37, Room 3050

department: CCR

institute: NCI

data_processing:
The demultiplexing, the primary analysis output, gene counting and TCR and BCR counting were performed by Cell Ranger Software. Base calling was performed using RTA 3.9.2, demultiplexing was performed using cellranger v6.1.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.1 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided human reference sequence (refdata-gex-GRCh38-2020-A).
PBMCs from the 59 patients yielded ≥ 3 cells per isolation with a total of 322897 cells that were merged using the Merge() function. After merging, cells with less than 200 nFeature RNA or more than 10% mitochondrial reads were excluded using Seurat v4.3.0
The V(D)J sequencing data were analyzed with the djvdj R package for single-cell V(D)J data.
Assembly: GRCh38
Supplementary files format and content: H5 file containing per-molecule information for all molecules that contain a valid barcode, a valid UMI, and were assigned with high confidence to a gene or Feature Barcode.
Supplementary files format and content: Filtered_contig_annotations.csv contains annotations of each high-confidence cell barcode.
Library strategy: TCR-Seq

source_name: Prostate cancer patient

extract_protocol:
Whole blood was collected and Lymphocyte separation medium was added and then the samples were centrifuged at 1400 rpm for 30 min. The lymphocyte layer was transferred to a new tube, 1X phosphate-buffered saline (PBS) was added and then centrifuged.The supernatant was discarded and the remaining sample was resuspended in PBS and centrifuged at 800 rpm for 8 mins. The supernatant was again discarded and the sample was then resuspend in freezing media: RPMI + 20% human AB serum.The cells in the samples were counted and frozen in 900 µl of freezing media and 100 µl of DMSO per cryovial.Vials were stored in liquid nitrogen.
Library construction was performed at the Single Cell Analysis Facility, a core service with the Center for Cancer Research at the NCI, Bethesda, MD. scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell 5’Reagent Kits V2 (10X Genomics; PN-1000263, PN-1000265, PN-1000190, PN-1000252, PN-1000253) following the manufacturer’s instruction. Briefly, cells were partitioned into nanoliter-scale Gel-beads-in-Emulsion (GEMs), generated by combining barcoded Gel Beads, a Master Mix containing  cells, and Partitioning Oil onto Chromium Next GEM Chip K. After successful completion of uniform emulsion consistency, the reverse transcription was run overnight to amplify full length cDNA. Simplified cDNA was then used to amplify full-length V(D)J segments, followed V(D)J library construction and 5' gene expression library construction. All the steps including TCR and BCR enrichment libraries and QC steps were performed as described in the 10X Genomics 5’ v2 Single Cell User Guide.

value: Blood

tag: race

value: African American (AA)

tag: lethal prostate_cancer_group

value: Lethal


title: Wild-type clone 1 biol rep 3

city: Boulder

first: Mingfeng

state: CO

address: 709 Mohawk Dr

institute: University of Colorado

description: Library name: C1-3

data_processing:
Quality control, read mapping, and quantification were performed using nf-core/rnaseq v3.20.0.
Assembly: The cleaned reads were aligned to the GRCh38.p13 human reference genome and quantified using GENCODE v38 annotations. The alignment process was performed using STAR v5.1.0, and the quantification process was performed using Salmon v1.10.3.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Cervical cancer

growth_protocol: The cells were cultured in high-glucose Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1× GlutaMAX-I, and 1× Penicillin-Streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Miniprep Plus Kits (Zymo Research).
Next-generation sequencing using rRNA-depletion libraries was performed by GENEWIZ.

value: Cervical cancer

value: Epithelial cervical adenocarcinoma cells

value: WT Halo-Tag RTEL1


title: SCAF2918t_24602_TCR

value: European American (EA)


title: pho4(B) strain T=15 min (pH 8.0), replicate B

description: Library name: B_T15_B


title: pho4(A) pho4(B) strain T=30 (pH 8.0), replicate B

description: Library name: AB_T30_B


title: SCAF2917t_22986_TCR


title: total RNA-seq from activated gamma-delta T cell (ENCLB092UGZ)

description:
https://www.encodeproject.org/experiments/ENCSR314ZXO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR314ZXO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB092UGZ

source_name: Homo sapiens female adult (33 years) activated gamma-delta T primary cell

value: activated gamma-delta T cell

value: 33 year

value: ENCBS833WME at ENCODE; https://www.encodeproject.org/ENCBS833WME/


title: A-5

city: qingdao

first: shijie

last: bi

address: No. 23, Hong Kong East Road

country: China

institute: ouc

description:
Library name: sample5
Column name in counts_allsamples.txt: A-5

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples
Differential expression analysis was performed using the DESeq25
Assembly: NCBI_GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumor

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
First, use the Single Cell Full Length mRNA-Amplification Kit to reverse transcribe and amplify RNA. For the cDNA that passes the quality inspection, use the cDNATruePrep DNA Library Prep Kit V2 for Illumina to construct the library in accordance with the instructions.

value: Tumor

value: melanoma cell

value: WT

tag: treatment

value: PBS

tag: batch

value: Day 10


title: A-3

description:
Library name: sample3
Column name in counts_allsamples.txt: A-3


title: total RNA-seq from T-helper 2 cell (ENCLB060MXP)

description:
https://www.encodeproject.org/experiments/ENCSR740VLU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR740VLU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB060MXP

source_name: Homo sapiens female adult (25 years) T-helper 2 primary cell

value: T-helper 2 cell

value: primary cell

value: female

value: adult

value: 25 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS070HAG at ENCODE; https://www.encodeproject.org/ENCBS070HAG/


title: Wild-type clone 1 biol rep 2

description: Library name: C1-2

value: Cervical cancer

value: Epithelial cervical adenocarcinoma cells

value: WT Halo-Tag RTEL1


title: pho4(B) strain T=15 min (pH 8.0), replicate A

description: Library name: B_T15_A

value: whole cell


title: normal bone marrow #1

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

description: human bone marrow mononuclear cells single cell Drop-seq

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.13.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2a.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.13.
Gene expression matrix was generated using Drop-seq tools v1.13.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

source_name: normal bone marrow

growth_protocol: Cryo-preserved bone marrow mononuclear cells or peripheral blood mononuclear cells from AML patients or healthy donors (STEMCELL Technologies) were thawed in a 37 °C water bath, dissociated by DNase I solution (New England Biolabs) treatment at a final concentration of 0.1 mg/mL and filtered through 40 μm cell strainers (Corning Life Sciences) to remove clumped cells. Isolated single cells were transferred into warm culture media (RPMI1640 supplemented with 10% FBS) and incubated at 37 °C for 2 hours. Then dead cells in the culture were eliminated using a dead cell removal kit from Miltenyi Biotec following the manufacturer’s protocol. The remaining viable single cells were counted and resuspended at 100 cells/ μl in a PBS-BSA solution.

extract_protocol:
Single-cell RNA sequencing was performed following the Drop-seq Online Protocol by Macosko et al (http://mccarrolllab.com/dropseq/) with minor modifications. Briefly, single cell suspension were loaded into the microfluidic device (FlowJEM) together with droplet-generating oil (Bio-Rad) and barcoded beads (MACOSKO-2011-10, Chemgenes) suspended in lysis buffer supplemented with RNase inhibitor (Lucigen) at a final concentration of 1 U/µL. Emulsions were incubated on ice for 30 minutes before droplet breakage and bead collection. Beads were subject to reverse transcription (Maxima H Minus Reverse Transcriptase: ThermoFisher; Template switch oligo: IDT) and Exo I (New England Biolabs) digestion. Next, 4000 beads were aliquoted into one PCR tube for amplification (KAPA HotStart ReadyMix: Kapa Biosystems). Products from multiple parallel PCRs were pooled together and purified using AMPure XP Beads (Beckman Coulter Life Sciences).
For each sample, 1 ng high quality cDNA was used for tagmentation and NGS library preparation using a Nextera XT kit (Illumina). High quality NGS libraries were sequenced on an Illumina NextSeq 550 (75-cycle kit) or NovaSeq 6000 (100-cycle kit) sequencers. All paired AML samples were processed and sequenced together to minimize batch effects.

tag: ex vivo treatment

value: untreated

value: bone marrow

tag: disease state

value: normal

tag: time point


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB158FCE)

description:
https://www.encodeproject.org/experiments/ENCSR313MPK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR313MPK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB158FCE

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-2 for 4 hours

value: CD4-positive, alpha-beta T cell

value: 40 year

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS116FWY at ENCODE; https://www.encodeproject.org/ENCBS116FWY/


title: pho4(A) pho4(B) strain T=30 (pH 8.0), replicate A

description: Library name: AB_T30_A

tag: tissue

tag: cell line

tag: genotype


title: SCAF2916t_22928_TCR

value: Blood

value: African American (AA)

value: Lethal


title: pho4(B) strain T=0 (pH 5.5), replicate C

description: Library name: B_T0_C


title: Wild-type clone 1 biol rep 1

description: Library name: C1-1

tag: cell type


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB858YHN)

description:
https://www.encodeproject.org/experiments/ENCSR310TTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR310TTV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB858YHN

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: ENCBS400RLG at ENCODE; https://www.encodeproject.org/ENCBS400RLG/


title: snRNA-seq of post-mortem human parietal cortex white matter, NeuN-Olig2-PU1-IRF8-Sox9+

city: London

first: Nathan

last: Skene

address: 80 Wood Lane

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: SK644S4
Brain bank case: PDC029; region block ID: P3B1; donor sex: male; donor age: 82 years; PMI: 48 h; RIN: 6.50; input tissue weight: 356 mg; brain region: parietal cortex white matter; sorting strategy: NeuN-Olig2-PU1-IRF8-Sox9+

library_source: transcriptomic single cell

data_processing:
Raw reads were processed with the Illumina DRAGEN single-cell RNA-seq pipeline version 4.4.6 using the hg38_alt_masked_v5 reference to generate per-sample filtered gene-by-barcode count matrices.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: gzip-compressed tab-delimited text file listing nucleus barcode identifiers for the filtered feature-barcode matrix.
Supplementary files format and content: features.tsv.gz: gzip-compressed tab-delimited text file listing feature identifiers, gene names, and feature types for the filtered feature-barcode matrix.
Supplementary files format and content: matrix.mtx.gz: gzip-compressed Matrix Market sparse count matrix containing expression counts for features by barcodes.

molecule: polyA RNA

source_name: parietal cortex white matter

growth_protocol: Frozen human post-mortem parietal cortex white matter was obtained from a neurologically unaffected Parkinson's UK Brain Bank donor; no cell growth protocol was used.

extract_protocol:
Nuclei were isolated from 356 mg frozen post-mortem brain tissue using an optimized iodixanol density-gradient protocol. Nuclei were stained for NeuN, OLIG2, IRF8, PU.1, and SOX9 and enriched by fluorescence-activated nuclei sorting on a BD FACSMelody. IRF8 and PU.1 were detected together on a shared PE channel.
Single-nucleus RNA-seq libraries were prepared from sorted nuclei using the Illumina Single Cell 3' RNA Prep, T2 kit (catalogue 20135689; PIP-seq chemistry) according to the manufacturer's instructions. Libraries were sequenced by Novogene on an Illumina NovaSeq X Plus using 150 bp paired-end reads.

treatment_protocol: Not applicable. Tissue was not subjected to an experimental treatment before processing.

value: parietal cortex white matter

value: SOX9-positive astrocytic nuclei

value: FANS sort:NeuN-Olig2-PU1-IRF8-Sox9+


title: SCAF2877t_27998_TCR


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-PU1-IRF8-Sox9-

description:
Library name: SK612S5
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 320 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-PU1-IRF8-Sox9-

data_processing:
Raw reads were processed to generate gene-by-barcode count matrices for each sorted sample. SK493_* samples were generated using 10x Genomics Cell Ranger (version 9.0.1) while the rest used Illumina DRAGEN single-cell RNA-seq pipeline (version 4.4.6).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: gzip-compressed tab-delimited text file listing cell/nucleus barcode identifiers for the filtered feature-barcode matrix.
Supplementary files format and content: features.tsv.gz: gzip-compressed tab-delimited text file listing gene/feature identifiers and names for the filtered feature-barcode matrix.
Supplementary files format and content: matrix.mtx.gz: gzip-compressed Matrix Market sparse count matrix containing expression counts for features by barcodes.

source_name: occipital cortex

growth_protocol: Frozen human post-mortem brain tissue was obtained from neurologically unaffected donor brain bank cases; no cell growth protocol was used.

extract_protocol:
Nuclei were isolated from frozen post-mortem brain tissue (approximately 250–350 mg per sample) using an in-house optimised protocol that included purification through a sucrose density gradient. Isolated nuclei were stained with nuclear markers to label specific nuclear populations of interest and enriched by fluorescence-activated nuclei sorting (FANS).
Two library preparation chemistries were used in this study. For samples SK493_1, SK493_2_batch1, and SK493_2_batch2, single-nucleus RNA-seq libraries were prepared from sorted nuclei using the 10x Genomics Chromium Next GEM Single Cell 3' GEM Kit v3.1 according to the manufacturer’s instructions. For samples all the other samples, libraries were prepared using the Illumina Single Cell 3' RNA Prep, T2 kit according to the manufacturer’s instructions. All libraries were sequenced at Novogene UK on an Illumina NovaSeq X Plus with 150 bp paired-end reads (70 Gb raw data per sample for the 10x libraries; 30 Gb per sample for the Illumina T2 libraries).

treatment_protocol: Not applicable. Tissue was not subjected to any experimental treatment prior to processing.

value: occipital cortex

value: sorted nuclei

value: FACS sort:NeuN-Olig2-PU1-IRF8-Sox9-


title: SCAF3011t_21030_TCR


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB918ZHE)

description:
https://www.encodeproject.org/experiments/ENCSR310GKZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR310GKZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB918ZHE

source_name: Homo sapiens male adult (38 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

tag: age

value: 38 year

tag: lab

tag: source

value: AllCells

tag: link

value: ENCBS365TJA at ENCODE; https://www.encodeproject.org/ENCBS365TJA/


title: pho4(B) strain T=0 (pH 5.5), replicate B

description: Library name: B_T0_B

value: whole cell


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-PU1+IRF8+Sox9-

description:
Library name: SK612S4
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 320 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-PU1+IRF8+Sox9-

tag: treatment

value: FACS sort:NeuN-Olig2-PU1+IRF8+Sox9-

tag: batch


title: pho4(B) strain T=0 (pH 5.5), replicate A

description: Library name: B_T0_A


title: SCAF2876t_26608_TCR

value: Blood

tag: race

value: African American (AA)

tag: lethal prostate_cancer_group

value: Lethal


title: SCAF2875t_26352_TCR

value: Nonlethal


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-PU1-IRF8-Sox9+

description:
Library name: SK612S3
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 320 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-PU1-IRF8-Sox9+

value: FACS sort:NeuN-Olig2-PU1-IRF8-Sox9+


title: pho4(A) strain T=60 min (pH 8.0), replicate C

description: Library name: A_T60_C


title: SCAF2874t_26082_TCR

value: European American (EA)


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2+PU1-IRF8-Sox9-

description:
Library name: SK612S2
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 320 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2+PU1-IRF8-Sox9-

value: FACS sort:NeuN-Olig2+PU1-IRF8-Sox9-


title: pho4(A) strain T=60 min (pH 8.0), replicate B

description: Library name: A_T60_B


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB089GTW)

description:
https://www.encodeproject.org/experiments/ENCSR306KPQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306KPQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB089GTW

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell

value: primary cell

value: female

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

value: ENCBS525BBK at ENCODE; https://www.encodeproject.org/ENCBS525BBK/


title: SCAF2873t_25197_TCR


title: SCAF2872t_24230_TCR


title: snRNA-seq of post-mortem human occipital cortex, NeuN+Olig2-PU1-IRF8-Sox9-

description:
Library name: SK612S1
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 320 mg; brain region: occipital cortex; sorting strategy: NeuN+Olig2-PU1-IRF8-Sox9-

value: occipital cortex

value: sorted nuclei

value: FACS sort:NeuN+Olig2-PU1-IRF8-Sox9-


title: total RNA-seq from T-cell (ENCLB522PKL)

description:
https://www.encodeproject.org/experiments/ENCSR303LFR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR303LFR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB522PKL

source_name: Homo sapiens male adult (38 years) T-cell primary cell

value: T-cell

value: male

value: 38 year

value: AllCells

value: ENCBS098TDL at ENCODE; https://www.encodeproject.org/ENCBS098TDL/


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-Sox9+

description:
Library name: SK591
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 338 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-Sox9+

value: FACS sort:NeuN-Olig2-Sox9+


title: SCAF2871t_22771_TCR

value: Blood

value: African American (AA)

value: Lethal


title: total RNA-seq from T-helper 17 cell (ENCLB303MFP)

description:
https://www.encodeproject.org/experiments/ENCSR302SSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR302SSR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB303MFP

source_name: Homo sapiens male adult (38 years) T-helper 17 primary cell

value: T-helper 17 cell

value: primary cell

value: ENCBS847LXV at ENCODE; https://www.encodeproject.org/ENCBS847LXV/


title: pho4(A) strain T=30 min (pH 8.0), replicate C

description: Library name: A_T30_C

value: whole cell


title: snRNA-seq of post-mortem human cerebellum, NeuN-Olig2-PU1+IRF8+Sox9-

description:
Library name: SK590S4
Brain bank case: PDC078; region block ID: CLB6; PMI: 18h; RIN: 7.00; cut weight: 271 mg; brain region: cerebellum; sorting strategy: NeuN-Olig2-PU1+IRF8+Sox9-

source_name: cerebellum

value: cerebellum

value: FACS sort:NeuN-Olig2-PU1+IRF8+Sox9-


title: pho4(A) strain T=30 min (pH 8.0), replicate B

description: Library name: A_T30_B

source_name: whole cell


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB800ACP)

description:
https://www.encodeproject.org/experiments/ENCSR298QSD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR298QSD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB800ACP

value: CD4-positive, alpha-beta T cell

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS940ELO at ENCODE; https://www.encodeproject.org/ENCBS940ELO/


title: SCAF2858t_22929_TCR

value: Nonlethal


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-IRF8+ replicate

description:
Library name: SK590S2
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 273 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-IRF8+_repeat

value: occipital cortex

value: sorted nuclei

value: FACS sort:NeuN-Olig2-IRF8+_repeat


title: pho4(A) strain T=60 min (pH 8.0), replicate A

description: Library name: A_T60_A


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB091BXT)

description:
https://www.encodeproject.org/experiments/ENCSR294VVV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR294VVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB091BXT

value: male

value: 42 year

value: AllCells

value: ENCBS464ZJI at ENCODE; https://www.encodeproject.org/ENCBS464ZJI/


title: SCAF2824t_24574_TCR

value: Blood

value: African American (AA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB349UMM)

description:
https://www.encodeproject.org/experiments/ENCSR307EHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307EHG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB349UMM

value: primary cell

value: female

value: 34 year

value: ENCBS300GOK at ENCODE; https://www.encodeproject.org/ENCBS300GOK/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB393YWF)

description:
https://www.encodeproject.org/experiments/ENCSR292CVA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR292CVA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB393YWF

value: CD4-positive, alpha-beta T cell

value: adult

value: 38 year

value: ENCBS364FPO at ENCODE; https://www.encodeproject.org/ENCBS364FPO/


title: pho4(A) strain T=15 min (pH 8.0), replicate C

description: Library name: A_T15_C

value: whole cell


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-PU1+Sox9-

description:
Library name: SK590S1
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 252 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-PU1+Sox9-

value: occipital cortex

value: sorted nuclei

value: FACS sort:NeuN-Olig2-PU1+Sox9-


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-PU1+

description:
Library name: SK567
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 320 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-PU1+


title: SCAF2823t_24397_TCR

value: European American (EA)


title: total RNA-seq from T-cell (ENCLB154IVT)

description:
https://www.encodeproject.org/experiments/ENCSR287FLI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR287FLI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB154IVT

source_name: Homo sapiens male adult (42 years) T-cell primary cell

value: T-cell

value: male

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS990ZXV at ENCODE; https://www.encodeproject.org/ENCBS990ZXV/


title: SCAF2822t_24392_TCR

source_name: Prostate cancer patient

value: Blood


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-IRF8+ batch2

description:
Library name: SK493_2_batch2
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 336 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-IRF8+_batch2

value: FACS sort:NeuN-Olig2-IRF8+_batch2


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB306JST)

description:
https://www.encodeproject.org/experiments/ENCSR286GSC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR286GSC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB306JST

value: CD4-positive, alpha-beta T cell

value: primary cell

value: ENCBS142UOB at ENCODE; https://www.encodeproject.org/ENCBS142UOB/


title: snRNA-seq of post-mortem human occipital cortex, NeuN-Olig2-IRF8+ batch1

description:
Library name: SK493_2_batch1
Brain bank case: PDC040; region block ID: P8A9; PMI: 15h; RIN: 6.10; cut weight: 336 mg; brain region: occipital cortex; sorting strategy: NeuN-Olig2-IRF8+_batch1

value: FACS sort:NeuN-Olig2-IRF8+_batch1


title: pho4(A) strain T=0 (pH 5.5), replicate C

description: Library name: A_T0_C

value: whole cell


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB913JII)

description:
https://www.encodeproject.org/experiments/ENCSR282KBZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR282KBZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB913JII

source_name: Homo sapiens male adult (38 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: adult

value: 38 year

value: ENCBS956RHO at ENCODE; https://www.encodeproject.org/ENCBS956RHO/


title: SCAF2820t_22915_TCR

value: African American (AA)

value: Lethal


title: pho4(A) strain T=0 (pH 5.5), replicate B

description: Library name: A_T0_B


title: SCAF2819t_22010_TCR

value: European American (EA)

value: Nonlethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB302BGG)

description:
https://www.encodeproject.org/experiments/ENCSR276BWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR276BWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB302BGG

value: male

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS987FUD at ENCODE; https://www.encodeproject.org/ENCBS987FUD/


title: Spatial co-profiling,human melanoma_r2, RNA

city: philadelphia

first: Pengfei

last: Guo

state: PA

address: 422 Curie Boulevard, Stellar Chance Labs, 711-712 (lab), philadelphia

institute: University of Pennsylvania

description:
Library name: Human_melanoma_r2_RNA
3'mRNA: read 1 contains transcript sequence; read 2 contains barcodes

data_processing:
Raw reads (fastq file) were aligned to the mouse or human genome using BWA (ATAC), BWA (Hi-C) or STAR (RNA). RNA counts were generated with featureCounts, ATAC  fragments were created with Sinto, and Hi-C pairs were generated with Pairtools.
Assembly: mm10 for mouse embryo and adult brain; hg38 for human melanoma
Supplementary files format and content: RNA.tar.gz: gene expression count matrix in mtx, tsv format
Supplementary files format and content: Image.tar.gz: spatial related images in tif, png, json, csv format
Supplementary files format and content: HIC.nodups.pairs.gz: Hi-C pairs in pairs format

source_name: Human melanoma

extract_protocol:
Frozen tissue sections were cryosectioned at 10 µm thickness, and processed for spatial Hi-C-RNA or ATAC library preparation using DBiT-seq.   Spatial barcoding was performed on cryosections using DBiT-seq.
Barcoded gDNA/cDNA (or ATAC fragments) were converted into Illumina-compatible sequencing libraries following standard protocols.

value: Human melanoma

value: tissue


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB649QGD)

description:
https://www.encodeproject.org/experiments/ENCSR273HGA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR273HGA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB649QGD

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-2 for 24 hours

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: 40 year

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS550HEP at ENCODE; https://www.encodeproject.org/ENCBS550HEP/


title: pho4(A) strain T=0 (pH 5.5), replicate A

description: Library name: A_T0_A

tag: tissue

value: whole cell


title: SCAF2818t_21943_TCR

value: Blood

value: African American (AA)


title: Spatial co-profiling,human melanoma_r2, Hi-C

description:
Library name: Human_melanoma_r2_HiC
Hi-C: read 1 contains genome sequence; read 2 contains barcodes

tag: cell line


title: wilt-type strain T=60 min (pH 8.0), replicate C

description: Library name: W_T60_C

tag: genotype

value: wild-type


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB676WFK)

description:
https://www.encodeproject.org/experiments/ENCSR271OTY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR271OTY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB676WFK

value: adult

value: 42 year

value: ENCBS532LAN at ENCODE; https://www.encodeproject.org/ENCBS532LAN/


title: TF ChIP-seq from K562 (ENCLB398WWX)

description:
https://www.encodeproject.org/experiments/ENCSR269ZGG/
***************
biological replicate number: 2
technical replicate number: 1
description: CEBPB ChIP-seq on K562 cells treated with shRNA targeting GATA1
experiment encode accession: ENCSR269ZGG
assay title: TF ChIP-seq
possible controls: ENCSR915CFB, ENCSR562EHT
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB398WWX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line expressing RNAi targeting H. sapiens GATA1

tag: antibody

value: CEBPB

tag: line

value: cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS363XIA at ENCODE; https://www.encodeproject.org/ENCBS363XIA/


title: wilt-type strain T=60 min (pH 8.0), replicate B

description: Library name: W_T60_B


title: SCAF2812t_27281_TCR

value: European American (EA)

value: Lethal


title: wilt-type strain T=60 min (pH 8.0), replicate A

description: Library name: W_T60_A


title: transverse colonoid line TC202, adult male, differentiation medium + 10mM isovalerate 48h

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

description: Library name: TC202_ISO_48H

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Raw count and Differentially expressed gene list

source_name: colon

growth_protocol: Human intestinal tissue procurement was approved by the Institutional Review Boards at Baylor College of Medicine. Tissue specimens were obtained from adult male donors with samples collected from the ascending or transverse colon. Human colonoid lines were established and maintained as three-dimensional (3D) cultures in Matrigel by the Texas Medical Center Digestive Disease Center Gastrointestinal Experimental Model Systems Core at Baylor College of Medicine, as previously described. For maintenance of 3D cultures, colonoids were grown in WRNE medium and passaged every 7 days. To generate 2D monolayers, colonoids cultured for 7 days in WRNE medium were harvested using calcium- and magnesium-free Dulbecco’s phosphate-buffered saline (DPBS; Invitrogen) containing 0.5 mM EDTA and centrifuged at 300 × g for 5 minutes at 4°C. Pelleted colonoids were enzymatically dissociated with 0.05% trypsin–EDTA (Invitrogen) for 5 minutes at 37°C. Trypsin activity was quenched by addition of CMGF- medium supplemented with 10% fetal bovine serum. Cells were further dissociated by repeated pipetting and passed through a 40-µm cell strainer to remove debris and cell aggregates. The flow-through was collected and centrifuged at 400 × g for 5 minutes at room temperature. Cell pellets were resuspended in WRNE medium supplemented with the ROCK inhibitor Y-27632 (StemCell Technologies; final concentration 10 µM) and Normocin. For Transwell cultures, inserts (Costar) were coated with collagen IV (Sigma-Aldrich; 33 µg/mL) and incubated overnight at 37°C. To maintain humidity during culture, sterile water was added to the inter-well space of 24-well plates (Corning). Approximately 2.5 × 10⁵ cells were seeded per Transwell insert in 100 µL of WRNE medium containing Y-27632 and Normocin, with 600 µL of the same medium added to the basolateral compartment. Twenty-four hours after seeding, culture media in both apical and basolateral compartments were replaced with differentiation medium supplemented with Y-27632 (10 µM) and Normocin. Monolayers were differentiated for two days prior to experimental treatment with branched-chain fatty acids sodium isovalerate (Pfaltz & Bauer) or differentiation media control conditions for 48h.

extract_protocol:
Total RNA was isolated with the Qiagen RNeasy® Mini Kit following the manufacturer’s protocol with the inclusion of the DNAse digestion step, and submitted to Novogene (Sacramento, CA) for poly(A)-based mRNA enrichment, library preparation, and NovaSeq PE150 sequencing (~6 Gb raw reads/sample).
Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 150 bp) was performed on an Illumina NovaSeq X Plus  for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample.

treatment_protocol: HIOs were cultured for 2 days in differentiation medium; media was replace with either differentiation media or differentiaion media + 10mM isovalerate. RNA was isolated after 2 or 48h of treatment

value: colon

value: organoid

tag: cell type

value: epithelium

value: control + 10mM isovalerate

tag: medium

value: Differentiation


title: TF ChIP-seq from K562 (ENCLB187TJH)

description:
https://www.encodeproject.org/experiments/ENCSR269ZGG/
***************
biological replicate number: 1
technical replicate number: 1
description: CEBPB ChIP-seq on K562 cells treated with shRNA targeting GATA1
experiment encode accession: ENCSR269ZGG
assay title: TF ChIP-seq
possible controls: ENCSR915CFB, ENCSR562EHT
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB187TJH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: ENCBS841JVC at ENCODE; https://www.encodeproject.org/ENCBS841JVC/


title: SCAF2811t_26136_TCR

value: Blood

value: African American (AA)


title: transverse colonoid line TC202, adult male, differentiation medium 2h

description: Library name: TC202_CON_2H

tag: treatment

value: control


title: wilt-type strain T=30 min (pH 8.0), replicate C

description: Library name: W_T30_C

value: whole cell

value: wild-type


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB717XMX)

description:
https://www.encodeproject.org/experiments/ENCSR256UBZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR256UBZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB717XMX

source_name: Homo sapiens male adult (42 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: 42 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS783UCX at ENCODE; https://www.encodeproject.org/ENCBS783UCX/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB868MGS)

description:
https://www.encodeproject.org/experiments/ENCSR255UHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR255UHN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB868MGS

value: CD4-positive, alpha-beta T cell

value: 38 year

value: ENCBS730BLK at ENCODE; https://www.encodeproject.org/ENCBS730BLK/


title: SCAF2809t_25015_TCR

tag: tissue

tag: race

value: European American (EA)

tag: lethal prostate_cancer_group


title: transverse colonoid line TC2005, adult male, differentiation medium + 10mM isovalerate 2h

description: Library name: TC2005_ISO_2H

value: colon

tag: cell line

value: organoid

value: epithelium

value: control + 10mM isovalerate

value: Differentiation


title: wilt-type strain T=30 min (pH 8.0), replicate A

description: Library name: W_T30_A

value: whole cell

tag: genotype

value: wild-type


title: SCAF2808t_22573_TCR

value: Blood

value: African American (AA)

value: Nonlethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB958RLA)

description:
https://www.encodeproject.org/experiments/ENCSR254ZLS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR254ZLS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB958RLA

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-15 for 4 hours

value: primary cell

value: female

value: adult

value: 40 year

value: John Stamatoyannopoulos, UW

tag: treatments

value: treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS937FCR at ENCODE; https://www.encodeproject.org/ENCBS937FCR/


title: transverse colonoid line TC2005, adult male, differentiation medium + 10mM isovalerate 48h

description: Library name: TC2005_ISO_48H

value: colon

tag: cell type


title: wilt-type strain T=15 min (pH 8.0), replicate C

description: Library name: W_T15_C


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB979RLZ)

description:
https://www.encodeproject.org/experiments/ENCSR254TFM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR254TFM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB979RLZ

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-15 for 24 hours

value: CD4-positive, alpha-beta T cell

value: AllCells

value: treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS523AVI at ENCODE; https://www.encodeproject.org/ENCBS523AVI/


title: wilt-type strain T=15 min (pH 8.0), replicate B

description: Library name: W_T15_B

value: whole cell


title: SCAF2807t_22213_TCR

value: Lethal


title: transverse colonoid line TC2005, adult male, differentiation medium 2h

description: Library name: TC2005_CON_2H

value: organoid

value: epithelium

value: control

tag: medium

value: Differentiation


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB685ZXV)

description:
https://www.encodeproject.org/experiments/ENCSR252PFT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR252PFT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB685ZXV

value: primary cell

tag: biosample encode accession

value: female

value: 34 year

value: ENCBS746YPU at ENCODE; https://www.encodeproject.org/ENCBS746YPU/


title: SCAF2806t_22135_TCR

value: Blood

value: European American (EA)

value: Nonlethal


title: transverse colonoid line TC2005, adult male, differentiation medium 48h

description: Library name: TC2005_CON_48H

value: colon


title: wilt-type strain T=15 min (pH 8.0), replicate A

description: Library name: W_T15_A

value: wild-type


title: SCAF2805t_21570_TCR


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB265CCL)

description:
https://www.encodeproject.org/experiments/ENCSR237SUT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR237SUT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB265CCL

value: CD4-positive, alpha-beta T cell

tag: encode accession

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS210WJU at ENCODE; https://www.encodeproject.org/ENCBS210WJU/


title: transverse colonoid line TC208, adult male, differentiation medium + 10mM isovalerate 2h

description: Library name: L208_ISO_2H

value: organoid

value: epithelium

value: control + 10mM isovalerate

value: Differentiation


title: wilt-type strain T=0 (pH 5.5), replicate C

description: Library name: W_T0_C

value: whole cell


title: total RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB141HIE)

description:
https://www.encodeproject.org/experiments/ENCSR234TAQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR234TAQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB141HIE

source_name: Homo sapiens male adult (56 years) effector memory CD4-positive, alpha-beta T primary cell

value: primary cell

tag: Sex

value: 56 year

value: ENCBS879UKF at ENCODE; https://www.encodeproject.org/ENCBS879UKF/


title: wilt-type strain T=0 (pH 5.5), replicate B

description: Library name: W_T0_B


title: SCAF2786t_25509_TCR

value: Blood

value: European American (EA)

value: Lethal


title: transverse colonoid line TC208, adult male, differentiation medium + 10mM isovalerate 48h

description: Library name: L208_ISO_48H

value: colon


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB709PTA)

description:
https://www.encodeproject.org/experiments/ENCSR228YDZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR228YDZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB709PTA

source_name: Homo sapiens male adult (38 years) effector memory CD8-positive, alpha-beta T primary cell

value: male

tag: dev stage

value: adult

value: ENCBS217TEH at ENCODE; https://www.encodeproject.org/ENCBS217TEH/


title: SCAF2785t_25265_TCR


title: transverse colonoid line TC208, adult male, differentiation medium 2h

description: Library name: L208_CON_2H

value: control


title: wilt-type strain T=0 (pH 5.5), replicate A

description: Library name: W_T0_A

value: wild-type


title: SCAF2784t_24520_TCR

value: African American (AA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB865TSX)

description:
https://www.encodeproject.org/experiments/ENCSR225VEP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR225VEP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB865TSX

source_name: Homo sapiens male adult (38 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

tag: age

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS815CQS at ENCODE; https://www.encodeproject.org/ENCBS815CQS/


title: transverse colonoid line TC208, adult male, differentiation medium 48h

description: Library name: L208_CON_48H

value: organoid

value: epithelium

tag: treatment

value: Differentiation


title: Ctrl mouse heart tissue sample C8

city: Solna

first: Nils-Göran

last: Larsson

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description: Library name: C8

data_processing:
Raw reads were filtered using fastp to remove adapter-containing reads, poly-N-containing reads, and low-quality reads.
Clean reads were aligned to the Mus musculus mm39/GRCm39 reference genome using HISAT2 v2.2.1.
Gene-level counts were generated using featureCounts v2.0.6.
Differential expression analysis was performed using DESeq2 v1.42.0 with Benjamini-Hochberg correction for multiple testing.
Assembly: mm39/GRCm39
Supplementary files format and content: Gene-level raw count matrices were generated for the RNA-seq samples.
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts for each sample.

source_name: heart

extract_protocol:
Total RNA was extracted from mouse heart tissue using the RNeasy Mini Kit (Qiagen) according to the manufacturer's tissue protocol.
Poly(A)-selected mRNA libraries were prepared from total RNA by Novogene using poly-T oligo-attached magnetic beads, followed by cDNA library construction and quality assessment by Qubit, real-time PCR, and Bioanalyzer analysis.

treatment_protocol: No experimental treatment was applied. Samples were grouped according to genotype: control and hMut.

value: heart

value: Ctrl


title: total RNA-seq from T-cell (ENCLB791SFA)

description:
https://www.encodeproject.org/experiments/ENCSR225DON/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR225DON
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB791SFA

source_name: Homo sapiens male adult (38 years) T-cell primary cell

value: T-cell

value: primary cell

tag: lab

value: ENCBS812CJU at ENCODE; https://www.encodeproject.org/ENCBS812CJU/


title: SCAF2783t_24358_TCR

value: Blood

value: European American (EA)


title: Ctrl mouse heart tissue sample C7

description: Library name: C7


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB028FAQ)

description:
https://www.encodeproject.org/experiments/ENCSR216POR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR216POR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB028FAQ

value: male

value: adult

tag: source

value: ENCBS759RYF at ENCODE; https://www.encodeproject.org/ENCBS759RYF/


title: SCAF2782t_23995_TCR

value: African American (AA)


title: ascending colonoid line Asc231, adult male, differentiation medium + 10mM isovalerate 48h

description: Library name: ASC231_ISO_48H

value: colon

value: control + 10mM isovalerate


title: Ctrl mouse heart tissue sample C6

description: Library name: C6


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB738CGW)

description:
https://www.encodeproject.org/experiments/ENCSR213LIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR213LIB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB738CGW

value: CD4-positive, alpha-beta T cell

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS100BYD at ENCODE; https://www.encodeproject.org/ENCBS100BYD/


title: ascending colonoid line Asc231, adult male, differentiation medium 2h

description: Library name: ASC231_CON_2H

tag: tissue

value: organoid

value: epithelium

value: control

value: Differentiation


title: Ctrl mouse heart tissue sample C5

description: Library name: C5

value: heart

value: Ctrl


title: SCAF2781t_22152_TCR

value: Blood

tag: race

value: Nonlethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB386PPY)

description:
https://www.encodeproject.org/experiments/ENCSR211PUA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR211PUA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB386PPY

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: primary cell

value: male

value: adult

value: 42 year

value: ENCBS695SVB at ENCODE; https://www.encodeproject.org/ENCBS695SVB/


title: SCAF2780t_22105_TCR

value: African American (AA)

tag: lethal prostate_cancer_group

value: Lethal


title: ascending colonoid line Asc231, adult male, differentiation medium 48h

description: Library name: ASC231_CON_48H

value: colon

tag: cell line


title: Ctrl mouse heart tissue sample C4

description: Library name: C4

tag: genotype


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB265KHD)

description:
https://www.encodeproject.org/experiments/ENCSR205XKX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR205XKX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB265KHD

value: CD8-positive, alpha-beta T cell

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS012UGE at ENCODE; https://www.encodeproject.org/ENCBS012UGE/


title: SCAF2779t_21906_TCR

value: European American (EA)


title: LEGH9

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: Library name: LEGH9

data_processing:
Transcript quantification was performed using Kallisto, and transcript-level abundances were summarized to gene-level counts using the tximport package.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes gene-level counts for each sample

source_name: Uterine cervix

extract_protocol:
Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue samples using the miRNeasy FFPE Kit (QIAGEN, Cat. No. 217504, Hilden, Germany) according to the manufacturer’s instructions.
RNA-seq libraries were generated using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) and the NEBNext Ultra II Directional RNA Library Prep Kit, according to the manufacturer’s instructions.

value: Uterine cervix

tag: Stage


title: Ctrl mouse heart tissue sample C3

description: Library name: C3

value: heart

value: Ctrl


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB455LPQ)

description:
https://www.encodeproject.org/experiments/ENCSR205GOW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR205GOW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB455LPQ

value: CD4-positive, alpha-beta T cell

value: 38 year

value: ENCBS785VEE at ENCODE; https://www.encodeproject.org/ENCBS785VEE/


title: SCAF3017_27500

data_processing:
The demultiplexing, the primary analysis output, gene counting and TCR and BCR counting were performed by Cell Ranger Software. Base calling was performed using RTA 3.9.2, demultiplexing was performed using cellranger v6.1.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.1 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided human reference sequence (refdata-gex-GRCh38-2020-A).
PBMCs from the 59 patients yielded ≥ 3 cells per isolation with a total of 322897 cells that were merged using the Merge() function. After merging, cells with less than 200 nFeature RNA or more than 10% mitochondrial reads were excluded using Seurat v4.3.0
The V(D)J sequencing data were analyzed with the djvdj R package for single-cell V(D)J data.
Assembly: GRCh38
Supplementary files format and content: H5 file containing per-molecule information for all molecules that contain a valid barcode, a valid UMI, and were assigned with high confidence to a gene or Feature Barcode.
Supplementary files format and content: Filtered_contig_annotations.csv contains annotations of each high-confidence cell barcode.

value: Blood


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB579ZSU)

description:
https://www.encodeproject.org/experiments/ENCSR308QRZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR308QRZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB579ZSU

source_name: Homo sapiens female adult (33 years) effector memory CD8-positive, alpha-beta T primary cell

value: primary cell

value: female

value: adult

value: 33 year

value: ENCBS413OBP at ENCODE; https://www.encodeproject.org/ENCBS413OBP/


title: LEGH8

description: Library name: LEGH8


title: Ctrl mouse heart tissue sample C2

description: Library name: C2


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB638XCV)

description:
https://www.encodeproject.org/experiments/ENCSR203CWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR203CWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB638XCV

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell

value: 40 year

value: ENCBS082YEW at ENCODE; https://www.encodeproject.org/ENCBS082YEW/


title: SCAF3016_25681

source_name: Prostate cancer patient

value: Nonlethal


title: Ctrl mouse heart tissue sample C1

description: Library name: C1


title: LEGH7

description: Library name: LEGH7


title: total RNA-seq from T-cell (ENCLB395VAO)

description:
https://www.encodeproject.org/experiments/ENCSR201NVJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR201NVJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB395VAO

source_name: Homo sapiens male adult (42 years) T-cell primary cell

value: T-cell

value: male

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS248SQW at ENCODE; https://www.encodeproject.org/ENCBS248SQW/


title: SCAF3015_24919

value: African American (AA)

value: Lethal


title: pho4(A) strain T=30 min (pH 8.0), replicate A

description: Library name: A_T30_A

source_name: whole cell

value: whole cell


title: LEGH6

description: Library name: LEGH6

value: Uterine cervix


title: hMut mouse heart tissue sample K9

description: Library name: K9

value: heart

value: hMut


title: pho4(A) strain T=15 min (pH 8.0), replicate B

description: Library name: A_T15_B


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB557OSU)

description:
https://www.encodeproject.org/experiments/ENCSR198YAQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR198YAQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB557OSU

source_name: Homo sapiens male adult (38 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: adult

value: 38 year

value: ENCBS046MBI at ENCODE; https://www.encodeproject.org/ENCBS046MBI/


title: SCAF3014_24610

value: Blood

value: European American (EA)


title: pho4(A) strain T=15 min (pH 8.0), replicate A

description: Library name: A_T15_A


title: LEGH5

description: Library name: LEGH5


title: hMut mouse heart tissue sample K8

description: Library name: K8


title: SCAF2821t_23198_TCR


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB556RQU)

description:
https://www.encodeproject.org/experiments/ENCSR197OZY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR197OZY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB556RQU

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: female

value: 34 year

value: ENCBS395ZXN at ENCODE; https://www.encodeproject.org/ENCBS395ZXN/


title: SCAF3013_27150

value: African American (AA)

value: Nonlethal


title: snRNA-seq of post-mortem human parietal cortex, NeuN-Olig2-IRF8+

description:
Library name: SK493_1
Brain bank case: PDC029; region block ID: P3B1; PMI: 48h; RIN: 6.50; cut weight: 370 mg; brain region: parietal cortex; sorting strategy: NeuN-Olig2-IRF8+

source_name: parietal cortex

value: parietal cortex

tag: cell type

value: sorted nuclei

value: FACS sort:NeuN-Olig2-IRF8+

tag: batch


title: LEGH3

description: Library name: LEGH3

value: Uterine cervix


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB107LEJ)

description:
https://www.encodeproject.org/experiments/ENCSR193WWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR193WWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB107LEJ

tag: biosample encode accession

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS267NTR at ENCODE; https://www.encodeproject.org/ENCBS267NTR/


title: hMut mouse heart tissue sample K7

description: Library name: K7

value: heart

value: hMut


title: SCAF3012_22690

value: Blood

value: Lethal


title: LEGH2

description: Library name: LEGH2


title: hMut mouse heart tissue sample K6

description: Library name: K6


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB073AXY)

description:
https://www.encodeproject.org/experiments/ENCSR191MTW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR191MTW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB073AXY

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

value: male

value: adult

value: 42 year

value: ENCBS591YQK at ENCODE; https://www.encodeproject.org/ENCBS591YQK/


title: SCAF3011_21030

value: African American (AA)


title: LEGH1

description: Library name: LEGH1


title: SCAF2817t_21365_TCR

value: Nonlethal


title: hMut mouse heart tissue sample K5

description: Library name: K5


title: SCAF2929_28161

value: European American (EA)


title: transverse colonoid line TC202, adult male, differentiation medium + 10mM isovalerate 2h

description: Library name: TC202_ISO_2H

source_name: colon

value: colon

value: organoid

value: epithelium

value: control + 10mM isovalerate

tag: medium

value: Differentiation


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB185OZW)

description:
https://www.encodeproject.org/experiments/ENCSR190JAK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR190JAK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB185OZW

tag: Sex

tag: dev stage

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS000FHM at ENCODE; https://www.encodeproject.org/ENCBS000FHM/


title: hMut mouse heart tissue sample K4

description: Library name: K4

value: heart

value: hMut


title: UEA7

description: Library name: UEA7

value: Uterine cervix

tag: age


title: SCAF2928_27424

value: Blood


title: total RNA-seq from T-cell (ENCLB437WFU)

description:
https://www.encodeproject.org/experiments/ENCSR189ADQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR189ADQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB437WFU

source_name: Homo sapiens female adult (33 years) T-cell primary cell

value: T-cell

value: primary cell

value: female

value: adult

value: 33 year

tag: lab

value: ENCBS777OHS at ENCODE; https://www.encodeproject.org/ENCBS777OHS/


title: UEA6

description: Library name: UEA6


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB245UPW)

description:
https://www.encodeproject.org/experiments/ENCSR188FWR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR188FWR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB245UPW

source_name: Homo sapiens male adult (30 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

value: male

value: 30 year

tag: source

value: ENCBS727MWA at ENCODE; https://www.encodeproject.org/ENCBS727MWA/


title: SCAF2927_27193

value: African American (AA)


title: hMut mouse heart tissue sample K3

description: Library name: K3


title: UEA4

description: Library name: UEA4


title: total RNA-seq from T-cell (ENCLB543XDQ)

description:
https://www.encodeproject.org/experiments/ENCSR184SAB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR184SAB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB543XDQ

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS486EXS at ENCODE; https://www.encodeproject.org/ENCBS486EXS/


title: SCAF2810t_26003_TCR

tag: tissue

value: Lethal


title: hMut mouse heart tissue sample K1

description: Library name: K1

value: heart


title: UEA3

description: Library name: UEA3


title: hMut mouse heart tissue sample K2

description: Library name: K2

value: hMut


title: SCAF2926_27140

tag: race


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB277QUQ)

description:
https://www.encodeproject.org/experiments/ENCSR183GSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR183GSI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB277QUQ

value: CD4-positive, alpha-beta T cell

value: 40 year

value: AllCells

value: ENCBS603JYZ at ENCODE; https://www.encodeproject.org/ENCBS603JYZ/


title: SCAF2925_25881

value: Blood

value: European American (EA)

tag: lethal prostate_cancer_group


title: UEA1

description: Library name: UEA1

value: Uterine cervix


title: Spatial co-profiling,mouse embryo E13.5_r2, RNA

description:
Library name: mouse_embryo_E13.5_r2_RNA
3'mRNA: read 1 contains transcript sequence; read 2 contains barcodes

source_name: Mouse embryo

value: Mouse embryo

tag: cell line

value: tissue

tag: treatment


title: transverse colonoid line TC202, adult male, differentiation medium 48h

description: Library name: TC202_CON_48H

value: colon

value: organoid

value: epithelium

value: control

value: Differentiation


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB590JMQ)

description:
https://www.encodeproject.org/experiments/ENCSR182HSC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR182HSC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB590JMQ

value: primary cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: ENCBS949CJA at ENCODE; https://www.encodeproject.org/ENCBS949CJA/


title: SCAF2924_24796


title: GAS7

description: Library name: GAS7

tag: Stage

value: ⅡB


title: Spatial co-profiling,mouse embryo E13.5_r2, Hi-C

description:
Library name: mouse_embryo_E13.5_r2_HiC
Hi-C: read 1 contains genome sequence; read 2 contains barcodes

tag: cell type

tag: genotype


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB834YBX)

description:
https://www.encodeproject.org/experiments/ENCSR181BTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR181BTV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB834YBX

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-15 for 1 hour

value: CD4-positive, alpha-beta T cell

tag: biosample encode accession

value: female

value: 34 year

value: AllCells

tag: treatments

value: treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS039XLU at ENCODE; https://www.encodeproject.org/ENCBS039XLU/


title: GAS6

description: Library name: GAS6

value: Uterine cervix

value: ⅣB


title: SCAF2923_23058

value: Blood

value: African American (AA)

value: Lethal


title: GAS4

description: Library name: GAS4


title: SCAF2922_26793


title: Spatial co-profiling,mouse embryo E13.5_r1, Hi-C

description:
Library name: mouse_embryo_E13.5_r1_HiC
Hi-C: read 1 contains genome sequence; read 2 contains barcodes

value: Mouse embryo

value: tissue

tag: batch


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB793LAM)

description:
https://www.encodeproject.org/experiments/ENCSR171AEU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR171AEU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB793LAM

value: primary cell

tag: encode accession

tag: Sex

value: adult

value: ENCBS180ZFO at ENCODE; https://www.encodeproject.org/ENCBS180ZFO/


title: SCAF2921_26678


title: Spatial co-profiling,mouse embryo E13.5_r1, RNA

description:
Library name: mouse_embryo_E13.5_r1_RNA
3'mRNA: read 1 contains transcript sequence; read 2 contains barcodes


title: GAS3

description: Library name: GAS3

tag: age


title: RNAseq_Khdrbs1-KO_rep3

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

country: Netherlands

institute: LUMC

description: Library name: RNAseq_Khdrbs1-KO_rep3

data_processing:
Sequences were trimmed using TrimGalore-0.6.5 with quality setting 30 and Cutadapt version 2.9. Trimmed reads were first mapped to GRCm39_MusMusculus using STAR (v2.7.7a ) with settings -sjdbGTFfile Mus_musculus.GRCm39.114.gtf and -outSAMmultNmax 1. For optimal quantification of alternative splicing events between samples, trimmed reads were re-mapped to GRCm39_MusMusculus using STAR (v2.7.7a), this time using settings -outSJfilterReads Unique, -outSAMstrandField intronMotif, -outFilterMultimapNmax 1, and providing a list of all individual SJ.out.tab files obtained from the first STAR runs in -sjdbFileChrStartEnd. Track figures around Polq exon 3 and 4 were generated in IGV (v2.19.6). For subsequent alternative splicing analyses, reads mapping to alternative chromosome patches were removed using Samtools (Version 1.11). Splicing analyses were performed using JUM (v3.0.0), testing three Wild type versus three Khdrbs1-KO samples. Included were splice junctions that received more than 10 unique mapped reads in at least 2 of the 3 samples per condition (5 for intron retention events). All alternative splicing events were obtained using pvalue setting 1. Read length was defined as 150bp. Alternative splicing events were annotated in JUM-C using a refFlat_GRCm39-file downloaded from the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables). Downstream data processing was performed in Excel. ΔPSI values represent Cassette exon inclusion frequency of Wild type minus Khdrbs1-KO; negative ΔPSI means more inclusion in Khdrbs1-KO compared to Wild type; positive ΔPSI means less inclusion in Khdrbs1-KO compared to Wild type .
Assembly: GRCm39
Supplementary files format and content: JUMoutput_WTvsKhdrbs1KO_CEevents.xlsx: Excel file containing all JUM alternative cassette exon inclusion events identified in three Wild type versus three Khdrbs1-KO samples

growth_protocol: The 129/Ola-derived IB10 mouse embryonic stem (mES) cells were cultured in Buffalo rat liver (BRL)-conditioned knockout Dulbecco’s modified Eagle’s medium (Gibco). The knockout Dulbecco’s modified Eagle’s medium was supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM GlutaMAX, 1 mM sodium pyruvate, 1× non-essential amino acids, 100 μM β-mercaptoethanol (all from Gibco), 10% fetal calf serum (Capricorn Scientific), and leukemia inhibitory factor. The mES cell lines were maintained on 0.1 % gelatin-coated plates. All cultures were incubated at 37°C with 5% CO2 and routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted from mES cells using the NucleoSpin RNA Mini Kit (Macherey-Nagel), following the manufacturer’s protocol. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer with RNA 6000 Nano chips (Agilent Technologies) to determine RNA Integrity Numbers. Only samples with RIN ≥9 were selected for downstream processing. To enable normalization and monitoring of technical variation, the ERCC RNA Spike-In Mix (Thermo Fisher Scientific) was added to each sample prior to library preparation.
RNA sequencing libraries were prepared by Macrogen Inc. (Seoul, South Korea) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina). Libraries were sequenced on an Illumina platform with 150 bp paired-end read configuration.

treatment_protocol: Cells were kept untreated

value: untreated (ERCC RNA Spike-In Mix (Thermo Fisher Scientific) was added to each sample prior to library preparation)


title: SCAF2920_26593

value: European American (EA)

value: Nonlethal


title: GAS1

description: Library name: GAS1


title: RNAseq_Khdrbs1-KO_rep2

description: Library name: RNAseq_Khdrbs1-KO_rep2

source_name: 129/Ola-derived IB10 mouse embryonic stem (mES) cells


title: SCAF2919_26565


title: RNAseq_Khdrbs1-KO_rep1

description: Library name: RNAseq_Khdrbs1-KO_rep1

value: 129/Ola-derived IB10 mouse embryonic stem (mES) cells


title: SCAF2918_24602


title: Spatial co-profiling,human melanoma, RNA

description:
Library name: Human_melanoma_RNA
3'mRNA: read 1 contains transcript sequence; read 2 contains barcodes

data_processing:
Raw reads (fastq file) were aligned to the mouse or human genome using BWA (ATAC), BWA (Hi-C) or STAR (RNA). RNA counts were generated with featureCounts, ATAC  fragments were created with Sinto, and Hi-C pairs were generated with Pairtools.
Assembly: mm10 for mouse embryo and adult brain; hg38 for human melanoma
Supplementary files format and content: RNA.tar.gz: gene expression count matrix in mtx, tsv format
Supplementary files format and content: Image.tar.gz: spatial related images in tif, png, json, csv format
Supplementary files format and content: HIC.nodups.pairs.gz: Hi-C pairs in pairs format
Supplementary files format and content: HIC_RNA.h5ad.gz: HIC_RNA processing data in h5ad format
Supplementary files format and content: ATAC.bed.gz: ATAC fragments in bed format

source_name: Human melanoma

value: Human melanoma


title: RNAseq_WT_rep3

description: Library name: RNAseq_WT_rep3

value: wild type


title: Spatial profiling, human melanoma, ATAC

description:
Library name: Human_melanoma_ATAC
ATAC: read 1 contains genome sequence; read 2 contains barcodes


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB803YCR)

description:
https://www.encodeproject.org/experiments/ENCSR148XTC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR148XTC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB803YCR

source_name: Homo sapiens female adult (33 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: female

tag: dev stage

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS806DSY at ENCODE; https://www.encodeproject.org/ENCBS806DSY/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB955XTD)

description:
https://www.encodeproject.org/experiments/ENCSR146QDU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146QDU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB955XTD

value: male

value: 38 year

tag: source

tag: link

value: ENCBS216AGH at ENCODE; https://www.encodeproject.org/ENCBS216AGH/


title: SCAF2917_22986

tag: tissue

value: Blood

tag: race

value: African American (AA)

value: Lethal


title: Spatial co-profiling,human melanoma, Hi-C

description:
Library name: Human_melanoma_HiC
Hi-C: read 1 contains genome sequence; read 2 contains barcodes


title: RNAseq_WT_rep2

description: Library name: RNAseq_WT_rep2

tag: cell line

value: untreated (ERCC RNA Spike-In Mix (Thermo Fisher Scientific) was added to each sample prior to library preparation)


title: SCAF2916_22928

tag: lethal prostate_cancer_group


title: SCAF2877_27998


title: total RNA-seq from T-cell (ENCLB728WXI)

description:
https://www.encodeproject.org/experiments/ENCSR142YRS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR142YRS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB728WXI

value: T-cell

value: primary cell

value: adult

value: ENCBS463NPC at ENCODE; https://www.encodeproject.org/ENCBS463NPC/


title: U1 GA and HelixH G12A/C122U variant

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

description:
Library name: U1.GA.HelixH.ID1
column name in the processed files: num_U1.GA.HelixH.ID1

data_processing:
RNAseq and splicing analysis were described earlier using DEDseq (https:// github.com/liwc01/DEDSeq, REF) with minor modifications.
RNA sequencing reads were mapped to human genome (hg19) using STAR (version 2.7.10b) (REF; PMID: 34911927); only uniquely mapped reads (with MAPQ > 10) with <5nt/100nt mismatches and properly paired reads were used.
For splicing analysis, all junction reads (read with a gap in alignment indicating splicing) were used, including the ones mapped to unannotated splice sites. Reads were counted for different exons (for cassette exon [CE]) or exonic regions (for A5′ss or A3′ss). For each splicing event, a percent-spliced-in (PSI) value was calculated using the percent of average read number supporting the inclusion among all reads supporting either the inclusion or the exclusion. A minimum of 10 for the denominator of PSI calculation was required. Otherwise, a ‘NA’ value would be generated. PSI values for biological replicates were averaged, and the PSI difference between the two treatment groups was calculated. For a statistical test, a 2 × 2 read counts table was made for each event, with rows for reads supporting inclusion or exclusion, and columns for the two comparing sample groups. Fisher’s exact test was used for the statistical tests. For biological replicates, each pair of the testing and control sample was analyzed by Fisher’s exact test and the geometric mean of all P-values was reported as a final P-value.  PSI change (deltaPSI) of >10% (or < −10%) and P < 0.001 was used to select splicing events being regulated by the treatment. PSI calculation, Fisher’s exact test, were performed using R (4.0.5).
Assembly: hg19
Supplementary files format and content: U1CKD_2CpdDR_293RNAseq.junction.counts.txt.gz: tab-delimited text file with rows representing splice junctions (from a 5'ss to a 3'ss) and columns representing the read counts in different RNAseq samples
Supplementary files format and content: U1CKD_2CpdDR_293RNAseq.Gene.counts.txt.gz: a tab-delimited text file with rows representing genes and columns representing read counts in RNAseq
Supplementary files format and content: U1_HelixH_GA_variants.junction.counts.txt.gz: tab-delimited text file with rows representing splice junctions (from a 5'ss to a 3'ss) and columns representing the read counts in different RNAseq samples

growth_protocol: HEK293T cells were grown in DMEM media with 10% FBS. 500,000 cells in 1.75mL of media were plated into a 6 well plate for approximately 6 hours.

extract_protocol:
RNA was isolated using KingFisherTM Apex instrument and the MagMAX™ mirVana™ Total RNA Isolation Kit (A27828) by Thermo Fisher according to manufacturer’s protocol.
Isolated RNA was submitted to Admera Health for library preparation (polyA selected, stranded) and mRNA-sequencing and >20M 150bp pair-end reads were returned.

treatment_protocol: Either siRNA negative control (ThermoFisher SilencerTM Negative control #2, AM4613) or U1C siRNA (ThermoFisher SilencerTM Select Pre-designed siRNA, S13225) were transfected for a final concentration of 25nM using Invitrogen Lipofectamine RNAiMax (13778-150). In brief, 10 uL 5uM siRNA was added to 115 uL of OptiMEM while 5 uL Lipofectamine added to 120 uL OptiMEM for 5 minutes before mixing the solutions and incubating for 20 minutes. 250uL of Lipofectamine:siRNA solution was gentle added to the 1.75mL cells. After 24 hours post-transfection, cells were treated with 10uL compound resuspended in DMSO. Final concentrations of branaplam were 1.2mM, 400nM, 100nM, 25nM, and 5nM. Final concentrations of risdiplam were 3.6mM, 1.2mM, 400nM, 200nM, and 50nM. Each compound treated experimental condition was treated and collected in duplicate while four DMSO only treated samples per siRNA transfection were collected. Synthesize of the U1 variants constructs, growth of HEK293 cells, transfection and RNA isolation were described in Bhattacharyya, et al 2021.

tag: treatment

value: U1 GA and HelixH G12A/C122U variant


title: total RNA-seq from T-cell (ENCLB330TQT)

description:
https://www.encodeproject.org/experiments/ENCSR142OOS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR142OOS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB330TQT

value: 42 year

value: ENCBS294XBJ at ENCODE; https://www.encodeproject.org/ENCBS294XBJ/


title: RNAseq_WT_rep1

description: Library name: RNAseq_WT_rep1

value: 129/Ola-derived IB10 mouse embryonic stem (mES) cells

value: wild type


title: SCAF2876_26608


title: U1 GA and HelixH C122G variant

description:
Library name: U1.GA.HelixH.Break2
column name in the processed files: num_U1.GA.HelixH.Break2

value: U1 GA and HelixH C122G variant


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB421CLC)

description:
https://www.encodeproject.org/experiments/ENCSR140GZF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR140GZF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB421CLC

value: CD4-positive, alpha-beta T cell

value: female

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS369APM at ENCODE; https://www.encodeproject.org/ENCBS369APM/


title: gavage vehicle LPLFD 3

description: Library name: LL11_109_gav_lpl_veh

growth_protocol: SPF and GF C57BL/6J mice were obtained from The Jackson Laboratory or the Center for Comparative Medicine at Baylor College of Medicine. Dams with 8-day-old pups were randomized to receive either a triple-irradiated control chow diet (20% kcal from protein, 15% kcal from fat, 65% kcal from carbohydrate; Research Diets #D21012505-1.5Viii) or a triple-irradiated low-protein, low-fat diet (LPLFD; 7% kcal from protein, 5% kcal from fat, 88% kcal from carbohydrate; Research Diets # D21012506-1.5Viii), both formulated to be isocaloric. Offspring were weaned at postnatal day 21 (DOL 21) onto the same diet as their dams and maintained ad libitum on these diets for an additional 5 weeks.

extract_protocol:
Colonic tissue was excised, opened longitudinally, and rinsed in ice-cold Ca2+ and Mg2+ free DPBS (Gibco) to remove luminal contents. Tissues were kept on ice until all samples were collected. Tissues were incubated in a chelation buffer (30 mM EDTA, 1.5 mM DTT in DPBS) on ice for 20 minutes, followed by transfer to a second EDTA-based dissociation solution (30 mM EDTA in DPBS) pre-warmed to 37°C and incubated for 10 minutes. Samples were shaken vigorously for ~30 seconds to detach the epithelium and the resulting suspension was collected while excluding residual tissue fragments. Cells were pelleted (800 × g, 4°C, 5 minutes) and either reconstituted in Trizol (Zymo Research) for RNA extraction, and submitted to Novogene (Sacramento, CA) for poly(A)-based mRNA enrichment, library preparation, and NovaSeq PE150 sequencing (~6 Gb raw reads/sample).
Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 150 bp) was performed on an Illumina NovaSeq X Plus  for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample.

treatment_protocol: At DOL 56, mice received 114 mM of either leucine or alanine (Millipore Sigma) by oral gavage twice daily for 2.5 days. Sterile water was used as vehicle control. In separate experiments, 100 mM sodium isovalerate (Pfaltz & Bauer) pH- and osmolality-matched saline was administered daily via rectal enema for 3 days. For enemas, mice were anesthetized with isoflurane, solutions were instilled via a flexible catheter, and animals were maintained in a head-down position for 1 minute to facilitate retention.

value: colon

tag: strain

tag: cell type

value: epithelium

tag: disease state

value: gavage vehicle LPLFD

value: male


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB519EMM)

description:
https://www.encodeproject.org/experiments/ENCSR137ZAT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR137ZAT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB519EMM

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: primary cell

tag: biosample encode accession

value: adult

value: ENCBS822OJB at ENCODE; https://www.encodeproject.org/ENCBS822OJB/


title: U1-GA variant

description:
Library name: U1.GA
column name in the processed files: num_U1.GA

value: U1-GA variant

tag: batch


title: SCAF2874_26082

value: Blood

value: European American (EA)

value: Nonlethal


title: gavage vehicle LPLFD 2

description: Library name: LL11_108_gav_lpl_veh


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB626USR)

description:
https://www.encodeproject.org/experiments/ENCSR134COS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR134COS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB626USR

value: CD4-positive, alpha-beta T cell

tag: encode accession

value: 42 year

value: ENCBS765KGF at ENCODE; https://www.encodeproject.org/ENCBS765KGF/


title: SCAF2873_25197

value: African American (AA)


title: mock, rep4

description:
Library name: Mock.4
column name in the processed files: num_Mock.4

value: mock, rep4


title: gavage vehicle LPLFD 1

description: Library name: LL11_107_gav_lpl_veh

tag: Sex


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB678OAU)

description:
https://www.encodeproject.org/experiments/ENCSR133IAE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133IAE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB678OAU

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-2 for 1 hour

value: female

tag: age

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS818ENX at ENCODE; https://www.encodeproject.org/ENCBS818ENX/


title: SCAF2872_24230


title: ascending colonoid line Asc231, adult male, differentiation medium + 10mM isovalerate 2h

description: Library name: ASC231_ISO_2H

value: colon

value: organoid

value: epithelium

value: control + 10mM isovalerate

tag: medium

value: Differentiation


title: snATAC-seq from B cell (ENCLB381YUB)

description:
https://www.encodeproject.org/experiments/ENCSR177OXQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR177OXQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB381YUB
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (22 years) B primary cell nuclear fraction

value: B cell

value: primary cell

value: male

tag: dev stage

value: adult

value: 22 year

tag: lab

value: Yijun Ruan, JAX

tag: subcellular fraction term name

value: nucleus

tag: source

value: ENCBS254AQR at ENCODE; https://www.encodeproject.org/ENCBS254AQR/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: mock, rep3

description:
Library name: Mock.3
column name in the processed files: num_Mock.3

tag: cell line

value: mock, rep3


title: gavage vehicle control 5

description: Library name: LL11_106_gav_con_veh

tag: tissue

value: gavage vehicle control


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB757WFU)

description:
https://www.encodeproject.org/experiments/ENCSR131HNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR131HNT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB757WFU

source_name: Homo sapiens male adult (38 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS464DSB at ENCODE; https://www.encodeproject.org/ENCBS464DSB/


title: SCAF2871_22771

source_name: Prostate cancer patient

value: Blood

tag: race

value: African American (AA)

tag: lethal prostate_cancer_group

value: Lethal


title: mock, rep2

description:
Library name: Mock.2
column name in the processed files: num_Mock.2

tag: treatment

value: mock, rep2