title: total RNA-seq from T-helper 17 cell (ENCLB474TWJ)

description:
https://www.encodeproject.org/experiments/ENCSR770ZYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR770ZYC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB474TWJ

source_name: Homo sapiens female adult (33 years) T-helper 17 primary cell

value: T-helper 17 cell

value: female

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS827BAF at ENCODE; https://www.encodeproject.org/ENCBS827BAF/


title: C-2

status: Public on Jul 24 2026

type: SRA

city: qingdao

first: shijie

last: bi

address: No. 23, Hong Kong East Road

country: China

institute: ouc

description:
Library name: sample12
Column name in counts_allsamples.txt: C-2

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: Tumor

tag: cell line

tag: cell type

value: melanoma cell

tag: genotype

value: WT

tag: treatment

value: VPE-PTEN

tag: batch

value: Day 10


title: MCF7 Vehicle DMSO 0.1%-1

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

country: USA

institute: University of South Carolina

description:
Library name: S85
ST-DMSO1
202507_InVitroCompiled_All_CPMTPM.xlsx

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Sequences were aligned to the GRCh38 using STAR v2.7.2b with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38 & GRCm39
Supplementary files format and content: 202507_InVitroCompiled_All_CPMTPM.xlsx file includes CPM/TPM values for each Samples, subsequent sheets include treatment group avarage CPM/TPM and DEG values.
Supplementary files format and content: 202507_InVivo_Human_genes_TPM file includes TPM values for each in vivo sample, subsequent sheets include treatment group avarage TPM and DEG values.

organism: Homo sapiens

source_name: Adherent epithelial cells

extract_protocol:
Total RNA was extracted using  Qiagen RNeasy Kits for RNA Purification kit as per manufacturer recommendations (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent) / 5200 Fragment Analyzer.
S01~S15 and S65~84 sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit, S85~S96 sequencing libraries were generated using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD.

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

value: 0.1 % DMSO


title: snATAC-seq from SK-N-SH (ENCLB018JAT)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR095KCD/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line SK-N-SH (RA treated)
experiment encode accession: ENCSR095KCD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB018JAT
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

library_source: genomic

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

molecule: genomic DNA

source_name: Homo sapiens SK-N-SH cell line treated with 6 uM all-trans-retinoic acid for 48 hours nuclear fraction

tag: line

value: SK-N-SH

value: cell line

tag: biosample encode accession

tag: Sex

tag: health state

value: Metastatic neuroblastoma from bone marrow

tag: dev stage

value: child

tag: age

value: 4 year

tag: lab

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

tag: source

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

tag: link

value: ENCBS620EDO at ENCODE; https://www.encodeproject.org/ENCBS620EDO/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: normal bone marrow #5

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

tag: tissue

value: bone marrow

tag: disease state

value: normal

tag: time point


title: total RNA-seq from T-cell (ENCLB461LJZ)

description:
https://www.encodeproject.org/experiments/ENCSR766GLB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR766GLB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB461LJZ

source_name: Homo sapiens female adult (33 years) T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours

value: T-cell

value: primary cell

tag: encode accession

value: female

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour;

value: ENCBS921RWD at ENCODE; https://www.encodeproject.org/ENCBS921RWD/


title: snATAC-seq from heart left ventricle (ENCLB107XTN)

description:
https://www.encodeproject.org/experiments/ENCSR088ZOL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR088ZOL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB107XTN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (31 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: male

value: 31 year

value: Michael Snyder, Stanford

value: Shin Lin

value: healthy

value: ENCBS505KRY at ENCODE; https://www.encodeproject.org/ENCBS505KRY/

value: Derived from ENCODE donor ENCDO862XAV; https://www.encodeproject.org/ENCDO862XAV/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB865YLY)

description:
https://www.encodeproject.org/experiments/ENCSR767VVE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR767VVE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB865YLY

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

value: female

value: 40 year

value: ENCBS331LIZ at ENCODE; https://www.encodeproject.org/ENCBS331LIZ/


title: normal bone marrow #4

value: untreated

value: bone marrow

value: normal


title: B-4

description:
Library name: sample9
Column name in counts_allsamples.txt: B-4

value: Tumor

tag: cell line

tag: cell type

value: melanoma cell

tag: genotype

value: WT

tag: treatment

value: VPE-WT

tag: batch

value: Day 10


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB565NWX)

description:
https://www.encodeproject.org/experiments/ENCSR765JAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR765JAZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB565NWX

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

value: CD8-positive, alpha-beta T cell

tag: biosample encode accession

tag: Sex

tag: dev stage

value: adult

tag: age

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS013UYP at ENCODE; https://www.encodeproject.org/ENCBS013UYP/


title: normal bone marrow #3-3


title: snATAC-seq from upper lobe of right lung (ENCLB623WSG)

description:
https://www.encodeproject.org/experiments/ENCSR086LCZ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human upper lobe of right lung
experiment encode accession: ENCSR086LCZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB623WSG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (60 years) upper lobe of right lung tissue, preserved by cryopreservation nuclear fraction

value: upper lobe of right lung

value: tissue

value: male

tag: health state

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: 60 year

tag: lab

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

tag: source

value: Yiing Lin, MD, PhD

value: ENCBS472WKJ at ENCODE; https://www.encodeproject.org/ENCBS472WKJ/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: TF ChIP-seq from HepG2 (ENCLB061YKD)

description:
https://www.encodeproject.org/experiments/ENCSR752CRD/
***************
biological replicate number: 1
technical replicate number: 1
description: JUND ChIP-seq on HepG2 cells treated with sgRNA targeting CEBPB
experiment encode accession: ENCSR752CRD
assay title: TF ChIP-seq
possible controls: ENCSR670SEW, ENCSR943SJY
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB061YKD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens CEBPB

tag: antibody

value: JUND

tag: line

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

tag: link

value: ENCBS287BGP at ENCODE; https://www.encodeproject.org/ENCBS287BGP/


title: B-3

description:
Library name: sample8
Column name in counts_allsamples.txt: B-3

tag: tissue

value: Tumor

value: melanoma cell

value: WT

value: VPE-WT

value: Day 10


title: snATAC-seq from heart left ventricle (ENCLB236RSZ)

description:
https://www.encodeproject.org/experiments/ENCSR084DVM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR084DVM
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB236RSZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (20 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

value: male

value: nonischemic

value: adult

value: 20 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS650GQB at ENCODE; https://www.encodeproject.org/ENCBS650GQB/

value: Derived from ENCODE donor ENCDO061UFT; https://www.encodeproject.org/ENCDO061UFT/


title: total RNA-seq from T-cell (ENCLB481SRC)

description:
https://www.encodeproject.org/experiments/ENCSR748EWB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR748EWB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB481SRC

source_name: Homo sapiens male adult (42 years) T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: T-cell

value: primary cell

tag: encode accession

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS565YBR at ENCODE; https://www.encodeproject.org/ENCBS565YBR/


title: normal bone marrow #3

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 (ENCLB405EQM)

description:
https://www.encodeproject.org/experiments/ENCSR744MZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR744MZD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB405EQM

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

value: CD4-positive, alpha-beta T cell

tag: biosample encode accession

value: female

value: 34 year

value: ENCBS541DIK at ENCODE; https://www.encodeproject.org/ENCBS541DIK/


title: normal bone marrow #2-2


title: snATAC-seq from heart left ventricle (ENCLB673HHC)

description:
https://www.encodeproject.org/experiments/ENCSR080TZR/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart left ventricle
experiment encode accession: ENCSR080TZR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB673HHC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (69 years) heart left ventricle tissue nuclear fraction

value: heart left ventricle

value: tissue

tag: Sex

value: male

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: nucleus

value: Shin Lin

value: ENCBS887VVW at ENCODE; https://www.encodeproject.org/ENCBS887VVW/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: normal bone marrow #2

value: untreated

value: bone marrow


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB923UTW)

description:
https://www.encodeproject.org/experiments/ENCSR738ZEH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR738ZEH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB923UTW

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

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: dev stage

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS954KJE at ENCODE; https://www.encodeproject.org/ENCBS954KJE/


title: snATAC-seq from heart left ventricle (ENCLB934LMM)

description:
https://www.encodeproject.org/experiments/ENCSR161IHV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR161IHV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB934LMM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (57 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

value: male

value: nonischemic

tag: age

value: 57 year

value: ENCBS159AKG at ENCODE; https://www.encodeproject.org/ENCBS159AKG/

value: Derived from ENCODE donor ENCDO639HZG; https://www.encodeproject.org/ENCDO639HZG/


title: snATAC-seq from SK-N-SH (ENCLB031QDV)

description:
https://www.encodeproject.org/experiments/ENCSR161GPE/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line SK-N-SH
experiment encode accession: ENCSR161GPE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB031QDV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: SK-N-SH

value: cell line

value: female

tag: health state

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: Michael Snyder, Stanford

value: nucleus

value: ATCC

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS474KMT at ENCODE; https://www.encodeproject.org/ENCBS474KMT/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCLB687ZOL)

description:
https://www.encodeproject.org/experiments/ENCSR736ZEJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR736ZEJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB687ZOL

source_name: Homo sapiens female adult (33 years) activated effector memory CD4-positive, alpha-beta T primary cell

value: primary cell

value: adult

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS150HAG at ENCODE; https://www.encodeproject.org/ENCBS150HAG/


title: E-1

description:
Library name: sample21
Column name in counts_allsamples.txt: E-1

source_name: Tumor

value: Tumor

tag: cell line

tag: cell type

value: melanoma cell

tag: genotype

value: WT

tag: treatment

value: VPE-PTEN+RG-NPs

tag: batch

value: Day 10


title: snATAC-seq from ovary (ENCLB751QZO)

description:
https://www.encodeproject.org/experiments/ENCSR075FKI/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human ovary
experiment encode accession: ENCSR075FKI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB751QZO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (59 years) ovary tissue, preserved by cryopreservation nuclear fraction

value: ovary

value: tissue

value: female

value: DM:yes; HTN:yes; CAD:no

value: 59 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS924VHJ at ENCODE; https://www.encodeproject.org/ENCBS924VHJ/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: MIAML-293-Re

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

source_name: leukemic bone marrow (AML)

tag: ex vivo treatment

value: untreated

tag: tissue

value: bone marrow

value: AML

value: at relapse


title: D-4

description:
Library name: sample19
Column name in counts_allsamples.txt: D-4

value: Tumor

value: melanoma cell

value: RG-NPs


title: A-2

description:
Library name: sample2
Column name in counts_allsamples.txt: A-2

value: WT

value: PBS

value: Day 10


title: TF ChIP-seq from K562 (ENCLB826NCM)

description:
https://www.encodeproject.org/experiments/ENCSR785RQR/
***************
biological replicate number: 1
technical replicate number: 1
description: JUND ChIP-seq on K562 cells treated with sgRNA targeting CEBPB
experiment encode accession: ENCSR785RQR
assay title: TF ChIP-seq
possible controls: ENCSR500KIT, ENCSR194GTV
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB826NCM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens CEBPB

tag: antibody

value: JUND

tag: line

value: cell line

tag: encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS357BSQ at ENCODE; https://www.encodeproject.org/ENCBS357BSQ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB555HDQ)

description:
https://www.encodeproject.org/experiments/ENCSR735EEM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR735EEM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB555HDQ

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: Sex

tag: dev stage

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS081TIJ at ENCODE; https://www.encodeproject.org/ENCBS081TIJ/


title: MIAML-293-Dx

value: untreated

value: bone marrow

tag: disease state

value: AML

tag: time point

value: at diagnosis


title: TF ChIP-seq from K562 (ENCLB089CPA)

description:
https://www.encodeproject.org/experiments/ENCSR075FCS/
***************
biological replicate number: 1
technical replicate number: 1
description: TEAD4 ChIP-seq on K562 cells treated with shRNA targeting MAFF
experiment encode accession: ENCSR075FCS
assay title: TF ChIP-seq
possible controls: ENCSR538UCE
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB089CPA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: cell line

tag: health state

tag: age

tag: lab

value: Michael Snyder, Stanford

value: ENCBS019EPP at ENCODE; https://www.encodeproject.org/ENCBS019EPP/


title: A-1

description:
Library name: sample1
Column name in counts_allsamples.txt: A-1

value: Tumor

tag: cell line

tag: cell type

value: melanoma cell

tag: genotype

value: WT

tag: treatment

value: PBS

tag: batch

value: Day 10


title: MCF7 500nM SNX631-2

description:
Library name: S89
ST-PAL2
202507_InVitroCompiled_All_CPMTPM.xlsx

source_name: Adherent epithelial cells

tag: tissue

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer


title: total RNA-seq from inflammatory macrophage (ENCLB460ZCH)

description:
https://www.encodeproject.org/experiments/ENCSR730DLN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR730DLN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB460ZCH

source_name: Homo sapiens male adult (24 years) inflammatory macrophage primary cell

value: inflammatory macrophage

value: primary cell

value: male

value: adult

value: 24 year

value: John Stamatoyannopoulos, UW

tag: source

value: Shelly Heimfeld

tag: link

value: ENCBS493FFZ at ENCODE; https://www.encodeproject.org/ENCBS493FFZ/


title: C-5

description:
Library name: sample15
Column name in counts_allsamples.txt: C-5

value: VPE-PTEN


title: snATAC-seq from heart left ventricle (ENCLB466PNW)

description:
https://www.encodeproject.org/experiments/ENCSR061BEN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR061BEN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB466PNW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (61 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: nonischemic (EF 23%, LVEDD 6.5)

value: 61 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS346JJG at ENCODE; https://www.encodeproject.org/ENCBS346JJG/

value: Derived from ENCODE donor ENCDO229CTV; https://www.encodeproject.org/ENCDO229CTV/


title: DPDH-3

city: Nanjing

first: weiwei

last: Zheng

state: Jiangsu

address: Xianlin Road 138

institute: Nanjing University of Chinese Medicine

description: Library name: Sample 6

data_processing:
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Brain

extract_protocol:
extracted by Trizol according to the USER GUID
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Brain

value: Primary cell

value: Endothelial cells


title: C-3

description:
Library name: sample13
Column name in counts_allsamples.txt: C-3

value: Tumor

value: melanoma cell

value: WT

value: Day 10


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB169CSJ)

description:
https://www.encodeproject.org/experiments/ENCSR730CSH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR730CSH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB169CSJ

source_name: Homo sapiens female adult (33 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

value: female

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS841FWI at ENCODE; https://www.encodeproject.org/ENCBS841FWI/


title: snATAC-seq from HCT116 (ENCLB830YVS)

description:
https://www.encodeproject.org/experiments/ENCSR058GOM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR058GOM
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB830YVS
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens HCT116 cell line nuclear fraction

tag: line

value: cell line

tag: Sex

value: male

value: colorectal carcinoma

tag: dev stage

value: 48 year

value: Mats Ljungman, UMichigan

tag: subcellular fraction term name

value: nucleus

value: ATCC

value: ENCBS183VWU at ENCODE; https://www.encodeproject.org/ENCBS183VWU/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: C-1

description:
Library name: sample11
Column name in counts_allsamples.txt: C-1

value: Tumor

value: melanoma cell

value: WT

value: VPE-PTEN

value: Day 10


title: B-5

description:
Library name: sample10
Column name in counts_allsamples.txt: B-5

value: VPE-WT


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB092LDM)

description:
https://www.encodeproject.org/experiments/ENCSR727RLJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR727RLJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB092LDM

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

tag: age

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS587WNV at ENCODE; https://www.encodeproject.org/ENCBS587WNV/


title: TF ChIP-seq from HepG2 (ENCLB047ULA)

description:
https://www.encodeproject.org/experiments/ENCSR054ZMK/
***************
biological replicate number: 1
technical replicate number: 1
description: NR2F2 ChIP-seq on HepG2 cells treated with shRNA targeting FOXA3
experiment encode accession: ENCSR054ZMK
assay title: TF ChIP-seq
possible controls: ENCSR142JFU, ENCSR441NSM
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB047ULA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting H. sapiens FOXA3

tag: antibody

value: cell line

tag: note

value: Homo sapiens HepG2 cell line transduced with doxycycline-inducible shRNA targeting non-targeting control. Cells were treated for 72 hours with 4ug/mL doxycycline prior to experiment harvest.

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

tag: lab

value: Michael Snyder, Stanford

value: ENCBS825SFH at ENCODE; https://www.encodeproject.org/ENCBS825SFH/


title: MIAML-210-Re-v2

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

tag: ex vivo treatment

value: untreated

value: bone marrow

tag: disease state

value: AML

tag: time point

value: at relapse


title: DPDH-1

description: Library name: Sample 4

tag: tissue

value: Brain

tag: cell line

value: Primary cell

tag: cell type

value: Endothelial cells


title: snATAC-seq from heart left ventricle (ENCLB815ROW)

description:
https://www.encodeproject.org/experiments/ENCSR051ECW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR051ECW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB815ROW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (55 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

tag: biosample encode accession

value: nonischemic (EF 25%, LVEDD 5.8)

value: adult

value: 55 year

tag: source

value: Shin Lin

tag: link

value: ENCBS652JMT at ENCODE; https://www.encodeproject.org/ENCBS652JMT/

value: Derived from ENCODE donor ENCDO865TFF; https://www.encodeproject.org/ENCDO865TFF/


title: MIAML-210-Dx-v2

value: at diagnosis


title: Krit1iECKO-3

description: Library name: Sample 3


title: snATAC-seq from pancreas (ENCLB969DOC)

description:
https://www.encodeproject.org/experiments/ENCSR042RUW/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human pancreas
experiment encode accession: ENCSR042RUW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB969DOC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (61 years) pancreas tissue, preserved by cryopreservation nuclear fraction

value: pancreas

tag: Sex

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

tag: dev stage

value: 61 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS805SGE at ENCODE; https://www.encodeproject.org/ENCBS805SGE/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: Krit1iECKO-2

description: Library name: Sample 2

value: Brain

value: Primary cell

value: Endothelial cells


title: MIAML-210-Re

value: untreated

value: bone marrow

value: AML

value: at relapse


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB053KSH)

description:
https://www.encodeproject.org/experiments/ENCSR721NBI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR721NBI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB053KSH

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

value: primary cell

tag: encode accession

value: male

value: adult

tag: age

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS768FYT at ENCODE; https://www.encodeproject.org/ENCBS768FYT/


title: MIAML-210-Dx

value: at diagnosis


title: snATAC-seq from heart left ventricle (ENCLB840CJW)

description:
https://www.encodeproject.org/experiments/ENCSR079TCC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR079TCC
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB840CJW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (68 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: ischemic

value: 68 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS623RZE at ENCODE; https://www.encodeproject.org/ENCBS623RZE/

value: Derived from ENCODE donor ENCDO239INK; https://www.encodeproject.org/ENCDO239INK/


title: snATAC-seq from HCT116 (ENCLB108WCL)

description:
https://www.encodeproject.org/experiments/ENCSR076QTT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR076QTT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB108WCL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF

tag: line

value: cell line

value: colorectal carcinoma

value: 48 year

value: Dr. Masato Kanemaki

value: ENCBS923KAP at ENCODE; https://www.encodeproject.org/ENCBS923KAP/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: snATAC-seq from activated B cell (ENCLB057YYG)

description:
https://www.encodeproject.org/experiments/ENCSR719QGN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR719QGN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB057YYG
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (22 years) activated B primary cell treated with 0.5 uM CpG ODN for 24 hours nuclear fraction

value: activated B cell

value: primary cell

value: male

value: adult

value: 22 year

value: Yijun Ruan, JAX

tag: subcellular fraction term name

value: nucleus

value: AllCells

tag: treatments

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS944UFG at ENCODE; https://www.encodeproject.org/ENCBS944UFG/

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


title: A-4

description:
Library name: sample4
Column name in counts_allsamples.txt: A-4

source_name: Tumor

value: Tumor

value: melanoma cell

tag: genotype

value: WT

tag: treatment

value: PBS

tag: batch

value: Day 10


title: Krit1iECKO-1

description: Library name: Sample 1

tag: tissue

value: Brain

value: Primary cell

value: Endothelial cells


title: snATAC-seq from placenta (ENCLB074VGH)

description:
https://www.encodeproject.org/experiments/ENCSR029KFQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR029KFQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB074VGH
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male embryo placenta tissue nuclear fraction

value: placenta

value: tissue

value: male

value: embryonic

value: not collected

tag: lab

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS256AHV at ENCODE; https://www.encodeproject.org/ENCBS256AHV/

value: Derived from ENCODE donor ENCDO023YQQ; https://www.encodeproject.org/ENCDO023YQQ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB150GAO)

description:
https://www.encodeproject.org/experiments/ENCSR719BLV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR719BLV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB150GAO

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

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 34 year

value: AllCells

value: ENCBS886TFW at ENCODE; https://www.encodeproject.org/ENCBS886TFW/


title: hSKP2-KI mouse ventral prostate bio rep 4

city: Orange

first: Liankun

last: Song

state: California

address: 101 the city dr. south, bldg55, rm260

institute: University of California, Irvine

description:
Library name: KI4
Column name in TPM_all_samples.csv: KI4

data_processing:
CLC genomic workbench 23.0.3
Raw sequencing reads were trimmed using quality score of 0.05 in CLC workbench.
Trimmed reads were mapped to reference sequence Mus_musculus_sequence_mm10_o in CLC workbench. (parameters: mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8)
Read counts extraction and normalization were performed in CLC workbench.
Assembly: GRCm38 (mm10)
Supplementary files format and content: CSV file include TPM values for each sample.

source_name: mouse ventral prostate

extract_protocol:
Ventral lobes of prostates from hSKP2-KI (n=4) and WT mice (n=4) at 12 months old age were freshly dissected and immediately homogenized in RNAStat (Amsbio, Friendswood, TX). The integrities of total RNA were analyzed by Agilent 2100 with an RNA integrity numbers ranging from 8 to 10.
Total mRNA was purified using poly-T oligo-attached magnetic beads and after fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were then checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution.

value: mouse ventral prostate

tag: cell type

value: primary tissue

value: FVB/N hSKP2 knock in


title: MIAML-137-Re

source_name: leukemic bone marrow (AML)

tag: ex vivo treatment

value: untreated

value: bone marrow

tag: disease state

value: AML

tag: time point

value: at relapse


title: snATAC-seq from adrenal gland (ENCLB152ADD)

description:
https://www.encodeproject.org/experiments/ENCSR028JGT/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human adrenal gland
experiment encode accession: ENCSR028JGT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB152ADD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (47 years) adrenal gland tissue, preserved by cryopreservation nuclear fraction

value: adrenal gland

value: tissue

tag: biosample encode accession

tag: health state

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: Michael Snyder, Stanford

value: nucleus

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS431JKP at ENCODE; https://www.encodeproject.org/ENCBS431JKP/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: MIAML-137-Dx

value: at diagnosis


title: hSKP2-KI mouse ventral prostate bio rep 3

description:
Library name: KI3
Column name in TPM_all_samples.csv: KI3

value: mouse ventral prostate


title: TF ChIP-seq from HepG2 (ENCLB337FRO)

description:
https://www.encodeproject.org/experiments/ENCSR028HEK/
***************
biological replicate number: 1
technical replicate number: 1
description: TEAD4 ChIP-seq on HepG2 cells treated with shRNA targeting FOXA3
experiment encode accession: ENCSR028HEK
assay title: TF ChIP-seq
possible controls: ENCSR142JFU, ENCSR981UIH
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB337FRO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

value: cell line

tag: encode accession

tag: Sex

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

value: ATCC

value: ENCBS657QMS at ENCODE; https://www.encodeproject.org/ENCBS657QMS/


title: MIAML-109-Re-v2

value: untreated

value: bone marrow

value: AML

value: at relapse


title: hSKP2-KI mouse ventral prostate bio rep 2

description:
Library name: KI2
Column name in TPM_all_samples.csv: KI2

value: primary tissue

tag: genotype

value: FVB/N hSKP2 knock in


title: snATAC-seq from heart left ventricle (ENCLB463JNA)

description:
https://www.encodeproject.org/experiments/ENCSR020FAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR020FAW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB463JNA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (21 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: healthy

value: adult

value: 21 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS107FQC at ENCODE; https://www.encodeproject.org/ENCBS107FQC/

value: Derived from ENCODE donor ENCDO934DRK; https://www.encodeproject.org/ENCDO934DRK/


title: MIAML-109-Dx-v2

tag: tissue

value: at diagnosis


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB982THT)

description:
https://www.encodeproject.org/experiments/ENCSR710NBJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR710NBJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB982THT

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

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: 42 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS249JKQ at ENCODE; https://www.encodeproject.org/ENCBS249JKQ/


title: hSKP2-KI mouse ventral prostate bio rep 1

description:
Library name: KI1
Column name in TPM_all_samples.csv: KI1

value: mouse ventral prostate

tag: cell type

value: primary tissue

value: FVB/N hSKP2 knock in


title: snATAC-seq from CD14-positive monocyte (ENCLB123KCP)

description:
https://www.encodeproject.org/experiments/ENCSR009WQK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR009WQK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB123KCP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (51 years) CD14-positive monocyte primary cell nuclear fraction

value: CD14-positive monocyte

value: adult

value: 51 year

value: Yijun Ruan, JAX

tag: subcellular fraction term name

value: nucleus

value: ENCBS093XSU at ENCODE; https://www.encodeproject.org/ENCBS093XSU/

value: Derived from ENCODE donor ENCDO346BRO; https://www.encodeproject.org/ENCDO346BRO/


title: MIAML-109-Re

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

tag: ex vivo treatment

value: untreated

value: bone marrow

tag: disease state

value: AML

value: at relapse


title: wild type mouse ventral prostate bio rep 4

description:
Library name: WT4
Column name in TPM_all_samples.csv: WT4

value: FVB/N wild type


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB799AQN)

description:
https://www.encodeproject.org/experiments/ENCSR702QOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR702QOF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB799AQN

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

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

value: male

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS013PXD at ENCODE; https://www.encodeproject.org/ENCBS013PXD/


title: snATAC-seq from heart left ventricle (ENCLB715YFN)

description:
https://www.encodeproject.org/experiments/ENCSR003DSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR003DSI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB715YFN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (50 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

tag: health state

value: ischemic (EF 49%, LVEDD 4.7) w/ Impella

value: adult

value: 50 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS662JCB at ENCODE; https://www.encodeproject.org/ENCBS662JCB/

value: Derived from ENCODE donor ENCDO602PYC; https://www.encodeproject.org/ENCDO602PYC/


title: MIAML-109-Dx

value: untreated

value: bone marrow

value: AML

tag: time point

value: at diagnosis


title: wild type mouse ventral prostate bio rep 3

description:
Library name: WT3
Column name in TPM_all_samples.csv: WT3

value: mouse ventral prostate

value: primary tissue

value: FVB/N wild type


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB515DVD)

description:
https://www.encodeproject.org/experiments/ENCSR697DWS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR697DWS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB515DVD

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

value: primary cell

value: female

value: 33 year

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS897GAI at ENCODE; https://www.encodeproject.org/ENCBS897GAI/


title: snATAC-seq from psoas muscle (ENCLB862ZLX)

description:
https://www.encodeproject.org/experiments/ENCSR000XQD/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR471YTA).
experiment encode accession: ENCSR000XQD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB862ZLX
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female child (16 years) psoas muscle tissue, preserved by flash-freezing nuclear fraction

value: psoas muscle

value: tissue

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS880DIS at ENCODE; https://www.encodeproject.org/ENCBS880DIS/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: MIAML-103-Re

value: untreated

value: bone marrow

value: AML

value: at relapse


title: wild type mouse ventral prostate bio rep 2

description:
Library name: WT2
Column name in TPM_all_samples.csv: WT2

value: mouse ventral prostate

value: primary tissue

value: FVB/N wild type


title: total RNA-seq from T-helper 2 cell (ENCLB026VWE)

description:
https://www.encodeproject.org/experiments/ENCSR696RIJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR696RIJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB026VWE

source_name: Homo sapiens female adult (33 years) T-helper 2 primary cell treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours

value: T-helper 2 cell

value: primary cell

tag: encode accession

value: female

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:16; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS369YUA at ENCODE; https://www.encodeproject.org/ENCBS369YUA/


title: MIAML-103-Dx

value: at diagnosis


title: Pre-infusion NK cells

city: Houston

first: DONGHAI

last: XIONG

state: TX

address: 6565 MD Anderson Blvd,

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: PreInfusion_NK
10x Genomics Chromium Single Cell 3' v3.1; library SC295_scRNA_1_S3

library_source: transcriptomic single cell

data_processing:
Reads were processed with 10x Genomics Cell Ranger v9.0.1 using the count pipeline.
Reads from the first sample (human CAR-NK cells) were aligned to the GRCh38 reference (refdata-gex-GRCh38-2020-A). Reads from the second sample (human and mouse cells mixture) were aligned to the human and mouse hybrid reference genome (refdata-gex-GRCh38-and-mm10-2020-A).
Cell Ranger filtered feature-barcode matrices were exported in Market Exchange (MEX) format; file names were prefixed with the sample name to ensure uniqueness.
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A) for PreInfusion_NK; GRCh38-and-mm10 hybrid (refdata-gex-GRCh38-and-mm10-2020-A) for PostChallenge_NK
Supplementary files format and content: Cell Ranger filtered feature-barcode matrix in Market Exchange (MEX) format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (genes), matrix.mtx.gz (UMI counts per gene per cell). Files renamed with a sample prefix so every file name is unique.

molecule: polyA RNA

source_name: umbilical cord blood

growth_protocol: Not applicable (cryopreserved CD5 CAR-NK cell product; see treatment protocol).

extract_protocol:
Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller. Single-cell gel beads-in-emulsion (GEMs) were generated and total RNA captured per the Chromium Single Cell 3' v3.1 protocol.
cDNA libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's instructions.

treatment_protocol: Two samples were subjected to scRNA-seq. The first sample is the human CD5 CAR-NK cells product before being injected to the mouse model ('PreInfusion_NK'). The second sample is prepared as follows: The human CD5 CAR-NK cells were injected into the mouse model with CD5+ CCRF tumor cells, 100 days later rechallenged with tumor cells; then the sample was collected 4 weeks after tumor rechallenge.

value: umbilical cord blood

value: CD5 CAR-NK cells

tag: treatment

value: pre-infusion (CD5 CAR-NK cell product prior to injection)


title: Control_STR_3

city: Charleston

first: Stefano

last: Berto

address: 68 President Street, BE208

institute: MUSC

description: Bulk RNA-seq

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M27). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Mouse mm10
Supplementary files format and content: Input tables are included as tab separated files.

source_name: Brain

extract_protocol:
Total RNAs were extracted from mouse PFC and STR at P24 using the miRNeasy Mini Kit (#217004, Qiagen, Hilden, Germany).
Total RNA with RIN values of ≥8.9 were used for RNA-seq library preparation. mRNA was purified from 500 ng total RNA, and used for cDNA library preparation by TruSeq Stranded mRNA Library Prep (#20020594, Illumina, San Diego, CA, USA). The quality of cDNA Libraries were determined by 2100 Bioanalyzer using Agilent High Sensitivity DNA Kit (#5067-4626, Agilent Technologies). Libraries were sequenced as 101 bp PE on Illumina NovaSeq6000.

value: Brain

tag: strain

value: Striatum

value: CTL

tag: time


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB018ERI)

description:
https://www.encodeproject.org/experiments/ENCSR689TCH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR689TCH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB018ERI

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

value: CD8-positive, alpha-beta T cell

tag: Sex

value: male

tag: dev stage

tag: age

value: 38 year

value: ENCBS427KYK at ENCODE; https://www.encodeproject.org/ENCBS427KYK/


title: Control_STR_2

description: Bulk RNA-seq

tag: tissue

tag: cell type

tag: genotype


title: MIAML-101-Dx

tag: ex vivo treatment

value: untreated

value: bone marrow

tag: disease state

value: AML


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB732IBL)

description:
https://www.encodeproject.org/experiments/ENCSR687NTR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR687NTR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB732IBL

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

value: female

value: adult

value: 40 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS452PRI at ENCODE; https://www.encodeproject.org/ENCBS452PRI/


title: Control_STR_1

description: Bulk RNA-seq

value: Brain

value: Striatum


title: B-2

description:
Library name: sample7
Column name in counts_allsamples.txt: B-2

source_name: Tumor

value: Tumor

tag: cell line

value: melanoma cell

value: WT

value: VPE-WT

tag: batch

value: Day 10


title: total RNA-seq from HG02635 (ENCLB776FAD)

description:
https://www.encodeproject.org/experiments/ENCSR710WEB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR710WEB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB776FAD
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02635 cell line

extract_protocol: not provided

tag: line

value: cell line

tag: encode accession

tag: note

value: HG02635 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS695XPC at ENCODE; https://www.encodeproject.org/ENCBS695XPC/


title: total RNA-seq from HG03085 (ENCLB293ZQM)

description:
https://www.encodeproject.org/experiments/ENCSR713PRS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR713PRS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB293ZQM
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03085 cell line

value: HG03085 LCLs; Donor from the Mende in Sierra Leone (MSL)

tag: Sex

value: female

value: adult

value: ENCBS564YWA at ENCODE; https://www.encodeproject.org/ENCBS564YWA/


title: MIAML-098-Dx

description: human leukemic blood PBMCs single cell Drop-seq

source_name: leukemic blood (AML)

value: untreated

value: blood

value: AML

tag: time point

value: at diagnosis


title: total RNA-seq from CD14-positive monocyte (ENCLB371OUP)

description:
https://www.encodeproject.org/experiments/ENCSR699PTC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR699PTC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB371OUP

source_name: Homo sapiens male adult (40 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

value: male

tag: dev stage

tag: age

value: 40 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS151NZI at ENCODE; https://www.encodeproject.org/ENCBS151NZI/


title: total RNA-seq from T-cell (ENCLB571XJL)

description:
https://www.encodeproject.org/experiments/ENCSR681UBL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR681UBL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB571XJL

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

value: T-cell

value: 38 year

value: AllCells

value: ENCBS536KEP at ENCODE; https://www.encodeproject.org/ENCBS536KEP/


title: total RNA-seq from HG03376 (ENCLB180CRK)

description:
https://www.encodeproject.org/experiments/ENCSR698TQK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR698TQK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB180CRK
nucleic acid starting quantity: 48
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03376 cell line

value: cell line

value: HG03376 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS820TRM at ENCODE; https://www.encodeproject.org/ENCBS820TRM/


title: MIAML-081-Re

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

source_name: leukemic bone marrow (AML)

value: untreated

tag: tissue

value: bone marrow

value: AML

value: at relapse


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB858YZD)

description:
https://www.encodeproject.org/experiments/ENCSR681CQP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR681CQP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB858YZD

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

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS573SUP at ENCODE; https://www.encodeproject.org/ENCBS573SUP/


title: Control_CTX_2

description: Bulk RNA-seq

value: Brain

tag: strain

tag: cell type

value: Prefrontal Cortex

tag: genotype

value: CTL

tag: time


title: MIAML-081-Dx

tag: ex vivo treatment

tag: disease state

value: at diagnosis


title: Control_CTX_1

description: Bulk RNA-seq


title: Control_CTX_3

description: Bulk RNA-seq


title: wild type mouse ventral prostate bio rep 1

description:
Library name: WT1
Column name in TPM_all_samples.csv: WT1

source_name: mouse ventral prostate

value: mouse ventral prostate

value: primary tissue

value: FVB/N wild type


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB419XSY)

description:
https://www.encodeproject.org/experiments/ENCSR692XQE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR692XQE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB419XSY

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

value: CD8-positive, alpha-beta T cell

tag: biosample encode accession

value: female

value: adult

value: 33 year

tag: lab

value: AllCells

value: ENCBS441QLV at ENCODE; https://www.encodeproject.org/ENCBS441QLV/


title: snATAC-seq from GM12878 (ENCLB416NQT)

description:
https://www.encodeproject.org/experiments/ENCSR680NPV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR680NPV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB416NQT
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens GM12878 cell line nuclear fraction

tag: line

value: cell line

tag: health state

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

tag: subcellular fraction term name

value: nucleus

value: Coriell

value: ENCBS186XGP at ENCODE; https://www.encodeproject.org/ENCBS186XGP/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: SK-MEL-1-3

city: Kunming

first: Li

middle: Qiao

last: hua

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

description: Library name: Sample 21

data_processing:
Raw data were filtered using fastp software (v 0.23.2), and reads were mapped to GRCh38 using HISAT2 (v 2.1.0), featureCounts (v 2.0.1) is used to count the reads mapped to each gene
Differential expression analysis between the two comparison sets was performed using DESeq2 software (1.40.2)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: skin

extract_protocol:
RNA extraction using the phenol/chloroform method,1 ug total RNA of each sample was used as the starting material to construct a transcriptome sequencing library
According to the operating instructions of VAHTS Universal V6 RNA-Seq Library Prepkit for Illumina (NR 604-01/02)

value: skin

tag: cell line

value: melanoma cell


title: MIAML-036-Re

value: untreated

value: bone marrow

value: AML

value: at relapse


title: SK-MEL-1-1

description: Library name: Sample 19


title: ADHD_STR_3

description: Bulk RNA-seq

value: Brain

value: Striatum

value: ADHD


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB242QZA)

description:
https://www.encodeproject.org/experiments/ENCSR675AMF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR675AMF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB242QZA

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

tag: encode accession

tag: Sex

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS058WOV at ENCODE; https://www.encodeproject.org/ENCBS058WOV/


title: total RNA-seq from GM19394 (ENCLB085HDH)

description:
https://www.encodeproject.org/experiments/ENCSR140MWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR140MWC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB085HDH
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19394 cell line

value: cell line

tag: note

value: GM19394 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

tag: dev stage

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS355ILH at ENCODE; https://www.encodeproject.org/ENCBS355ILH/


title: WM-115-2

description: Library name: Sample 23

tag: tissue

value: skin

tag: cell type

value: melanoma cell


title: MIAML-036-Dx

value: untreated

value: bone marrow

value: AML

tag: time point

value: at diagnosis


title: SC-4-3

description: Library name: Sample 18

source_name: skin epidermis

value: skin epidermis

value: hTERT-overexpressing melanocyte clone

value: epidermal melanocyte


title: MIAML-098-Re

tag: ex vivo treatment

value: blood

value: at relapse


title: ADHD_STR_2

description: Bulk RNA-seq

source_name: Brain

value: Brain

tag: strain

value: Striatum

tag: genotype

value: ADHD

tag: time


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB939HBS)

description:
https://www.encodeproject.org/experiments/ENCSR667LBE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR667LBE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB939HBS

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

value: male

value: adult

tag: age

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS697HYI at ENCODE; https://www.encodeproject.org/ENCBS697HYI/


title: SC-4-2

description: Library name: Sample 17

tag: cell line


title: MIAML-015-Re

value: untreated

value: bone marrow

tag: disease state

value: AML


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB349ORQ)

description:
https://www.encodeproject.org/experiments/ENCSR665YFR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR665YFR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB349ORQ

tag: encode accession

tag: Sex

value: ENCBS522ZGZ at ENCODE; https://www.encodeproject.org/ENCBS522ZGZ/


title: SC-4-1

description: Library name: Sample 16

value: skin epidermis

value: hTERT-overexpressing melanocyte clone

value: epidermal melanocyte


title: ADHD_STR_1

description: Bulk RNA-seq

value: Brain

value: Striatum


title: MIAML-015-Dx

value: at diagnosis


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB424SNM)

description:
https://www.encodeproject.org/experiments/ENCSR662SUW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR662SUW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB424SNM

source_name: Homo sapiens female adult (33 years) stimulated activated CD4-positive, alpha-beta T primary cell

value: primary cell

value: female

value: 33 year

tag: source

tag: link

value: ENCBS324RLM at ENCODE; https://www.encodeproject.org/ENCBS324RLM/


title: ADHD_CTX_3

description: Bulk RNA-seq

value: Prefrontal Cortex

value: ADHD


title: SK-MEL-1-2

description: Library name: Sample 20

value: skin

value: melanoma cell


title: SC-3-3

description: Library name: Sample 15


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB064PCH)

description:
https://www.encodeproject.org/experiments/ENCSR686VCH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR686VCH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB064PCH

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

value: CD4-positive, alpha-beta T cell

tag: dev stage

value: adult

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS311RBJ at ENCODE; https://www.encodeproject.org/ENCBS311RBJ/


title: MIAML-006-Re

value: untreated

tag: tissue

value: bone marrow

value: AML

value: at relapse


title: ADHD_CTX_2

description: Bulk RNA-seq

value: Brain

tag: cell type


title: SC-3-2

description: Library name: Sample 14

value: skin epidermis

value: hTERT-overexpressing melanocyte clone

value: epidermal melanocyte


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB574ROY)

description:
https://www.encodeproject.org/experiments/ENCSR662GSD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR662GSD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB574ROY

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

value: primary cell

value: male

value: 42 year

value: ENCBS470GVS at ENCODE; https://www.encodeproject.org/ENCBS470GVS/


title: MIAML-006-Dx

tag: time point

value: at diagnosis


title: ADHD_CTX_1

description: Bulk RNA-seq

value: Prefrontal Cortex

value: ADHD


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB229VLL)

description:
https://www.encodeproject.org/experiments/ENCSR656FTZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR656FTZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB229VLL

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: adult

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS340VTZ at ENCODE; https://www.encodeproject.org/ENCBS340VTZ/


title: SC-3-1

description: Library name: Sample 13

value: skin epidermis


title: 95

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

data_processing:
Read quality was assessed using FastQC v0.12.1 and adapter trimming was performed using Trimmomatic v0.39.
Alignment was performed with STAR v2.7.11b. Genome indices were created using Mus_musculus.GRCm39.dna.chromosome.fa and Mus_musculus.GRCm39.104.gtf.
Gene counts were determined using STAR v2.7.3a.
Assembly: mm10 (build 39)
Supplementary files format and content: STAR-aligned counts were transformed with the variance stabilizing transformation method in DESeq2.
Supplementary files format and content: Tab-delimited text files represent the number of aligned PE reads to each gene.

source_name: Adult male mouse dosed every 4 days for 84 days

extract_protocol:
Frozen mouse liver (~100 mg) was homogenized in 1 mL of TriZOL with chrome-steel beads using a Mixer Mill 300 (Life Sciences, Carlsbad, CA) for 4 minutes. Following, total RNA was extracted per the manufacturer’s instructions with an additional 5:1 phenol:chloroform extraction step (Sigma Aldrich, St. Louis, MO). RNA purity (260/280 ratio) and concentration (ng/µL) were assessed with a NanoDrop 1000 spectrophotometer. RNA quality was determined using an Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RINs) ≥7.
Library preparation was performed using an mRNA-seq Lib Prep Kit for Illumina (RK20302).

treatment_protocol: Mice were orally gavaged with TCDD in sesame oil vehicle every 4 days for 84 days. Half of the mice were exposed to simvastatin in their diet.

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

tag: vendor

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB903QDK)

description:
https://www.encodeproject.org/experiments/ENCSR655SGT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR655SGT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB903QDK

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: primary cell

tag: biosample encode accession

value: female

value: adult

tag: age

value: 40 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

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

value: ENCBS602NOQ at ENCODE; https://www.encodeproject.org/ENCBS602NOQ/


title: 94

value: Liver

tag: strain

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: mRNA-seq Lib Prep Kit for Illumina (RK20302)


title: SC-1-2

description: Library name: Sample 11

value: skin epidermis

tag: cell line

value: hTERT-overexpressing melanocyte clone

value: epidermal melanocyte


title: H19

type: RNA

city: Oslo

first: Berit

middle: Sletbakk

last: Brusletto

address: Kirkeveien 166

department: Oslo University Hospital

country: Norway

institute: Medical Biochemisty

description: Gene expression data from plasma Evs from healthy controls

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Transcriptome 2.0 Arrays (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix.

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.

label: biotin

source_name: Extracellular vesicles

label_protocol: Total RNA from EVs from each plasma sample was subjected to the GeneChip WT Pico Reagent Kit following the manufacturer’s protocol for whole-genome gene expression analysis (Affymetrix)

extract_protocol: The ExoRNeasy Serum/Plasma Midi Kit (Qiagen), designed for the combined isolation of vesicles and total RNA from EVs, was used to isolate total RNA from the EVs.

treatment_protocol: EVs were isolated from the plasma samples using size-exclusion chromatography (SEC) with a qEV original 70 nm column and Izon Automatic Fraction Collector (AFC) (Izon Science, Oxford, UK).

tag: tissue

value: plasma extra vesicles (Evs)

tag: subject status

value: healthy controls


title: SC-1-3

description: Library name: Sample 12

tag: cell type


title: 92

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

tag: bedding

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: total RNA-seq from T-cell (ENCLB952WZD)

description:
https://www.encodeproject.org/experiments/ENCSR632GUZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR632GUZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB952WZD

source_name: Homo sapiens female adult (33 years) T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: T-cell

value: primary cell

tag: encode accession

value: female

tag: dev stage

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

tag: link

value: ENCBS917YKI at ENCODE; https://www.encodeproject.org/ENCBS917YKI/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB570ZEU)

description:
https://www.encodeproject.org/experiments/ENCSR631SUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR631SUM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB570ZEU

value: CD4-positive, alpha-beta T cell

value: 40 year

value: ENCBS099HXK at ENCODE; https://www.encodeproject.org/ENCBS099HXK/


title: WM-115-1

description: Library name: Sample 22

value: skin

value: melanoma cell


title: SC-1-1

description: Library name: Sample 10

value: skin epidermis

value: hTERT-overexpressing melanocyte clone

value: epidermal melanocyte


title: H21

value: plasma extra vesicles (Evs)

value: healthy controls


title: H20


title: 91

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

tag: vendor

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

value: mRNA-seq Lib Prep Kit for Illumina (RK20302)


title: P6-3

description: Library name: Sample 9

value: skin epidermis

value: primary human epidermal melanocytes

value: epidermal melanocyte


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB678WXQ)

description:
https://www.encodeproject.org/experiments/ENCSR631PKY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR631PKY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB678WXQ

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

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

value: male

value: adult

tag: age

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS749VSH at ENCODE; https://www.encodeproject.org/ENCBS749VSH/


title: 89

value: Liver

tag: strain

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

tag: library name


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB111KHR)

description:
https://www.encodeproject.org/experiments/ENCSR631KDU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR631KDU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB111KHR

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS722HJY at ENCODE; https://www.encodeproject.org/ENCBS722HJY/


title: P6-2

description: Library name: Sample 8

tag: tissue

value: skin epidermis

tag: cell line

value: primary human epidermal melanocytes

tag: cell type

value: epidermal melanocyte


title: 88

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

value: mRNA-seq Lib Prep Kit for Illumina (RK20302)


title: total RNA-seq from T-helper 1 cell (ENCLB825LQB)

description:
https://www.encodeproject.org/experiments/ENCSR626GTK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR626GTK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB825LQB

source_name: Homo sapiens male adult (56 years) T-helper 1 primary cell

value: T-helper 1 cell

value: primary cell

tag: encode accession

value: male

tag: dev stage

value: adult

value: 56 year

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS875JUM at ENCODE; https://www.encodeproject.org/ENCBS875JUM/


title: NM7

description: Gene expression data from plasma Evs from meningococcal meningitis (MM) patient

value: plasma extra vesicles (Evs)

tag: subject status

value: meningococcal meningitis (MM) patient


title: NM8


title: total RNA-seq from HG03096 (ENCLB694UWO)

description:
https://www.encodeproject.org/experiments/ENCSR714BDB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR714BDB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB694UWO
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03096 cell line

tag: line

value: cell line

tag: note

value: HG03096 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: Stephen Montgomery, Stanford

value: Coriell

tag: link

value: ENCBS418CNS at ENCODE; https://www.encodeproject.org/ENCBS418CNS/


title: NM12


title: P6-1

description: Library name: Sample 7

value: skin epidermis

value: primary human epidermal melanocytes

value: epidermal melanocyte


title: 86

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

tag: vendor

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

value: mRNA-seq Lib Prep Kit for Illumina (RK20302)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB585FDC)

description:
https://www.encodeproject.org/experiments/ENCSR622RGO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR622RGO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB585FDC

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: female

value: adult

tag: age

value: 40 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS438HFP at ENCODE; https://www.encodeproject.org/ENCBS438HFP/


title: NM11

tag: tissue

value: plasma extra vesicles (Evs)

value: meningococcal meningitis (MM) patient


title: 85

value: Liver

tag: strain

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

tag: library name


title: MIX-3

description: Library name: Sample 6

value: skin epidermis

tag: cell line

value: hTERT-overexpressing melanocytes, bulk population

tag: cell type

value: epidermal melanocyte


title: MIX-2

description: Library name: Sample 5


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB714AQC)

description:
https://www.encodeproject.org/experiments/ENCSR621JBA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR621JBA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB714AQC

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

value: male

tag: dev stage

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS528UIV at ENCODE; https://www.encodeproject.org/ENCBS528UIV/


title: 82

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

value: mRNA-seq Lib Prep Kit for Illumina (RK20302)


title: NM10

value: plasma extra vesicles (Evs)

tag: subject status

value: meningococcal meningitis (MM) patient


title: NM9


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB611RCT)

description:
https://www.encodeproject.org/experiments/ENCSR616VHK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR616VHK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB611RCT

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS771TNW at ENCODE; https://www.encodeproject.org/ENCBS771TNW/


title: MIX-1

description: Library name: Sample 4

value: skin epidermis

value: hTERT-overexpressing melanocytes, bulk population

value: epidermal melanocyte


title: 80

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

tag: vendor

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB433EEX)

description:
https://www.encodeproject.org/experiments/ENCSR615FXW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR615FXW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB433EEX

source_name: Homo sapiens female adult (33 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: female

value: adult

tag: age

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS394GQJ at ENCODE; https://www.encodeproject.org/ENCBS394GQJ/


title: A-375-3

description: Library name: Sample 3

source_name: skin

tag: tissue

value: skin

value: melanoma cell


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB354FBZ)

description:
https://www.encodeproject.org/experiments/ENCSR614CXA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR614CXA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB354FBZ

value: male

value: 42 year

value: ENCBS800MAS at ENCODE; https://www.encodeproject.org/ENCBS800MAS/


title: NS13

description: Gene expression data from plasma Evs from meningococcal septic shock (MSS) patient

value: plasma extra vesicles (Evs)


title: A-375-2

description: Library name: Sample 2

tag: cell line


title: 79

value: Liver

tag: strain

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name

value: mRNA-seq Lib Prep Kit for Illumina (RK20302)


title: 78

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Millipore-Sigma

value: diet


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB443XFI)

description:
https://www.encodeproject.org/experiments/ENCSR607OCT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR607OCT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB443XFI

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

value: male

tag: dev stage

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS905UKX at ENCODE; https://www.encodeproject.org/ENCBS905UKX/


title: NS18

value: plasma extra vesicles (Evs)

tag: subject status

value: meningococcal septic shock (MSS) patient


title: A-375-1

description: Library name: Sample 1

value: skin

tag: cell type

value: melanoma cell


title: NS17


title: 77

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

value: mRNA-seq Lib Prep Kit for Illumina (RK20302)


title: B-1

description:
Library name: sample6
Column name in counts_allsamples.txt: B-1

source_name: Tumor

value: Tumor

value: melanoma cell

tag: genotype

value: WT

tag: treatment

value: VPE-WT

tag: batch

value: Day 10