title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB674MPZ)

description:
https://www.encodeproject.org/experiments/ENCSR598XPW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR598XPW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB674MPZ

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: female

value: adult

tag: age

value: 34 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS290ZTR at ENCODE; https://www.encodeproject.org/ENCBS290ZTR/


title: NS16

status: Public on Jul 24 2026

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 meningococcal septic shock (MSS) patient

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

molecule: total RNA

organism: Homo sapiens

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


title: 76

type: SRA

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

country: USA

institute: Michigan State University

library_source: transcriptomic

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.

organism: Mus musculus

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

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)

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: iPSC-CM, Day 25, EV-miRNA, biol rep 3

city: Suita

first: Yuki

last: Saito

state: Osaka

address: Life System Building, 1-3 Yamadaoka

department: Department of Future Medicine

country: Japan

institute: Osaka Univ.

description: Library name: Sample 9

library_source: other

data_processing:
Sequencing was performed on a NovaSeq 6000 platform (Illumina).
The sequenced reads were mapped to human mature miRNA sequences annotated in miRBase (version 22.1) using Bowtie2, and SAMtools.
Assembly: miRBase (human, version 22.1)
Supplementary files format and content: csv files include raw counts or TPM values for each Sample

molecule: other

source_name: iPSC-CM

growth_protocol: Cardiogenic differentiation of human iPSC was performed using a chemically defined protocol using activator and inhibitors of the Wnt signaling pathway.

extract_protocol:
EV-derived miRNAs were extracted from conditioned media collected at each differentiation stage using the exoEasy Maxi Kit for Exosome Isolation (QIAGEN) according to the kit protocol.
Library preparation was performed using a NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (NEB) according to the manufacturer’s instructions. The resulting libraries were size-selected by agarose gel electrophoresis and purified using a QIAquick Gel Extraction Kit (QIAGEN).

tag: cell type

value: iPSC-CM


title: NS15

value: plasma extra vesicles (Evs)

value: meningococcal septic shock (MSS) patient


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB576SVE)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR598HFA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR598HFA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB576SVE

library_source: genomic

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

molecule: genomic DNA

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

tag: encode accession

value: female

tag: dev stage

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS643RYO at ENCODE; https://www.encodeproject.org/ENCBS643RYO/


title: 74

value: Liver

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB964LTP)

description:
https://www.encodeproject.org/experiments/ENCSR597FRN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR597FRN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB964LTP

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: ENCBS638GEC at ENCODE; https://www.encodeproject.org/ENCBS638GEC/


title: iPSC-CM, Day 25, EV-miRNA, biol rep 2

description: Library name: Sample 8

value: iPSC-CM


title: iPSC-CM, Day 25, EV-miRNA, biol rep 1

description: Library name: Sample 7


title: NS14

tag: tissue

value: plasma extra vesicles (Evs)

tag: subject status

value: meningococcal septic shock (MSS) patient


title: 73

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: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: P1

description: Gene expression data from plasma Evs from systemic pneumococcal disease (SPD) patient

value: plasma extra vesicles (Evs)


title: iPSC-CM, Day 16, EV-miRNA, biol rep 3

description: Library name: Sample 6

value: iPSC-CM


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB976USZ)

description:
https://www.encodeproject.org/experiments/ENCSR595BNL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR595BNL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB976USZ

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

value: female

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS195YKZ at ENCODE; https://www.encodeproject.org/ENCBS195YKZ/


title: 72

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

value: Accustandard

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

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


title: P2

value: plasma extra vesicles (Evs)

value: systemic pneumococcal disease (SPD) patient


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB832YTV)

description:
https://www.encodeproject.org/experiments/ENCSR587LNN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR587LNN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB832YTV

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS517WPX at ENCODE; https://www.encodeproject.org/ENCBS517WPX/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB864AHS)

description:
https://www.encodeproject.org/experiments/ENCSR586OMC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR586OMC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB864AHS

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

value: male

value: 42 year

value: ENCBS894QIE at ENCODE; https://www.encodeproject.org/ENCBS894QIE/


title: 71

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: vendor

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

tag: dose

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name


title: iPSC-CM, Day 16, EV-miRNA, biol rep 2

description: Library name: Sample 5

tag: cell type

value: iPSC-CM


title: iPSC-CM, Day 16, EV-miRNA, biol rep 1

description: Library name: Sample 4


title: P6

value: plasma extra vesicles (Evs)

value: systemic pneumococcal disease (SPD) patient


title: 70

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: oral gavage

value: microgram per kilogram

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


title: total RNA-seq from T-helper 2 cell (ENCLB392BDJ)

description:
https://www.encodeproject.org/experiments/ENCSR582NNM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR582NNM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB392BDJ

source_name: Homo sapiens female adult (33 years) T-helper 2 primary cell treated with 50 U/mL Interleukin-2 for 16 hours

value: T-helper 2 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

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS517UOY at ENCODE; https://www.encodeproject.org/ENCBS517UOY/


title: undifferentiated iPS cells, EV-miRNA, biol rep 3

description: Library name: Sample 3

source_name: iPSC

value: iPSC


title: P5

value: plasma extra vesicles (Evs)

value: systemic pneumococcal disease (SPD) patient


title: 68

value: Liver

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

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: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: P4

tag: tissue

value: plasma extra vesicles (Evs)

value: systemic pneumococcal disease (SPD) patient


title: total RNA-seq from T-cell (ENCLB729LTV)

description:
https://www.encodeproject.org/experiments/ENCSR580MYI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR580MYI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB729LTV

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

value: T-cell

value: primary cell

tag: biosample encode accession

value: female

value: adult

tag: age

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS243EYE at ENCODE; https://www.encodeproject.org/ENCBS243EYE/


title: MIAML-279-Re

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

description: human leukemic 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: leukemic bone marrow (AML)

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

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

tag: ex vivo treatment

value: untreated

value: bone marrow

tag: disease state

value: AML

tag: time point

value: at relapse


title: undifferentiated iPS cells, EV-miRNA, biol rep 2

description: Library name: Sample 2

value: iPSC


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB581ZPO)

description:
https://www.encodeproject.org/experiments/ENCSR575WTO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR575WTO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB581ZPO

value: CD4-positive, alpha-beta T cell

value: 34 year

tag: link

value: ENCBS242UUS at ENCODE; https://www.encodeproject.org/ENCBS242UUS/


title: undifferentiated iPS cells, EV-miRNA, biol rep 1

description: Library name: Sample 1


title: P3

value: plasma extra vesicles (Evs)

tag: subject status

value: systemic pneumococcal disease (SPD) patient


title: capture Hi-C from HepG2 (ENCLB580EAD)

description:
https://www.encodeproject.org/experiments/ENCSR374AJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: promoter capture Hi-C in HepG2 cells
experiment encode accession: ENCSR374AJQ
assay title: capture Hi-C
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB580EAD
fragmentation methods: see document
size range: 200-600

source_name: Homo sapiens HepG2 cell line

tag: line

value: cell line

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS832YMN at ENCODE; https://www.encodeproject.org/ENCBS832YMN/


title: 67

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)

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

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


title: capture Hi-C from HepG2 (ENCLB914VHU)

description:
https://www.encodeproject.org/experiments/ENCSR374AJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: promoter capture Hi-C in HepG2 cells
experiment encode accession: ENCSR374AJQ
assay title: capture Hi-C
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB914VHU
fragmentation methods: see document
size range: 200-600

value: cell line

tag: biosample encode accession

tag: encode accession

tag: Sex

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

value: Michael Snyder, Stanford

tag: source

value: ATCC

value: ENCBS279TVV at ENCODE; https://www.encodeproject.org/ENCBS279TVV/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB311ODE)

description:
https://www.encodeproject.org/experiments/ENCSR563HOA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR563HOA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB311ODE

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

value: CD8-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS557XFE at ENCODE; https://www.encodeproject.org/ENCBS557XFE/


title: 65

tag: tissue

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

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

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: iPSC-CM, Day 25, RNA, biol rep 3

description: Library name: Sample 9

data_processing:
Sequencing was performed on a NovaSeq 6000 platform (Illumina).
The sequenced reads were mapped to the human reference genome sequences (hg38) using HISAT2.
Assembly: human hg38
Supplementary files format and content: csv files include raw counts or TPM values for each Sample

extract_protocol:
Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA Library Prep kit (Illumina) according to the manufacturer’s instructions.

tag: cell type

value: iPSC-CM


title: 64

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB156VXO)

description:
https://www.encodeproject.org/experiments/ENCSR555ZBQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR555ZBQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB156VXO

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS366UPI at ENCODE; https://www.encodeproject.org/ENCBS366UPI/


title: iPSC-CM, Day 25, RNA, biol rep 2

description: Library name: Sample 8

value: iPSC-CM


title: capture Hi-C from K562 (ENCLB660JUS)

description:
https://www.encodeproject.org/experiments/ENCSR193DKN/
***************
biological replicate number: 1
technical replicate number: 1
description: promoter capture Hi-C in K562 cells
experiment encode accession: ENCSR193DKN
assay title: capture Hi-C
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB660JUS
fragmentation methods: see document
size range: 200-600

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS053BOX at ENCODE; https://www.encodeproject.org/ENCBS053BOX/


title: DPDH-2

city: Nanjing

first: weiwei

last: Zheng

state: Jiangsu

address: Xianlin Road 138

country: China

institute: Nanjing University of Chinese Medicine

description: Library name: Sample 5

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

tag: cell line

value: Primary cell

value: Endothelial cells


title: 62

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 CD8-positive, alpha-beta T cell (ENCLB832OOE)

description:
https://www.encodeproject.org/experiments/ENCSR551PHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR551PHJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB832OOE

value: CD8-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: dev stage

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS578AHA at ENCODE; https://www.encodeproject.org/ENCBS578AHA/


title: iPSC-CM, Day 25, RNA, biol rep 1

description: Library name: Sample 7

value: iPSC-CM


title: 61

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

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: library name


title: capture Hi-C from K562 (ENCLB827SLN)

description:
https://www.encodeproject.org/experiments/ENCSR193DKN/
***************
biological replicate number: 2
technical replicate number: 1
description: promoter capture Hi-C in K562 cells
experiment encode accession: ENCSR193DKN
assay title: capture Hi-C
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB827SLN
fragmentation methods: see document
size range: 200-600

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

tag: age

value: 53 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: ATCC

tag: link

value: ENCBS742VVG at ENCODE; https://www.encodeproject.org/ENCBS742VVG/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB764QCF)

description:
https://www.encodeproject.org/experiments/ENCSR550SAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR550SAN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB764QCF

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS303QUQ at ENCODE; https://www.encodeproject.org/ENCBS303QUQ/


title: polyA plus RNA-seq from GM19238 (ENCLB592IYL)

description:
https://www.encodeproject.org/experiments/ENCSR955MJB/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19238 RNA Seq
experiment encode accession: ENCSR955MJB
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB592IYL
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19238 cell line

tag: line

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS510BCA at ENCODE; https://www.encodeproject.org/ENCBS510BCA/


title: 35_2

tag: tissue

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: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

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


title: iPSC-CM, Day 16, RNA, biol rep 3

description: Library name: Sample 6

tag: cell type

value: iPSC-CM


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB954YEU)

description:
https://www.encodeproject.org/experiments/ENCSR547BMD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR547BMD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB954YEU

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: adult

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS443AGL at ENCODE; https://www.encodeproject.org/ENCBS443AGL/


title: iPSC-CM, Day 16, RNA, biol rep 2

description: Library name: Sample 5


title: polyA plus RNA-seq from GM19238 (ENCLB195LZU)

description:
https://www.encodeproject.org/experiments/ENCSR955MJB/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19238 RNA Seq
experiment encode accession: ENCSR955MJB
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB195LZU
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

tag: health state

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS948GPA at ENCODE; https://www.encodeproject.org/ENCBS948GPA/


title: 165

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

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB604QUS)

description:
https://www.encodeproject.org/experiments/ENCSR545NOS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR545NOS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB604QUS

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: biosample encode accession

tag: encode accession

tag: Sex

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS390AUU at ENCODE; https://www.encodeproject.org/ENCBS390AUU/


title: polyA plus RNA-seq from GM19147 (ENCLB755LZM)

description:
https://www.encodeproject.org/experiments/ENCSR946IFS/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19147 RNA Seq
experiment encode accession: ENCSR946IFS
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB755LZM
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19147 cell line

value: cell line

value: female

value: unknown

tag: dev stage

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS609ZTM at ENCODE; https://www.encodeproject.org/ENCBS609ZTM/


title: iPSC-CM, Day 16, RNA, biol rep 1

description: Library name: Sample 4

source_name: iPSC-CM

value: iPSC-CM


title: 163

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

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

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: Carbon dioxide euthanasia

tag: library name

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


title: total RNA-seq from suppressor macrophage (ENCLB053EOY)

description:
https://www.encodeproject.org/experiments/ENCSR545EEX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR545EEX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB053EOY

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

value: suppressor macrophage

value: primary cell

value: male

value: adult

tag: age

value: 24 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Shelly Heimfeld

tag: link

value: ENCBS228ZPK at ENCODE; https://www.encodeproject.org/ENCBS228ZPK/


title: undifferentiated iPS cells, RNA, biol rep 3

description: Library name: Sample 3

value: iPSC


title: polyA plus RNA-seq from GM19147 (ENCLB761PFS)

description:
https://www.encodeproject.org/experiments/ENCSR946IFS/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19147 RNA Seq
experiment encode accession: ENCSR946IFS
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB761PFS
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: line

value: cell line

value: female

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS006ETI at ENCODE; https://www.encodeproject.org/ENCBS006ETI/


title: 144

tag: tissue

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: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: undifferentiated iPS cells, RNA, biol rep 2

description: Library name: Sample 2

tag: cell type

value: iPSC


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB162BFO)

description:
https://www.encodeproject.org/experiments/ENCSR544WYT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR544WYT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB162BFO

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: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS292DLQ at ENCODE; https://www.encodeproject.org/ENCBS292DLQ/


title: polyA plus RNA-seq from GM12282 (ENCLB256ZRR)

description:
https://www.encodeproject.org/experiments/ENCSR919QJN/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12282 RNA Seq
experiment encode accession: ENCSR919QJN
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB256ZRR
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM12282 cell line

value: cell line

value: male

tag: health state

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS395EKJ at ENCODE; https://www.encodeproject.org/ENCBS395EKJ/


title: 143

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

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB475VAZ)

description:
https://www.encodeproject.org/experiments/ENCSR542LAG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR542LAG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB475VAZ

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: biosample encode accession

tag: encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS318HWA at ENCODE; https://www.encodeproject.org/ENCBS318HWA/


title: undifferentiated iPS cells, RNA, biol rep 1

description: Library name: Sample 1

source_name: iPSC

value: iPSC


title: 142

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

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

tag: dose

value: Carbon dioxide euthanasia

tag: library name


title: total RNA-seq from effector CD8-positive, alpha-beta T cell (ENCLB134FGJ)

description:
https://www.encodeproject.org/experiments/ENCSR541BVY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541BVY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB134FGJ

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

value: primary cell

value: male

value: adult

tag: age

value: 42 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS725NBN at ENCODE; https://www.encodeproject.org/ENCBS725NBN/


title: polyA plus RNA-seq from GM12282 (ENCLB410UTX)

description:
https://www.encodeproject.org/experiments/ENCSR919QJN/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12282 RNA Seq
experiment encode accession: ENCSR919QJN
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB410UTX
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: line

value: cell line

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS346KMC at ENCODE; https://www.encodeproject.org/ENCBS346KMC/


title: Retroperitoneal leiomyosarcoma

first: James

middle: Paul

last: Agolia

address: 257 Campus Dr West

department: Surgery

institute: Stanford University

description:
Library name: RPLMS1
10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQs were aligned to GRCh38-2020-A using  cellranger-7.1.0.
Assembly: GRCh38-2020-A
Supplementary files format and content: raw and filtered .h5 cellranger outputs

source_name: Retroperitoneal leiomyosarcoma

extract_protocol:
At the time of tumor resection, a sample of the resected tumor was collected. The specimen was transported on ice in Miltenyi MACS tissue storage solution to Retro Bio.
Library preparation was performed by Retro Bio using 10x Genomics Single Cell 5' PE chemistry.

tag: tissue

value: Retroperitoneal leiomyosarcoma


title: polyA plus RNA-seq from GM19141 (ENCLB443CWO)

description:
https://www.encodeproject.org/experiments/ENCSR882MBJ/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19141 RNA Seq
experiment encode accession: ENCSR882MBJ
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB443CWO
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19141 cell line

tag: health state

value: ENCBS133DEO at ENCODE; https://www.encodeproject.org/ENCBS133DEO/


title: 140

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)

tag: water

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

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


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB508QMA)

description:
https://www.encodeproject.org/experiments/ENCSR534JDX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR534JDX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB508QMA

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

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS017DZX at ENCODE; https://www.encodeproject.org/ENCBS017DZX/


title: CE4

city: Xinjiang

first: Xiumin

address: 137 South Liyushan Road

institute: Tumor Hospital Affiliated to Xinjiang Medical University

description:
Library name: CE4
CE4

data_processing:
The raw sequencing data were analyzed using the ACGT101-miR analysis pipeline, and the specific steps were as follows: 1. Raw data processing: perform base calling to obtain raw reads; remove adapter sequences, low-quality reads (Q value < 20), reads with length < 18 nt or > 30 nt, and contaminating sequences to obtain clean data. 2. Small RNA screening: screen small RNAs of 18-30 nt from clean data, which is the target range of miRNAs. 3. Sequence filtering: align the screened small RNAs with mRNA, Rfam (non-coding RNA database) and Repbase (repeat sequence database) to remove mRNA fragments, rRNA, tRNA, snRNA, snoRNA and repeat sequences, retaining potential miRNA sequences. 4. miRNA identification: align the potential miRNA sequences with the corresponding species genome (human genome) to identify known miRNAs and predict novel miRNAs. 5. Differential expression analysis: compare the miRNA expression levels between the echinococcosis patient group and the healthy control group, screen differentially expressed miRNAs (fold change > 2 or < 0.5, P value < 0.05) using statistical software. 6. Target gene prediction and enrichment analysis: predict the target genes of differentially expressed miRNAs using target gene prediction software (such as TargetScan, miRanda); perform Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis on the target genes to explore the biological functions and signaling pathways involved in differentially expressed miRNAs.
Assembly: GRCh38 (Human Genome Reference Consortium build 38, the latest standard human genome assembly, suitable for serum exosomal miRNA identification and alignment of human-derived miRNAs in this project)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: serum

extract_protocol:
1. Take the frozen serum samples out of the -80°C refrigerator, thaw them on ice, and centrifuge at 4000 rpm, 4°C for 20 minutes to further remove residual cell debris and impurities, and collect the supernatant. 2. Purify exosomes from the supernatant by size exclusion chromatography (SEC): first, equilibrate the SEC column with pre-cooled PBS (RNase-free) to ensure the column is free of impurities and air bubbles; then load the supernatant onto the column, elute with PBS at a constant flow rate, and collect elution fractions sequentially. 3. Conduct quality control on the collected fractions: take a small amount of each fraction for ultra-high-speed centrifugation (100000 rpm, 4°C for 70 minutes), observe whether exosome precipitates are formed; combine the fractions containing exosomes, and centrifuge again to concentrate exosomes, which are used for subsequent identification and RNA extraction.
1. Construct small RNA libraries using the Illumina TruSeq Small RNA Library Prep Kit, strictly following the kit instructions: ligate 3' and 5' adapters to the purified exosomal small RNA, perform reverse transcription to synthesize cDNA, and amplify the cDNA by PCR to obtain the small RNA library. 2. Qualify the constructed library: detect the library size (target size 140-160 bp) by agarose gel electrophoresis, and determine the library concentration and uniformity by quantitative PCR (qPCR). 3. Perform single-end 50 bp sequencing on the qualified libraries using the Illumina Hiseq 2000/2500 sequencing platform. During the sequencing process, set up quality control samples to monitor the sequencing quality (sequencing error rate < 1%, Q30 value > 85%).

value: serum

tag: cell type

value: exosome

tag: treatment

value: Echinococcus granulosus infection


title: polyA plus RNA-seq from GM19141 (ENCLB945RSG)

description:
https://www.encodeproject.org/experiments/ENCSR882MBJ/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19141 RNA Seq
experiment encode accession: ENCSR882MBJ
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB945RSG
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

tag: biosample encode accession

tag: encode accession

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS994KAE at ENCODE; https://www.encodeproject.org/ENCBS994KAE/


title: CE3

description:
Library name: CE3
CE3


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB657QWS)

description:
https://www.encodeproject.org/experiments/ENCSR533VJD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR533VJD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB657QWS

value: CD4-positive, alpha-beta T cell

tag: Sex

tag: dev stage

value: 42 year

value: ENCBS248UGO at ENCODE; https://www.encodeproject.org/ENCBS248UGO/


title: polyA plus RNA-seq from GM18486 (ENCLB304HDA)

description:
https://www.encodeproject.org/experiments/ENCSR849TZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: GM18486 RNA Seq
experiment encode accession: ENCSR849TZZ
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB304HDA
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM18486 cell line

value: male

value: ENCBS787GVN at ENCODE; https://www.encodeproject.org/ENCBS787GVN/


title: 137

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

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

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB422VCK)

description:
https://www.encodeproject.org/experiments/ENCSR532WIC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR532WIC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB422VCK

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

tag: age

value: 34 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS779JKC at ENCODE; https://www.encodeproject.org/ENCBS779JKC/


title: CE2

description:
Library name: CE2
CE2

tag: tissue

value: serum

value: exosome

value: Echinococcus granulosus infection


title: polyA plus RNA-seq from GM18486 (ENCLB249WEO)

description:
https://www.encodeproject.org/experiments/ENCSR849TZZ/
***************
biological replicate number: 2
technical replicate number: 1
description: GM18486 RNA Seq
experiment encode accession: ENCSR849TZZ
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB249WEO
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: line

value: cell line

value: male

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS576WWP at ENCODE; https://www.encodeproject.org/ENCBS576WWP/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB940SIQ)

description:
https://www.encodeproject.org/experiments/ENCSR527RCU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR527RCU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB940SIQ

value: 40 year

value: ENCBS926ZDR at ENCODE; https://www.encodeproject.org/ENCBS926ZDR/


title: 136

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)

tag: water

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: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

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


title: CE1

description:
Library name: CE1
CE1

value: serum

tag: cell type

value: exosome

tag: treatment

value: Echinococcus granulosus infection


title: polyA plus RNA-seq from GM20506 (ENCLB050YAS)

description:
https://www.encodeproject.org/experiments/ENCSR847UYP/
***************
biological replicate number: 2
technical replicate number: 1
description: GM20506 RNA Seq
experiment encode accession: ENCSR847UYP
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB050YAS
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM20506 cell line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: health state

value: unknown

tag: dev stage

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS849LOX at ENCODE; https://www.encodeproject.org/ENCBS849LOX/


title: 135

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

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

tag: library name


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB533KLJ)

description:
https://www.encodeproject.org/experiments/ENCSR524GMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR524GMW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB533KLJ

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

tag: age

value: 42 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS985EKC at ENCODE; https://www.encodeproject.org/ENCBS985EKC/


title: polyA plus RNA-seq from GM20506 (ENCLB114NPD)

description:
https://www.encodeproject.org/experiments/ENCSR847UYP/
***************
biological replicate number: 1
technical replicate number: 1
description: GM20506 RNA Seq
experiment encode accession: ENCSR847UYP
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB114NPD
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: line

value: cell line

value: female

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS762PCJ at ENCODE; https://www.encodeproject.org/ENCBS762PCJ/


title: control1

description:
Library name: control1
control1

tag: tissue

value: serum

tag: cell type

value: exosome

value: control


title: 134

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)

tag: water

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: 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 effector memory CD4-positive, alpha-beta T cell (ENCLB911YNQ)

description:
https://www.encodeproject.org/experiments/ENCSR521WKX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR521WKX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB911YNQ

source_name: Homo sapiens male adult (24 years) effector memory CD4-positive, alpha-beta T primary cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: male

value: adult

value: 24 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS573BMS at ENCODE; https://www.encodeproject.org/ENCBS573BMS/


title: control2

description:
Library name: control2
control2

value: serum

value: exosome

tag: treatment

value: control


title: polyA plus RNA-seq from GM18508 (ENCLB481SQW)

description:
https://www.encodeproject.org/experiments/ENCSR843URE/
***************
biological replicate number: 2
technical replicate number: 1
description: GM18508 RNA Seq
experiment encode accession: ENCSR843URE
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB481SQW
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM18508 cell line

value: cell line

value: female

tag: dev stage

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS531UWN at ENCODE; https://www.encodeproject.org/ENCBS531UWN/


title: total RNA-seq from T-helper 1 cell (ENCLB552KVF)

description:
https://www.encodeproject.org/experiments/ENCSR520OSH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR520OSH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB552KVF

source_name: Homo sapiens male adult (30 years) T-helper 1 primary cell

value: T-helper 1 cell

value: 30 year

value: ENCBS173OEK at ENCODE; https://www.encodeproject.org/ENCBS173OEK/


title: control3

description:
Library name: control3
control3


title: 132

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

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 (ENCLB718BXH)

description:
https://www.encodeproject.org/experiments/ENCSR519ARV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR519ARV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB718BXH

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

tag: age

value: 34 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS285UED at ENCODE; https://www.encodeproject.org/ENCBS285UED/


title: polyA plus RNA-seq from GM18508 (ENCLB335BPI)

description:
https://www.encodeproject.org/experiments/ENCSR843URE/
***************
biological replicate number: 1
technical replicate number: 1
description: GM18508 RNA Seq
experiment encode accession: ENCSR843URE
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB335BPI
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: line

value: cell line

value: Erez Aiden, Baylor

value: Coriell

tag: link

value: ENCBS324OEB at ENCODE; https://www.encodeproject.org/ENCBS324OEB/


title: control4

description:
Library name: control4
control4

tag: tissue

value: serum

tag: cell type

value: exosome

value: control


title: 131

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)

tag: water

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: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name


title: polyA plus RNA-seq from GM12878 (ENCLB425ARQ)

description:
https://www.encodeproject.org/experiments/ENCSR839BHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 RNA Seq
experiment encode accession: ENCSR839BHJ
assay title: polyA plus RNA-seq
encode release date: 2025-09-22
lab: Erez Aiden, Baylor
library encode accession: ENCLB425ARQ
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM12878 cell line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: health state

value: unknown

value: adult

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS318LIJ at ENCODE; https://www.encodeproject.org/ENCBS318LIJ/


title: Ramos, ST14 knockout clone 3

city: Taipei

first: Yi-Lin

last: Chiu

address: No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

country: Taiwan

institute: National Defense Medical Center

description:
Library name: Sample4
1610

data_processing:
Raw sequencing reads were assessed for quality using FastQC. Adapter sequences and low-quality bases were trimmed using vendor-provided preprocessing workflows.
Transcript-level quantification was performed using Salmon (v1.10.0) and kallisto (v0.46.1), both employing lightweight mapping strategies (quasi-mapping for Salmon and pseudoalignment for kallisto).
Assembly: GRCh38
Supplementary files format and content: Expression values were reported as TPM (transcripts per million) and estimated counts.

source_name: Ramos

growth_protocol: A total of 10^7 cells were incubated in RPMI medium at a concentration of 10^6 cells/mL at 37°C, and collected after 24 hours.

extract_protocol:
Cells were lysed and total RNA was extracted with QIAzol/RNeasy.
Total RNA (1 µg) was used for library construction. Poly(A)+ mRNA was isolated using oligo(dT) magnetic beads and fragmented using divalent cations at elevated temperature. First- and second-strand cDNA synthesis was performed using random primers. Double-stranded cDNA underwent end repair, A-tailing, and adaptor ligation. Size selection was performed using magnetic beads, followed by PCR amplification with indexed primers. Library preparation was performed by Genewiz on an Illumina NovaSeq 6000 platform using 2×150 bp paired-end mode.

tag: cell line

value: Ramos

value: Burkitt lymphoma

tag: genotype

value: ST14 knockout


title: polyA plus RNA-seq from GM12878 (ENCLB028VGZ)

description:
https://www.encodeproject.org/experiments/ENCSR839BHJ/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12878 RNA Seq
experiment encode accession: ENCSR839BHJ
assay title: polyA plus RNA-seq
encode release date: 2025-09-22
lab: Erez Aiden, Baylor
library encode accession: ENCLB028VGZ
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: dev stage

value: ENCBS795XYX at ENCODE; https://www.encodeproject.org/ENCBS795XYX/


title: 133

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

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

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


title: total RNA-seq from T-cell (ENCLB255PMO)

description:
https://www.encodeproject.org/experiments/ENCSR518BIO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR518BIO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB255PMO

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

value: T-cell

value: primary cell

value: male

value: adult

tag: age

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS412UJU at ENCODE; https://www.encodeproject.org/ENCBS412UJU/


title: 130

tag: tissue

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)

tag: water

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: total RNA-seq from T-cell (ENCLB400YFL)

description:
https://www.encodeproject.org/experiments/ENCSR517VKJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR517VKJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB400YFL

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

value: T-cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS004HMK at ENCODE; https://www.encodeproject.org/ENCBS004HMK/


title: Ramos, ST14 knockout clone 2

description:
Library name: Sample3
1607

tag: cell line

value: Ramos

tag: cell type

value: Burkitt lymphoma

tag: genotype

value: ST14 knockout


title: 129

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

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

tag: library name

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB865SKR)

description:
https://www.encodeproject.org/experiments/ENCSR517QID/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR517QID
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB865SKR

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

tag: dev stage

value: adult

tag: age

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS729VKZ at ENCODE; https://www.encodeproject.org/ENCBS729VKZ/


title: Ramos, ST14 knockout clone 1

description:
Library name: Sample2
1601

value: Ramos

value: Burkitt lymphoma

value: ST14 knockout


title: polyA plus RNA-seq from GM20530 (ENCLB957DTK)

description:
https://www.encodeproject.org/experiments/ENCSR835TRJ/
***************
biological replicate number: 2
technical replicate number: 1
description: GM20530 RNA Seq
experiment encode accession: ENCSR835TRJ
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB957DTK
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM20530 cell line

tag: line

value: cell line

tag: health state

value: unknown

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Coriell

value: ENCBS214MIL at ENCODE; https://www.encodeproject.org/ENCBS214MIL/


title: 128

tag: tissue

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

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: polyA plus RNA-seq from GM20530 (ENCLB485CRD)

description:
https://www.encodeproject.org/experiments/ENCSR835TRJ/
***************
biological replicate number: 1
technical replicate number: 1
description: GM20530 RNA Seq
experiment encode accession: ENCSR835TRJ
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB485CRD
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

value: unknown

value: Erez Aiden, Baylor

value: Coriell

tag: link

value: ENCBS230MIW at ENCODE; https://www.encodeproject.org/ENCBS230MIW/


title: Ramos, parental

description:
Library name: Sample1
Rms

tag: cell line

value: Ramos

tag: cell type

value: Burkitt lymphoma

tag: genotype

value: WT


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB668MPF)

description:
https://www.encodeproject.org/experiments/ENCSR516UIC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR516UIC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB668MPF

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

value: primary cell

value: male

tag: dev stage

value: adult

tag: age

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS127YZW at ENCODE; https://www.encodeproject.org/ENCBS127YZW/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB329SSU)

description:
https://www.encodeproject.org/experiments/ENCSR515XBO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR515XBO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB329SSU

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

value: CD4-positive, alpha-beta T cell

value: 42 year

value: ENCBS419UFX at ENCODE; https://www.encodeproject.org/ENCBS419UFX/


title: SCAF3017b_27500_BCR

city: Bethesda

first: Huaitian

last: Liu

state: MD

address: Building 37, Room 3050

department: CCR

institute: NCI

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

source_name: Prostate cancer patient

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

value: Blood

tag: race

value: African American (AA)

tag: lethal prostate_cancer_group

value: Lethal


title: 127

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

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name

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


title: polyA plus RNA-seq from GM18519 (ENCLB222QRN)

description:
https://www.encodeproject.org/experiments/ENCSR829TTU/
***************
biological replicate number: 1
technical replicate number: 1
description: GM18519 RNA Seq
experiment encode accession: ENCSR829TTU
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB222QRN
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM18519 cell line

tag: line

value: cell line

value: male

tag: health state

value: unknown

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Coriell

value: ENCBS660EPR at ENCODE; https://www.encodeproject.org/ENCBS660EPR/


title: polyA plus RNA-seq from GM18519 (ENCLB433IHK)

description:
https://www.encodeproject.org/experiments/ENCSR829TTU/
***************
biological replicate number: 2
technical replicate number: 1
description: GM18519 RNA Seq
experiment encode accession: ENCSR829TTU
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB433IHK
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: biosample encode accession

tag: encode accession

tag: Sex

value: ENCBS713DJT at ENCODE; https://www.encodeproject.org/ENCBS713DJT/


title: 126

tag: tissue

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

tag: vendor

value: Accustandard

value: Room temperature

value: sesame oil

tag: dose


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB403FHU)

description:
https://www.encodeproject.org/experiments/ENCSR515OTH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR515OTH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB403FHU

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

tag: dev stage

value: adult

tag: age

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS285OMM at ENCODE; https://www.encodeproject.org/ENCBS285OMM/


title: SCAF3016b_25681_BCR

value: Blood

tag: race

value: European American (EA)

tag: lethal prostate_cancer_group

value: Nonlethal


title: total RNA-seq from central memory CD4-positive, alpha-beta T cell (ENCLB166HCR)

description:
https://www.encodeproject.org/experiments/ENCSR509WMO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR509WMO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB166HCR

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

value: male

value: 42 year

value: ENCBS538RBT at ENCODE; https://www.encodeproject.org/ENCBS538RBT/


title: SCAF3015b_24919_BCR

value: African American (AA)

value: Lethal


title: polyA plus RNA-seq from GM19225 (ENCLB585RUM)

description:
https://www.encodeproject.org/experiments/ENCSR817BUE/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19225 RNA Seq
experiment encode accession: ENCSR817BUE
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB585RUM
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19225 cell line

tag: line

value: cell line

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS275HID at ENCODE; https://www.encodeproject.org/ENCBS275HID/


title: 124

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

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name

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


title: polyA plus RNA-seq from GM19225 (ENCLB517ETB)

description:
https://www.encodeproject.org/experiments/ENCSR817BUE/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19225 RNA Seq
experiment encode accession: ENCSR817BUE
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB517ETB
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

tag: biosample encode accession

tag: encode accession

value: female

tag: health state

value: unknown

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Coriell

value: ENCBS554JMW at ENCODE; https://www.encodeproject.org/ENCBS554JMW/


title: 123

tag: tissue

value: Liver

tag: strain

value: Charles Rivers Laboratories

tag: Sex

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

tag: vendor

value: Accustandard

value: Room temperature


title: SCAF3014b_24610_BCR

value: Blood

tag: race

value: European American (EA)


title: 122

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: polyA plus RNA-seq from GM12890 (ENCLB959FKX)

description:
https://www.encodeproject.org/experiments/ENCSR805MXI/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12890 RNA Seq
experiment encode accession: ENCSR805MXI
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB959FKX
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM12890 cell line

tag: line

value: cell line

value: female

value: unknown

tag: dev stage

value: Erez Aiden, Baylor

value: Coriell

tag: link

value: ENCBS033RJT at ENCODE; https://www.encodeproject.org/ENCBS033RJT/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB714YBM)

description:
https://www.encodeproject.org/experiments/ENCSR507PXP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR507PXP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB714YBM

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

value: adult

tag: age

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS830QIZ at ENCODE; https://www.encodeproject.org/ENCBS830QIZ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB692FWL)

description:
https://www.encodeproject.org/experiments/ENCSR508LYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR508LYC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB692FWL

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

value: 40 year

value: ENCBS520CLW at ENCODE; https://www.encodeproject.org/ENCBS520CLW/


title: SCAF3013b_27150_BCR

value: Blood

value: African American (AA)

tag: lethal prostate_cancer_group

value: Nonlethal


title: polyA plus RNA-seq from GM12890 (ENCLB066AWS)

description:
https://www.encodeproject.org/experiments/ENCSR805MXI/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12890 RNA Seq
experiment encode accession: ENCSR805MXI
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB066AWS
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

tag: biosample encode accession

value: female

value: ENCBS376CUL at ENCODE; https://www.encodeproject.org/ENCBS376CUL/


title: 121

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

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name

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


title: 138

tag: tissue

value: Liver

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)


title: Control ChIP-seq from K562 (ENCLB842KYO)

description:
https://www.encodeproject.org/experiments/ENCSR500KIT/
***************
biological replicate number: 1
technical replicate number: 1
description: JUND ChIP-seq on K562 cells treated with control sgRNA
experiment encode accession: ENCSR500KIT
assay title: Control ChIP-seq
possible controls: ENCSR402HVP
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB842KYO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line

tag: antibody

value: JUND

value: cell line

tag: encode accession

tag: note

value: Homo sapiens K562 cell line transduced with doxycycline-inducible shRNA targeting MAFF. Cells were treated for 72 hours with 4ug/mL doxycycline prior to experiment harvest.

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: ATCC

value: ENCBS229MUI at ENCODE; https://www.encodeproject.org/ENCBS229MUI/


title: 120

value: Liver

tag: strain

value: Charles Rivers Laboratories

tag: Sex

tag: bedding

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

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 (ENCLB178QZQ)

description:
https://www.encodeproject.org/experiments/ENCSR499DSM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR499DSM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB178QZQ

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

value: male

tag: dev stage

value: adult

tag: age

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS305BER at ENCODE; https://www.encodeproject.org/ENCBS305BER/


title: polyA plus RNA-seq from GM18510 (ENCLB142EUN)

description:
https://www.encodeproject.org/experiments/ENCSR775XLU/
***************
biological replicate number: 2
technical replicate number: 1
description: GM18510 RNA Seq
experiment encode accession: ENCSR775XLU
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB142EUN
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM18510 cell line

tag: line

value: cell line

value: not collected

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS529RSZ at ENCODE; https://www.encodeproject.org/ENCBS529RSZ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB570NCP)

description:
https://www.encodeproject.org/experiments/ENCSR497SHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR497SHC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB570NCP

value: female

value: 40 year

value: ENCBS020LNF at ENCODE; https://www.encodeproject.org/ENCBS020LNF/


title: polyA plus RNA-seq from GM19099 (ENCLB216FUY)

description:
https://www.encodeproject.org/experiments/ENCSR707NLA/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19099 RNA Seq
experiment encode accession: ENCSR707NLA
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB216FUY
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19099 cell line

value: ENCBS040LBN at ENCODE; https://www.encodeproject.org/ENCBS040LBN/


title: 119

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

tag: tissue

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

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name

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


title: SCAF2929b_28161_BCR

value: Blood

tag: race

value: European American (EA)

tag: lethal prostate_cancer_group

value: Nonlethal


title: 117

value: Liver

tag: strain

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB948TMS)

description:
https://www.encodeproject.org/experiments/ENCSR495IOL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR495IOL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB948TMS

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

tag: Sex

value: female

value: adult

value: 40 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS720JSA at ENCODE; https://www.encodeproject.org/ENCBS720JSA/


title: SCAF2928b_27424_BCR

value: Blood

value: African American (AA)

value: Nonlethal


title: polyA plus RNA-seq from GM19099 (ENCLB058BYH)

description:
https://www.encodeproject.org/experiments/ENCSR707NLA/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19099 RNA Seq
experiment encode accession: ENCSR707NLA
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB058BYH
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

tag: biosample encode accession

tag: health state

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS687JUM at ENCODE; https://www.encodeproject.org/ENCBS687JUM/


title: SCAF3012b_22690_BCR

value: Lethal


title: 116

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

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 CD8-positive, alpha-beta T cell (ENCLB791LQX)

description:
https://www.encodeproject.org/experiments/ENCSR493UEI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR493UEI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB791LQX

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

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

tag: dev stage

value: adult

tag: age

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS756STA at ENCODE; https://www.encodeproject.org/ENCBS756STA/


title: polyA plus RNA-seq from GM19138 (ENCLB351LFN)

description:
https://www.encodeproject.org/experiments/ENCSR682NEW/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19138 RNA Seq
experiment encode accession: ENCSR682NEW
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB351LFN
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19138 cell line

tag: line

value: cell line

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS146YQO at ENCODE; https://www.encodeproject.org/ENCBS146YQO/


title: SCAF2927b_27193_BCR

tag: tissue

value: Blood

value: African American (AA)


title: 115

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

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia

tag: library name