title: polyA plus RNA-seq from GM19138 (ENCLB716XUE)

description:
https://www.encodeproject.org/experiments/ENCSR682NEW/
***************
biological replicate number: 2
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: ENCLB716XUE
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

tag: encode accession

tag: Sex

value: male

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS047VCM at ENCODE; https://www.encodeproject.org/ENCBS047VCM/


title: SCAF2926b_27140_BCR

status: Public on Jul 24 2026

type: SRA

city: Bethesda

first: Huaitian

last: Liu

state: MD

address: Building 37, Room 3050

department: CCR

country: USA

institute: NCI

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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.

tag: tissue

value: Blood

tag: race

value: African American (AA)

tag: lethal prostate_cancer_group

value: Lethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB408HVC)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR493ROS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR493ROS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB408HVC

library_source: genomic

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

molecule: genomic DNA

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

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

value: female

tag: dev stage

value: adult

tag: age

value: 40 year

tag: lab

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:4; duration_units:hour;

tag: link

value: ENCBS889AOZ at ENCODE; https://www.encodeproject.org/ENCBS889AOZ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB988ZIP)

description:
https://www.encodeproject.org/experiments/ENCSR491OTO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR491OTO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB988ZIP

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

value: 34 year

value: ENCBS835MYS at ENCODE; https://www.encodeproject.org/ENCBS835MYS/


title: SCAF2925b_25881_BCR

value: European American (EA)


title: polyA plus RNA-seq from GM18510 (ENCLB615NJY)

description:
https://www.encodeproject.org/experiments/ENCSR775XLU/
***************
biological replicate number: 1
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: ENCLB615NJY
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: ENCBS189LNZ at ENCODE; https://www.encodeproject.org/ENCBS189LNZ/


title: 114

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

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

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: polyA plus RNA-seq from GM12154 (ENCLB587TMU)

description:
https://www.encodeproject.org/experiments/ENCSR609DRM/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12154 RNA Seq
experiment encode accession: ENCSR609DRM
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB587TMU
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM12154 cell line

value: cell line

tag: encode accession

tag: Sex

value: male

tag: health state

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS978YJB at ENCODE; https://www.encodeproject.org/ENCBS978YJB/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB912TQP)

description:
https://www.encodeproject.org/experiments/ENCSR491BTW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR491BTW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB912TQP

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

tag: dev stage

value: adult

tag: age

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS398UTF at ENCODE; https://www.encodeproject.org/ENCBS398UTF/


title: SCAF2924b_24796_BCR

tag: tissue

value: Blood

tag: race

value: European American (EA)

tag: lethal prostate_cancer_group


title: SCAF3011b_21030_BCR

value: African American (AA)


title: 113

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

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: 112

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)


title: polyA plus RNA-seq from GM12154 (ENCLB669VFD)

description:
https://www.encodeproject.org/experiments/ENCSR609DRM/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12154 RNA Seq
experiment encode accession: ENCSR609DRM
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB669VFD
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: line

value: cell line

value: male

value: unknown

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Coriell

tag: link

value: ENCBS138YLE at ENCODE; https://www.encodeproject.org/ENCBS138YLE/


title: SCAF2923b_23058_BCR

value: Blood

value: African American (AA)

value: Lethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB033AXC)

description:
https://www.encodeproject.org/experiments/ENCSR490SPA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR490SPA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB033AXC

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS715FZB at ENCODE; https://www.encodeproject.org/ENCBS715FZB/


title: 111

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: polyA plus RNA-seq from GM18861 (ENCLB660QLF)

description:
https://www.encodeproject.org/experiments/ENCSR581EYM/
***************
biological replicate number: 2
technical replicate number: 1
description: GM18861 RNA Seq
experiment encode accession: ENCSR581EYM
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB660QLF
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM18861 cell line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

value: adult

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS876AFA at ENCODE; https://www.encodeproject.org/ENCBS876AFA/


title: polyA plus RNA-seq from GM18861 (ENCLB196JJW)

description:
https://www.encodeproject.org/experiments/ENCSR581EYM/
***************
biological replicate number: 1
technical replicate number: 1
description: GM18861 RNA Seq
experiment encode accession: ENCSR581EYM
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB196JJW
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: dev stage

value: ENCBS584DVA at ENCODE; https://www.encodeproject.org/ENCBS584DVA/


title: total RNA-seq from suppressor macrophage (ENCLB519AKK)

description:
https://www.encodeproject.org/experiments/ENCSR487JSW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR487JSW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB519AKK

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

value: suppressor macrophage

value: primary cell

value: male

tag: age

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS306JME at ENCODE; https://www.encodeproject.org/ENCBS306JME/


title: SCAF2922b_26793_BCR

tag: tissue

value: Blood

tag: race

value: African American (AA)

tag: lethal prostate_cancer_group


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB924HEY)

description:
https://www.encodeproject.org/experiments/ENCSR490OGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR490OGB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB924HEY

value: CD4-positive, alpha-beta T cell

value: 34 year

value: AllCells

value: ENCBS034GWE at ENCODE; https://www.encodeproject.org/ENCBS034GWE/


title: 110

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

tag: library name

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


title: 109

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: polyA plus RNA-seq from GM18907 (ENCLB848NMQ)

description:
https://www.encodeproject.org/experiments/ENCSR571CLM/
***************
biological replicate number: 2
technical replicate number: 1
description: GM18907 RNA Seq
experiment encode accession: ENCSR571CLM
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB848NMQ
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM18907 cell line

tag: line

value: cell line

value: female

tag: health state

value: unknown

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Coriell

tag: link

value: ENCBS451OIY at ENCODE; https://www.encodeproject.org/ENCBS451OIY/


title: SCAF2920b_26593_BCR

value: Blood

value: European American (EA)

value: Nonlethal


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCLB265SWQ)

description:
https://www.encodeproject.org/experiments/ENCSR480RHI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR480RHI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB265SWQ

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

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS335DVW at ENCODE; https://www.encodeproject.org/ENCBS335DVW/


title: SCAF2921b_26678_BCR

value: African American (AA)

value: Lethal


title: polyA plus RNA-seq from GM18907 (ENCLB327XKD)

description:
https://www.encodeproject.org/experiments/ENCSR571CLM/
***************
biological replicate number: 1
technical replicate number: 1
description: GM18907 RNA Seq
experiment encode accession: ENCSR571CLM
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB327XKD
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: female

value: ENCBS189XPN at ENCODE; https://www.encodeproject.org/ENCBS189XPN/


title: BMDMs MDA5KO 3

city: Tokyo

first: Takashi

last: Ishii

address: 7-3-1, Hongo, BUnkyo-ku

country: Japan

institute: The University of Tokyo

data_processing:
CLC genomics workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameter- mismath cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file with FPKM

source_name: bone marrow

extract_protocol:
Total RNA was extracted with a NucleoSpin® RNA plus kit according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following the manufacturer’s protocols

value: bone marrow

tag: cell type

value: Macrophages

tag: genotype


title: SCAF2919b_26565_BCR

value: Blood


title: polyA plus RNA-seq from GM19257 (ENCLB651TKP)

description:
https://www.encodeproject.org/experiments/ENCSR558XAR/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19257 RNA Seq
experiment encode accession: ENCSR558XAR
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB651TKP
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19257 cell line

tag: biosample encode accession

tag: encode accession

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS130TTK at ENCODE; https://www.encodeproject.org/ENCBS130TTK/


title: BMDMs MDA5KO 2


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB093YGI)

description:
https://www.encodeproject.org/experiments/ENCSR479TXY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR479TXY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB093YGI

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

value: primary cell

tag: Sex

value: male

tag: dev stage

value: adult

value: 42 year

value: ENCBS952CGO at ENCODE; https://www.encodeproject.org/ENCBS952CGO/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB707FLX)

description:
https://www.encodeproject.org/experiments/ENCSR478YJK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR478YJK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB707FLX

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

value: CD4-positive, alpha-beta T cell

tag: age

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS999NYR at ENCODE; https://www.encodeproject.org/ENCBS999NYR/


title: polyA plus RNA-seq from GM19257 (ENCLB265SAY)

description:
https://www.encodeproject.org/experiments/ENCSR558XAR/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19257 RNA Seq
experiment encode accession: ENCSR558XAR
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB265SAY
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: female

value: ENCBS435ZXU at ENCODE; https://www.encodeproject.org/ENCBS435ZXU/


title: SCAF2918b_24602_BCR

tag: tissue

value: Blood

tag: race

value: European American (EA)


title: BMDMs MDA5KO 1

value: bone marrow

value: Macrophages


title: polyA plus RNA-seq from GM19204 (ENCLB866ASF)

description:
https://www.encodeproject.org/experiments/ENCSR517FYU/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19204 RNA Seq
experiment encode accession: ENCSR517FYU
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB866ASF
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19204 cell line

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS458ROW at ENCODE; https://www.encodeproject.org/ENCBS458ROW/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB688CAB)

description:
https://www.encodeproject.org/experiments/ENCSR470ZTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR470ZTV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB688CAB

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

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 42 year

value: ENCBS558CTX at ENCODE; https://www.encodeproject.org/ENCBS558CTX/


title: SCAF2917b_22986_BCR

source_name: Prostate cancer patient

value: African American (AA)

tag: lethal prostate_cancer_group

value: Lethal


title: total RNA-seq from effector CD8-positive, alpha-beta T cell (ENCLB791UXW)

description:
https://www.encodeproject.org/experiments/ENCSR473ETU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR473ETU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB791UXW

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

value: female

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS219KZS at ENCODE; https://www.encodeproject.org/ENCBS219KZS/


title: SCAF2916b_22928_BCR

value: Blood


title: polyA plus RNA-seq from GM19204 (ENCLB776HEO)

description:
https://www.encodeproject.org/experiments/ENCSR517FYU/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19204 RNA Seq
experiment encode accession: ENCSR517FYU
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB776HEO
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: unknown

value: Erez Aiden, Baylor

value: ENCBS116IXP at ENCODE; https://www.encodeproject.org/ENCBS116IXP/


title: BMDMs WT 3

value: bone marrow

value: Macrophages

value: WT


title: BMDMs WT 2


title: total RNA-seq from T-helper 2 cell (ENCLB425ZNX)

description:
https://www.encodeproject.org/experiments/ENCSR467JQS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR467JQS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB425ZNX

source_name: Homo sapiens male adult (38 years) T-helper 2 primary cell

value: T-helper 2 cell

value: primary cell

value: male

value: adult

value: 38 year

value: ENCBS203FJK at ENCODE; https://www.encodeproject.org/ENCBS203FJK/


title: polyA plus RNA-seq from GM19114 (ENCLB220ZTT)

description:
https://www.encodeproject.org/experiments/ENCSR459TWG/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19114 RNA Seq
experiment encode accession: ENCSR459TWG
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB220ZTT
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19114 cell line

value: female

value: Coriell

value: ENCBS555KGN at ENCODE; https://www.encodeproject.org/ENCBS555KGN/


title: SCAF2877b_27998_BCR

value: Blood

value: African American (AA)

value: Lethal


title: SCAF2876b_26608_BCR


title: CD11b+ macrophages MDA5KO 3

source_name: lung

value: lung


title: total RNA-seq from T-helper 1 cell (ENCLB270SRD)

description:
https://www.encodeproject.org/experiments/ENCSR467GYH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR467GYH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB270SRD

source_name: Homo sapiens male adult (24 years) T-helper 1 primary cell

value: T-helper 1 cell

value: 24 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS769TAJ at ENCODE; https://www.encodeproject.org/ENCBS769TAJ/


title: BMDMs WT 1

value: bone marrow

value: Macrophages

value: WT


title: polyA plus RNA-seq from GM19114 (ENCLB044JPR)

description:
https://www.encodeproject.org/experiments/ENCSR459TWG/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19114 RNA Seq
experiment encode accession: ENCSR459TWG
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB044JPR
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: unknown

value: Erez Aiden, Baylor

value: ENCBS530MDM at ENCODE; https://www.encodeproject.org/ENCBS530MDM/


title: polyA plus RNA-seq from GM11840 (ENCLB039SGV)

description:
https://www.encodeproject.org/experiments/ENCSR426RVG/
***************
biological replicate number: 2
technical replicate number: 1
description: GM11840 RNA Seq
experiment encode accession: ENCSR426RVG
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB039SGV
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM11840 cell line

value: female

value: Coriell

value: ENCBS284YAV at ENCODE; https://www.encodeproject.org/ENCBS284YAV/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB728RBV)

description:
https://www.encodeproject.org/experiments/ENCSR464ODS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR464ODS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB728RBV

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: adult

value: 33 year

value: ENCBS071QXU at ENCODE; https://www.encodeproject.org/ENCBS071QXU/


title: SCAF2875b_26352_BCR

value: Blood

value: African American (AA)

value: Nonlethal


title: CD11b+ macrophages MDA5KO 2

value: lung

value: Macrophages


title: total RNA-seq from effector CD8-positive, alpha-beta T cell (ENCLB215JLX)

description:
https://www.encodeproject.org/experiments/ENCSR463BAI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR463BAI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB215JLX

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

value: male

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS953FEN at ENCODE; https://www.encodeproject.org/ENCBS953FEN/


title: SCAF2874b_26082_BCR

value: European American (EA)


title: polyA plus RNA-seq from GM11840 (ENCLB990BBX)

description:
https://www.encodeproject.org/experiments/ENCSR426RVG/
***************
biological replicate number: 1
technical replicate number: 1
description: GM11840 RNA Seq
experiment encode accession: ENCSR426RVG
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB990BBX
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: female

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS373MWC at ENCODE; https://www.encodeproject.org/ENCBS373MWC/


title: CD11b+ macrophages MDA5KO 1


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB245FHF)

description:
https://www.encodeproject.org/experiments/ENCSR454MAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR454MAP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB245FHF

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

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

value: 42 year

value: ENCBS478ORV at ENCODE; https://www.encodeproject.org/ENCBS478ORV/


title: SCAF2873b_25197_BCR

value: Blood

value: African American (AA)


title: polyA plus RNA-seq from GM18498 (ENCLB742EKB)

description:
https://www.encodeproject.org/experiments/ENCSR398UQG/
***************
biological replicate number: 2
technical replicate number: 1
description: GM18498 RNA Seq
experiment encode accession: ENCSR398UQG
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB742EKB
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM18498 cell line

value: male

value: ENCBS332MGA at ENCODE; https://www.encodeproject.org/ENCBS332MGA/


title: CD11b+ macrophages WT 3

value: lung

value: Macrophages

value: WT


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB211BTP)

description:
https://www.encodeproject.org/experiments/ENCSR451YWJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR451YWJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB211BTP

value: CD8-positive, alpha-beta T cell

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS962NKN at ENCODE; https://www.encodeproject.org/ENCBS962NKN/


title: CD11b+ macrophages WT 2


title: SCAF2872b_24230_BCR

value: European American (EA)


title: polyA plus RNA-seq from GM18498 (ENCLB426REQ)

description:
https://www.encodeproject.org/experiments/ENCSR398UQG/
***************
biological replicate number: 1
technical replicate number: 1
description: GM18498 RNA Seq
experiment encode accession: ENCSR398UQG
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB426REQ
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS506CII at ENCODE; https://www.encodeproject.org/ENCBS506CII/


title: SCAF2871b_22771_BCR

value: Lethal


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB020UHA)

description:
https://www.encodeproject.org/experiments/ENCSR439ZSL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR439ZSL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB020UHA

value: primary cell

value: adult

value: 42 year

value: ENCBS994KNH at ENCODE; https://www.encodeproject.org/ENCBS994KNH/


title: polyA plus RNA-seq from GM19239 (ENCLB857VPT)

description:
https://www.encodeproject.org/experiments/ENCSR350PLV/
***************
biological replicate number: 2
technical replicate number: 1
description: GM19239 RNA Seq
experiment encode accession: ENCSR350PLV
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB857VPT
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM19239 cell line

value: male

value: unknown

value: ENCBS328PJT at ENCODE; https://www.encodeproject.org/ENCBS328PJT/


title: CD11b+ macrophages WT 1

value: lung

value: Macrophages

value: WT


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB828KRQ)

description:
https://www.encodeproject.org/experiments/ENCSR438JKO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR438JKO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB828KRQ

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

value: CD4-positive, alpha-beta T cell

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS563RWH at ENCODE; https://www.encodeproject.org/ENCBS563RWH/


title: SCAF2858b_22929_BCR

value: Blood

value: African American (AA)

value: Nonlethal


title: polyA plus RNA-seq from GM19239 (ENCLB440XWM)

description:
https://www.encodeproject.org/experiments/ENCSR350PLV/
***************
biological replicate number: 1
technical replicate number: 1
description: GM19239 RNA Seq
experiment encode accession: ENCSR350PLV
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB440XWM
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS673IHT at ENCODE; https://www.encodeproject.org/ENCBS673IHT/


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB628RCL)

description:
https://www.encodeproject.org/experiments/ENCSR436PAE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR436PAE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB628RCL

source_name: Homo sapiens male adult (30 years) effector memory CD8-positive, alpha-beta T primary cell

value: primary cell

value: male

value: adult

value: 30 year

value: ENCBS806UML at ENCODE; https://www.encodeproject.org/ENCBS806UML/


title: pho4(A) pho4(B) strain Low Pi, replicate C

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

description: Library name: AB_L_C

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

organism: Komagataella phaffii GS115

source_name: whole cell

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

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

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

value: whole cell

tag: cell line


title: polyA plus RNA-seq from GM07037 (ENCLB875NDO)

description:
https://www.encodeproject.org/experiments/ENCSR345CKK/
***************
biological replicate number: 1
technical replicate number: 1
description: GM07037 RNA Seq
experiment encode accession: ENCSR345CKK
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB875NDO
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM07037 cell line

value: female

value: unknown

value: ENCBS030VQT at ENCODE; https://www.encodeproject.org/ENCBS030VQT/


title: SCAF2824b_24574_BCR


title: pho4(A) pho4(B) strain Low Pi, replicate B

description: Library name: AB_L_B


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB094JJD)

description:
https://www.encodeproject.org/experiments/ENCSR436BAK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR436BAK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB094JJD

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

value: CD8-positive, alpha-beta T cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS807XXG at ENCODE; https://www.encodeproject.org/ENCBS807XXG/


title: SCAF2823b_24397_BCR

source_name: Prostate cancer patient

value: Blood

value: European American (EA)


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCLB826TVO)

description:
https://www.encodeproject.org/experiments/ENCSR427HHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR427HHG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB826TVO

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

value: ENCBS600QKZ at ENCODE; https://www.encodeproject.org/ENCBS600QKZ/


title: polyA plus RNA-seq from GM07037 (ENCLB166JHO)

description:
https://www.encodeproject.org/experiments/ENCSR345CKK/
***************
biological replicate number: 2
technical replicate number: 1
description: GM07037 RNA Seq
experiment encode accession: ENCSR345CKK
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB166JHO
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS002MQZ at ENCODE; https://www.encodeproject.org/ENCBS002MQZ/


title: polyA plus RNA-seq from GM12286 (ENCLB825PLR)

description:
https://www.encodeproject.org/experiments/ENCSR289KIV/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12286 RNA Seq
experiment encode accession: ENCSR289KIV
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB825PLR
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM12286 cell line

value: male

value: ENCBS614LGR at ENCODE; https://www.encodeproject.org/ENCBS614LGR/


title: SCAF2822b_24392_BCR


title: pho4(A) pho4(B) strain Low Pi, replicate A

description: Library name: AB_L_A

value: whole cell


title: pho4(A) pho4(B) strain High Pi, replicate C

description: Library name: AB_H_C


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB274ROM)

description:
https://www.encodeproject.org/experiments/ENCSR423XHS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR423XHS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB274ROM

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: ENCBS544MIH at ENCODE; https://www.encodeproject.org/ENCBS544MIH/


title: polyA plus RNA-seq from GM12286 (ENCLB738TDY)

description:
https://www.encodeproject.org/experiments/ENCSR289KIV/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12286 RNA Seq
experiment encode accession: ENCSR289KIV
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB738TDY
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: unknown

value: ENCBS345DKB at ENCODE; https://www.encodeproject.org/ENCBS345DKB/


title: pho4(A) pho4(B) strain High Pi, replicate B

description: Library name: AB_H_B


title: SCAF2821b_23198_BCR

value: Blood

value: European American (EA)

value: Lethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB754LJT)

description:
https://www.encodeproject.org/experiments/ENCSR422HVC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR422HVC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB754LJT

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-2 for 1 hour

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

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

value: ENCBS341LGN at ENCODE; https://www.encodeproject.org/ENCBS341LGN/


title: SCAF2820b_22915_BCR

value: African American (AA)


title: pho4(A) pho4(B) strain High Pi, replicate A

description: Library name: AB_H_A

value: whole cell


title: total RNA-seq from activated gamma-delta T cell (ENCLB033EOZ)

description:
https://www.encodeproject.org/experiments/ENCSR420NCN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR420NCN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB033EOZ

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

value: activated gamma-delta T cell

value: primary cell

value: male

value: 42 year

value: ENCBS148UZT at ENCODE; https://www.encodeproject.org/ENCBS148UZT/


title: polyA plus RNA-seq from GM11920 (ENCLB085YRB)

description:
https://www.encodeproject.org/experiments/ENCSR289AAO/
***************
biological replicate number: 1
technical replicate number: 1
description: GM11920 RNA Seq
experiment encode accession: ENCSR289AAO
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB085YRB
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM11920 cell line

tag: line

value: cell line

value: female

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS552LPD at ENCODE; https://www.encodeproject.org/ENCBS552LPD/


title: polyA plus RNA-seq from GM11920 (ENCLB617ZPX)

description:
https://www.encodeproject.org/experiments/ENCSR289AAO/
***************
biological replicate number: 2
technical replicate number: 1
description: GM11920 RNA Seq
experiment encode accession: ENCSR289AAO
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB617ZPX
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

tag: health state

value: ENCBS101AOC at ENCODE; https://www.encodeproject.org/ENCBS101AOC/


title: SCAF2819b_22010_BCR

value: Blood

value: European American (EA)

value: Nonlethal


title: pho4(B) strain Low Pi, replicate C

description: Library name: B_L_C


title: SCAF2818b_21943_BCR

value: African American (AA)


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCLB933FJX)

description:
https://www.encodeproject.org/experiments/ENCSR409FWR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR409FWR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB933FJX

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

value: adult

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS247LUN at ENCODE; https://www.encodeproject.org/ENCBS247LUN/


title: polyA plus RNA-seq from GM11993 (ENCLB308XVJ)

description:
https://www.encodeproject.org/experiments/ENCSR195LZH/
***************
biological replicate number: 1
technical replicate number: 1
description: GM11993 RNA Seq
experiment encode accession: ENCSR195LZH
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB308XVJ
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM11993 cell line

tag: source

value: ENCBS995ATL at ENCODE; https://www.encodeproject.org/ENCBS995ATL/


title: pho4(B) strain Low Pi, replicate B

description: Library name: B_L_B

value: whole cell


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB288TKF)

description:
https://www.encodeproject.org/experiments/ENCSR408SVX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR408SVX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB288TKF

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: 38 year

tag: link

value: ENCBS440YJC at ENCODE; https://www.encodeproject.org/ENCBS440YJC/


title: SCAF2817b_21365_BCR


title: polyA plus RNA-seq from GM11993 (ENCLB606ANR)

description:
https://www.encodeproject.org/experiments/ENCSR195LZH/
***************
biological replicate number: 2
technical replicate number: 1
description: GM11993 RNA Seq
experiment encode accession: ENCSR195LZH
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB606ANR
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: female

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS017TVZ at ENCODE; https://www.encodeproject.org/ENCBS017TVZ/


title: pho4(B) strain Low Pi, replicate A

description: Library name: B_L_A


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB068DHQ)

description:
https://www.encodeproject.org/experiments/ENCSR407ILD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR407ILD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB068DHQ

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

value: adult

value: ENCBS990AHT at ENCODE; https://www.encodeproject.org/ENCBS990AHT/


title: pho4(B) strain High Pi, replicate C

description: Library name: B_H_C


title: SCAF2812b_27281_BCR

value: Blood

value: European American (EA)

value: Lethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB054YBD)

description:
https://www.encodeproject.org/experiments/ENCSR406AIN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR406AIN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB054YBD

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

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS432SIT at ENCODE; https://www.encodeproject.org/ENCBS432SIT/


title: polyA plus RNA-seq from GM20787 (ENCLB345LKA)

description:
https://www.encodeproject.org/experiments/ENCSR150XQV/
***************
biological replicate number: 2
technical replicate number: 1
description: GM20787 RNA Seq
experiment encode accession: ENCSR150XQV
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB345LKA
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM20787 cell line

value: male

value: ENCBS748UWQ at ENCODE; https://www.encodeproject.org/ENCBS748UWQ/


title: polyA plus RNA-seq from GM20787 (ENCLB119IFA)

description:
https://www.encodeproject.org/experiments/ENCSR150XQV/
***************
biological replicate number: 1
technical replicate number: 1
description: GM20787 RNA Seq
experiment encode accession: ENCSR150XQV
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB119IFA
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: ENCBS799IZP at ENCODE; https://www.encodeproject.org/ENCBS799IZP/


title: SCAF2811b_26136_BCR

value: African American (AA)


title: pho4(B) strain High Pi, replicate B

description: Library name: B_H_B

value: whole cell


title: total RNA-seq from central memory CD4-positive, alpha-beta T cell (ENCLB550VZV)

description:
https://www.encodeproject.org/experiments/ENCSR403NDE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR403NDE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB550VZV

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

value: primary cell

value: 38 year

value: ENCBS437FID at ENCODE; https://www.encodeproject.org/ENCBS437FID/


title: SCAF2810b_26003_BCR


title: polyA plus RNA-seq from GM12889 (ENCLB433LAI)

description:
https://www.encodeproject.org/experiments/ENCSR113EAE/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12889 RNA Seq
experiment encode accession: ENCSR113EAE
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB433LAI
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM12889 cell line

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS532VPT at ENCODE; https://www.encodeproject.org/ENCBS532VPT/


title: total RNA-seq from effector CD8-positive, alpha-beta T cell (ENCLB489GTD)

description:
https://www.encodeproject.org/experiments/ENCSR402WEM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR402WEM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB489GTD

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

value: female

value: adult

value: 33 year

value: ENCBS619YQR at ENCODE; https://www.encodeproject.org/ENCBS619YQR/


title: pho4(B) strain High Pi, replicate A

description: Library name: B_H_A

source_name: whole cell


title: SCAF2809b_25015_BCR

value: Blood

value: European American (EA)


title: polyA plus RNA-seq from GM12889 (ENCLB859RLA)

description:
https://www.encodeproject.org/experiments/ENCSR113EAE/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12889 RNA Seq
experiment encode accession: ENCSR113EAE
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB859RLA
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: male

value: ENCBS656PHO at ENCODE; https://www.encodeproject.org/ENCBS656PHO/


title: pho4(A) strain Low Pi, replicate C

description: Library name: A_L_C

value: whole cell


title: SCAF2808b_22573_BCR

value: African American (AA)

value: Nonlethal


title: polyA plus RNA-seq from GM18505 (ENCLB070HNY)

description:
https://www.encodeproject.org/experiments/ENCSR006SBQ/
***************
biological replicate number: 1
technical replicate number: 1
description: GM18505 RNA Seq
experiment encode accession: ENCSR006SBQ
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB070HNY
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

source_name: Homo sapiens GM18505 cell line

value: ENCBS189DGI at ENCODE; https://www.encodeproject.org/ENCBS189DGI/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB405ZYH)

description:
https://www.encodeproject.org/experiments/ENCSR399CLZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR399CLZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB405ZYH

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

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS627TZB at ENCODE; https://www.encodeproject.org/ENCBS627TZB/


title: pho4(A) strain Low Pi, replicate B

description: Library name: A_L_B


title: snATAC-seq from HepG2 (ENCLB950WXC)

description:
https://www.encodeproject.org/experiments/ENCSR398OHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR398OHC
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB950WXC
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens HepG2 cell line nuclear fraction

value: hepatocellular carcinoma

value: child

value: 15 year

value: Mats Ljungman, UMichigan

tag: subcellular fraction term name

value: nucleus

value: ATCC

value: ENCBS741RCV at ENCODE; https://www.encodeproject.org/ENCBS741RCV/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: SCAF2807b_22213_BCR

source_name: Prostate cancer patient

value: Blood

value: African American (AA)

value: Lethal


title: polyA plus RNA-seq from GM18505 (ENCLB457AHQ)

description:
https://www.encodeproject.org/experiments/ENCSR006SBQ/
***************
biological replicate number: 2
technical replicate number: 1
description: GM18505 RNA Seq
experiment encode accession: ENCSR006SBQ
assay title: polyA plus RNA-seq
encode release date: 2025-09-30
lab: Erez Aiden, Baylor
library encode accession: ENCLB457AHQ
nucleic acid starting quantity: 1000
nucleic acid starting quantity units: ng
instrument model: Ultima Genomics

value: cell line

value: female

value: unknown

value: Erez Aiden, Baylor

value: Coriell

value: ENCBS345FNK at ENCODE; https://www.encodeproject.org/ENCBS345FNK/


title: pho4(A) strain Low Pi, replicate A

description: Library name: A_L_A

value: whole cell

tag: genotype


title: SCAF2806b_22135_BCR

value: European American (EA)

value: Nonlethal


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB861XKP)

description:
https://www.encodeproject.org/experiments/ENCSR398FYY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR398FYY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB861XKP

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

value: primary cell

tag: biosample encode accession

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS744JZA at ENCODE; https://www.encodeproject.org/ENCBS744JZA/


title: pho4(A) strain High Pi, replicate C

description: Library name: A_H_C


title: Fennel leaf, supplemental red LED light, biological rep 3

city: Blacksburg

first: Jingsi

address: 360 Duck Pond Drive

department: Food Science and Technology

institute: Virginia Tech

description: Library name: RED3

data_processing:
RNA-seq reads from the three biological replicates were merged and assembled into a de novo transcriptome from all available reads using Trinity (version 2.15.1), with the resulting assembly containing 211,514 contigs.
Assembly: De novo transcriptome assembly generated using Trinity (version 2.15.1) since no reference genome was available for Foeniculum vulgare
Supplementary files format and content: CSV file containing raw gene-level read counts generated from de novo transcriptome assembly

organism: Anethum foeniculum

source_name: Leaf

extract_protocol:
Total RNA was extracted from approximately 50 mg of fennel leaf tissue using the Qiagen RNeasy Plant Mini Kit (Hilden, Germany) and treated with the Qiagen RNase-free DNase Set (Hilden, Germany) according to manufacturer’s instructions.
Library preparation and RNA-seq were conducted by Novogene (Sacramento, CA) using the Illumina NovaSeq platform (HWI-ST1276) with paired-end, 150 bp read sequencing strategy.

value: Leaf

tag: treatment

value: Ambient sunlight and supplemental red LED light


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB869AMN)

description:
https://www.encodeproject.org/experiments/ENCSR397FKH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR397FKH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB869AMN

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

value: CD8-positive, alpha-beta T cell

tag: encode accession

tag: Sex

value: 38 year

value: ENCBS100AJW at ENCODE; https://www.encodeproject.org/ENCBS100AJW/


title: SCAF2805b_21570_BCR

value: Blood


title: Fennel leaf, supplemental red LED light, biological rep 2

description: Library name: RED2


title: pho4(A) strain High Pi, replicate B

description: Library name: A_H_B


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB097DAN)

description:
https://www.encodeproject.org/experiments/ENCSR396TZQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR396TZQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB097DAN

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

value: CD4-positive, alpha-beta T cell

value: female

tag: dev stage

tag: age

value: 33 year

value: ENCBS279ORW at ENCODE; https://www.encodeproject.org/ENCBS279ORW/


title: SCAF2786b_25509_BCR

tag: tissue

tag: race

value: European American (EA)

value: Lethal


title: pho4(A) strain High Pi, replicate A

description: Library name: A_H_A

value: whole cell

tag: cell line


title: Fennel leaf, supplemental red LED light, biological rep 1

description: Library name: RED1


title: total RNA-seq from inflammatory macrophage (ENCLB530UHC)

description:
https://www.encodeproject.org/experiments/ENCSR395TPM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR395TPM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB530UHC

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

value: inflammatory macrophage

value: primary cell

value: male

value: adult

value: 24 year

value: Shelly Heimfeld

value: ENCBS946FSM at ENCODE; https://www.encodeproject.org/ENCBS946FSM/


title: SCAF2785b_25265_BCR

tag: lethal prostate_cancer_group


title: Fennel leaf, control, biological rep 3

description: Library name: CTRL3

value: Leaf

value: Control (ambient sunlight)


title: wilt-type strain Low Pi, replicate C

description: Library name: W_L_C

value: wild-type


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB800RKQ)

description:
https://www.encodeproject.org/experiments/ENCSR388BAM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR388BAM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB800RKQ

value: CD8-positive, alpha-beta T cell

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS767HJT at ENCODE; https://www.encodeproject.org/ENCBS767HJT/


title: Fennel leaf, control, biological rep 2

description: Library name: CTRL2


title: SCAF2784b_24520_BCR

value: Blood

value: African American (AA)


title: wilt-type strain Low Pi, replicate B

description: Library name: W_L_B

value: whole cell


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB203SHA)

description:
https://www.encodeproject.org/experiments/ENCSR387QNB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR387QNB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB203SHA

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

value: CD4-positive, alpha-beta T cell

value: primary cell

value: ENCBS308FTF at ENCODE; https://www.encodeproject.org/ENCBS308FTF/


title: SCAF2783b_24358_BCR

value: European American (EA)


title: total RNA-seq from T follicular helper cell (ENCLB752NTN)

description:
https://www.encodeproject.org/experiments/ENCSR383IYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR383IYX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB752NTN

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

value: T follicular helper cell

value: female

value: adult

value: 33 year

value: ENCBS745KVK at ENCODE; https://www.encodeproject.org/ENCBS745KVK/


title: wilt-type strain Low Pi, replicate A

description: Library name: W_L_A

value: wild-type


title: Fennel leaf, control, biological rep 1

description: Library name: CTRL1

value: Leaf

value: Control (ambient sunlight)


title: splenic CD90+cells from 3-week-old Clec9a-cre Stat1-flox/flox mice and Stat1-flox/flox littermates. HTO.

city: Planegg

first: Barbara

last: Schraml

address: Großhaderner Strasse 9

country: Germany

institute: LMU Munich

description: Library name: scRNAseq_Clec9a-cre_Stat1-flox_CD90-pos_HTO

library_source: other

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

molecule: protein

source_name: Spleen

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

value: Spleen

tag: cell type

value: CD90+ Lymphocytes

value: Clec9a-cre Stat1-flox; Stat1-flox


title: wilt-type strain High Pi, replicate C

description: Library name: W_H_C


title: SCAF2781b_22152_BCR

value: Blood

value: African American (AA)

value: Nonlethal


title: splenic CD90+cells from 3-week-old Clec9a-cre Stat1-flox/flox mice and Stat1-flox/flox littermates. GEX.

description: Library name: scRNAseq_Clec9a-cre_Stat1-flox_CD90-pos


title: wilt-type strain High Pi, replicate B

description: Library name: W_H_B

value: whole cell


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB177ADG)

description:
https://www.encodeproject.org/experiments/ENCSR380HRM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR380HRM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB177ADG

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: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS155RSZ at ENCODE; https://www.encodeproject.org/ENCBS155RSZ/


title: SCAF2780b_22105_BCR

value: Lethal


title: splenic CD11c+MHCII+ DCs from 3-week-old Clec9a-cre Stat1-flox/flox mice and Stat1-flox/flox littermates. HTO.

description: Library name: scRNAseq_Clec9a-cre_Stat1-flox_DC_HTO

value: Dendritic cells


title: wilt-type strain High Pi, replicate A

description: Library name: W_H_A

value: wild-type


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCLB759OCF)

description:
https://www.encodeproject.org/experiments/ENCSR378SSX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR378SSX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB759OCF

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

value: male

value: adult

value: 42 year

value: ENCBS177EYY at ENCODE; https://www.encodeproject.org/ENCBS177EYY/


title: SCAF2779b_21906_BCR

value: Blood

value: European American (EA)


title: splenic CD11c+MHCII+ DCs from 3-week-old Clec9a-cre Stat1-flox/flox mice and Stat1-flox/flox littermates. GEX.

description: Library name: scRNAseq_Clec9a-cre_Stat1-flox_DC

value: Spleen

value: Clec9a-cre Stat1-flox; Stat1-flox


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB637ZHS)

description:
https://www.encodeproject.org/experiments/ENCSR377DQZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR377DQZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB637ZHS

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

value: CD4-positive, alpha-beta T cell

value: female

value: 40 year

tag: treatments

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

value: ENCBS646EZD at ENCODE; https://www.encodeproject.org/ENCBS646EZD/


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

description: Library name: AB_T60_C

value: whole cell


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

description: Library name: scRNAseq_DC_across_age_spleen_3+6_HTO

value: Clec9a-cre Rosa26-TOM


title: SCAF3017t_27500_TCR

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

value: African American (AA)

value: Lethal


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

description: Library name: AB_T60_B


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCLB867RCD)

description:
https://www.encodeproject.org/experiments/ENCSR375TBP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR375TBP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB867RCD

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

value: primary cell

value: male

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS244OKF at ENCODE; https://www.encodeproject.org/ENCBS244OKF/


title: SCAF3016t_25681_TCR

value: Blood

value: European American (EA)

value: Nonlethal


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

description: Library name: AB_T60_A

source_name: whole cell


title: total RNA-seq from T-cell (ENCLB498RQK)

description:
https://www.encodeproject.org/experiments/ENCSR371BHW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR371BHW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB498RQK

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

value: T-cell

value: female

value: adult

value: 33 year

tag: source

value: ENCBS844UBD at ENCODE; https://www.encodeproject.org/ENCBS844UBD/


title: splenic CD11c+MHCII+ Dendritic cells from 1-week and 4-week-old mice. HTO.

description: Library name: scRNAseq_DC_across_age_spleen_1+4_HTO

value: Spleen

value: Dendritic cells

value: Clec9a-cre Rosa26-TOM


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB885PIK)

description:
https://www.encodeproject.org/experiments/ENCSR370ORE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR370ORE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB885PIK

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: 40 year

tag: link

value: ENCBS239UKP at ENCODE; https://www.encodeproject.org/ENCBS239UKP/


title: SCAF3014t_24610_TCR


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

description: Library name: AB_T30_C

value: whole cell


title: splenic CD11c+MHCII+ Dendritic cells from 1-week and 4-week-old mice. GEX.

description: Library name: scRNAseq_DC_across_age_spleen_1+4


title: total RNA-seq from T-cell (ENCLB883NGH)

description:
https://www.encodeproject.org/experiments/ENCSR368ZJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR368ZJO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB883NGH

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS915ZNP at ENCODE; https://www.encodeproject.org/ENCBS915ZNP/


title: SCAF3013t_27150_TCR

value: Blood

value: African American (AA)

value: Nonlethal


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

city: London

first: Nathan

last: Skene

address: 80 Wood Lane

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: SK644S5
Brain bank case: PDC029; region block ID: P3B1; donor sex: male; donor age: 82 years; PMI: 48 h; RIN: 6.50; input tissue weight: 356 mg; brain region: parietal cortex white matter; sorting strategy: NeuN-Olig2-PU1-IRF8-Sox9-

library_source: transcriptomic single cell

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

molecule: polyA RNA

source_name: parietal cortex white matter

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

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

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

value: parietal cortex white matter

value: all-marker-negative nuclei

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

tag: batch


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB490MPN)

description:
https://www.encodeproject.org/experiments/ENCSR366ANX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR366ANX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB490MPN

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

value: CD8-positive, alpha-beta T cell

value: male

value: adult

value: 42 year

value: ENCBS204OPD at ENCODE; https://www.encodeproject.org/ENCBS204OPD/


title: SCAF3012t_22690_TCR

source_name: Prostate cancer patient

value: Lethal


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB345UVX)

description:
https://www.encodeproject.org/experiments/ENCSR358DGI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR358DGI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB345UVX

value: primary cell

value: ENCBS488CZZ at ENCODE; https://www.encodeproject.org/ENCBS488CZZ/


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

description:
Library name: SK644S3
Brain bank case: PDC029; region block ID: P3B1; donor sex: male; donor age: 82 years; PMI: 48 h; RIN: 6.50; input tissue weight: 356 mg; brain region: parietal cortex white matter; sorting strategy: NeuN-Olig2-PU1+IRF8+Sox9-

value: IRF8/PU.1-positive microglial nuclei

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


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

description: Library name: AB_T15_C

value: whole cell

tag: genotype


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

description: Library name: AB_T15_B


title: SCAF2929t_28161_TCR

value: Blood

value: European American (EA)


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

description:
Library name: SK644S2
Brain bank case: PDC029; region block ID: P3B1; donor sex: male; donor age: 82 years; PMI: 48 h; RIN: 6.50; input tissue weight: 356 mg; brain region: parietal cortex white matter; sorting strategy: NeuN-Olig2+PU1-IRF8-Sox9-

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


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

description: Library name: AB_T15_A


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB382NTR)

description:
https://www.encodeproject.org/experiments/ENCSR342HIN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR342HIN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB382NTR

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

value: CD4-positive, alpha-beta T cell

tag: biosample encode accession

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS388UST at ENCODE; https://www.encodeproject.org/ENCBS388UST/


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

description:
Library name: SK644S1
Brain bank case: PDC029; region block ID: P3B1; donor sex: male; donor age: 82 years; PMI: 48 h; RIN: 6.50; input tissue weight: 356 mg; brain region: parietal cortex white matter; sorting strategy: NeuN+Olig2-PU1-IRF8-Sox9-

value: parietal cortex white matter

value: NeuN-positive neuronal nuclei

tag: treatment

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


title: snATAC-seq from MCF-7 (ENCLB785RQF)

description:
https://www.encodeproject.org/experiments/ENCSR341TTX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR341TTX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB785RQF
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens MCF-7 cell line nuclear fraction

tag: line

value: cell line

value: female

tag: health state

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

value: Mats Ljungman, UMichigan

tag: subcellular fraction term name

value: nucleus

value: ATCC

value: ENCBS458XLY at ENCODE; https://www.encodeproject.org/ENCBS458XLY/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: SCAF2927t_27193_TCR

value: Blood

value: African American (AA)


title: ATPase-dead clone 19 biol rep 3

city: Boulder

first: Mingfeng

state: CO

address: 709 Mohawk Dr

institute: University of Colorado

description: Library name: C19-3

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

source_name: Cervical cancer

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

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

value: Cervical cancer

value: Epithelial cervical adenocarcinoma cells

value: ATPase-dead Halo-Tag RTEL1


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

description: Library name: AB_T0_B

value: whole cell


title: SCAF2926t_27140_TCR

value: Lethal


title: ATPase-dead clone 19 biol rep 2

description: Library name: C19-2


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

description: Library name: AB_T0_A


title: total RNA-seq from inflammatory macrophage (ENCLB296EGS)

description:
https://www.encodeproject.org/experiments/ENCSR338VRX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR338VRX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB296EGS

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

value: inflammatory macrophage

value: primary cell

tag: encode accession

tag: Sex

value: male

tag: dev stage

tag: age

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS128PAI at ENCODE; https://www.encodeproject.org/ENCBS128PAI/


title: SCAF2925t_25881_TCR

tag: tissue

tag: race

value: European American (EA)

tag: lethal prostate_cancer_group


title: ATPase-dead clone 19 biol rep 1

description: Library name: C19-1

tag: cell line

tag: cell type


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

description: Library name: B_T60_C


title: SCAF2924t_24796_TCR


title: ATPase-dead clone 17 biol rep 3

description: Library name: C17-3


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

description: Library name: B_T60_B


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB792EKD)

description:
https://www.encodeproject.org/experiments/ENCSR337CAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR337CAN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB792EKD

value: CD4-positive, alpha-beta T cell

value: female

value: adult

value: 34 year

tag: lab

tag: source

value: AllCells

tag: link

value: ENCBS845HWQ at ENCODE; https://www.encodeproject.org/ENCBS845HWQ/


title: SCAF2923t_23058_TCR

value: Blood

value: African American (AA)


title: ATPase-dead clone 17 biol rep 2

description: Library name: C17-2

value: Cervical cancer

value: Epithelial cervical adenocarcinoma cells

tag: genotype

value: ATPase-dead Halo-Tag RTEL1


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

description: Library name: B_T60_A

value: whole cell


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB843ZJD)

description:
https://www.encodeproject.org/experiments/ENCSR334JVS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR334JVS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB843ZJD

value: primary cell

tag: biosample encode accession

value: male

value: 42 year

value: ENCBS324CKZ at ENCODE; https://www.encodeproject.org/ENCBS324CKZ/


title: SCAF2922t_26793_TCR


title: ATPase-dead clone 17 biol rep 1

description: Library name: C17-1


title: total RNA-seq from T-cell (ENCLB534BVE)

description:
https://www.encodeproject.org/experiments/ENCSR337PXJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR337PXJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB534BVE

value: T-cell

value: 33 year

value: John Stamatoyannopoulos, UW

value: ENCBS367CPC at ENCODE; https://www.encodeproject.org/ENCBS367CPC/


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

description: Library name: B_T30_C


title: SCAF2921t_26678_TCR

value: Lethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB512GEC)

description:
https://www.encodeproject.org/experiments/ENCSR330KBN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR330KBN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB512GEC

value: CD4-positive, alpha-beta T cell

value: female

value: adult

value: 40 year

value: AllCells

value: ENCBS521OXE at ENCODE; https://www.encodeproject.org/ENCBS521OXE/


title: Wild-type clone 15 biol rep 3

description: Library name: C15-3

value: Cervical cancer

value: Epithelial cervical adenocarcinoma cells

value: WT Halo-Tag RTEL1


title: snATAC-seq from lung (ENCLB005VVB)

description:
https://www.encodeproject.org/experiments/ENCSR083HFN/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC on human lung Please note that this experiment is part of 10x multiome and has a corresponding scRNA experiment (ENCSR225OII)
experiment encode accession: ENCSR083HFN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB005VVB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (47 years) lung tissue, preserved by flash-freezing nuclear fraction

value: lung

value: tissue

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

value: 47 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS709MGO at ENCODE; https://www.encodeproject.org/ENCBS709MGO/

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


title: SCAF2782b_23995_BCR

value: Blood

value: African American (AA)


title: normal bone marrow #2-3

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

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

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

source_name: normal bone marrow

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

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

tag: ex vivo treatment

value: untreated

value: bone marrow

tag: disease state

value: normal

tag: time point


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

description: Library name: B_T30_B

value: whole cell


title: total RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB565RVK)

description:
https://www.encodeproject.org/experiments/ENCSR380UXM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR380UXM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB565RVK

source_name: Homo sapiens female adult (25 years) effector memory CD4-positive, alpha-beta T primary cell

value: primary cell

tag: encode accession

value: female

value: adult

value: 25 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS420MGJ at ENCODE; https://www.encodeproject.org/ENCBS420MGJ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB839IGB)

description:
https://www.encodeproject.org/experiments/ENCSR324GEQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR324GEQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB839IGB

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

value: CD4-positive, alpha-beta T cell

tag: Sex

value: 34 year

value: ENCBS207OQX at ENCODE; https://www.encodeproject.org/ENCBS207OQX/


title: SCAF2920t_26593_TCR

value: European American (EA)

value: Nonlethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB615TOI)

description:
https://www.encodeproject.org/experiments/ENCSR321JCI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR321JCI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB615TOI

tag: dev stage

value: ENCBS164YSC at ENCODE; https://www.encodeproject.org/ENCBS164YSC/


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

description: Library name: B_T30_A


title: Wild-type clone 15 biol rep 2

description: Library name: C15-2

value: Cervical cancer

value: Epithelial cervical adenocarcinoma cells

value: WT Halo-Tag RTEL1


title: SCAF2919t_26565_TCR

value: Blood

value: African American (AA)