title: MPRA from MIN6 (ENCLB613LYD)

description:
https://www.encodeproject.org/experiments/ENCSR981ILP/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TCF7L2 enhancer.
experiment encode accession: ENCSR981ILP
assay title: MPRA
possible controls: ENCSR361QPQ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB613LYD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: not collected

value: unknown

value: Nadav Ahituv, UCSF

tag: source

value: ENCBS450ZQL at ENCODE; https://www.encodeproject.org/ENCBS450ZQL/


title: DNase-seq from K562 (ENCLB136OUN)

status: Public on Mar 06 2026

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR840YOF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB136OUN

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: John Stamatoyannopoulos, UW

value: ATCC

tag: link

value: ENCBS874WPD at ENCODE; https://www.encodeproject.org/ENCBS874WPD/


title: R-003-iA_C

city: Atlanta

first: Benjamin

last: Siciliano

state: GA

address: 615 Michael Street

institute: Emory University

description: Library name: Sample 27

library_source: transcriptomic

data_processing:
RNA-seq reads were trimmed via Trimmomatic and aligned against the human reference transcriptome (GRCh38.p14) via Salmon. Transcriptome-wide gene counts were obtained through gene-level transcript summarization with the tximeta R package. FPKM values were calculated using the DESeq2 R package by normalizing the counts with its built-in size factor estimation and subsequently adjusting for gene length.
Assembly: hg38
Supplementary files format and content: FPKM

molecule: total RNA

source_name: Patient-derived hiPSC

extract_protocol:
Total RNA was extracted from each of the nine hiPSC-derived astrocyte cell lines via TRIzol reagent (Invitrogen, 15596026) per the manufacturer’s instructions. Total RNA from each line was treated with DNase I (Zymo Research, E1010) and then cleaned and concentrated via the Clean & Concentrator Kit (Zymo Research, D4033). A NanoDrop One/OneC Microvolume UV‒Vis Spectrophotometer (Thermo Scientific, ND-ONE-W) was then used to determine the RNA yield from each of the nine RNA extractions. For RNA sequencing (RNA-seq), 150-cycle PE sequencing via the Illumina HiSeq2500 platform was performed by Admera Health (South Plainfield, New Jersey, United States) with 1 µg of RNase-free RNA (>10 ng/μL, RIN > 7) per technical triplicate for each of the nine lines.
An RNA-seq library was generated utilizing the Illumina mRNA sample prep kit (Illumina, RS-100-0801) according to the manufacturer's protocol in 3 technical replicates for each sample. The library constructs' size and concentration were verified with a bioanalyzer before sequencing on the Illumina NovaSeq6000. The raw reads' quality was evaluated to confirm the success of the library preparation and sequencing processes.

tag: cell line

value: Patient-derived hiPSC

tag: cell type

value: hiPSC-derived astrocyte

tag: genotype

value: SSRI responder


title: R-003-iA_B

description: Library name: Sample 26


title: Experiment1_D7_Prdm1cKO_GEX

city: Pittsburgh

first: Harinder

last: Singh

state: PA

address: 5051 Centre Avenue

department: Center for Systems Immunology and Department of Immunology

institute: University of Pittsburgh

description:
Library name: Sample 6
10X genomics - 5Prime - V2

library_source: transcriptomic single cell

data_processing:
For all scRNA-Seq experiments, UMI counts were calculated using CellRanger (v.6.1.2) and reads were aligned using mm10 as the reference genome. CellRanger filtered feature sparse matrix counts files from the NP+B220+ splenocyte sample obtained on 14 d.p.i. (HDF5 format) were supplied for unsupervised cell-clustering analysis using the ICGS2 algorithm in the software AltAnalyze using default parameters2. ICGS2 delineates non-negative matrix factorization (NMF) clusters and unique marker genes. Cell-type/state labels were initially based on ICGS2 cluster-specific marker gene-set enrichment (GO-Elite) and then further refined with manual curation using literature-associated markers. A small proportion of non-B-lineage cells were identified based on their marker gene profiles and were excluded from the downstream analysis.
ICGS2 cell clusters for NP+B220+ splenocytes isolated from WT on 14 d.p.i. were used as the reference for all remaining single-cell RNA-seq  experiments presented (supervised classification). Label transfer was performed in the software cellHarmony using centroid-based classification and a minimum Pearson correlation coefficient of 0.7 on the log2 scaled gene expression counts, to exclude low-quality alignments.
Single-cell VDJ sequencing data were processed using Cellranger VDJ (v.6.1.2) reference for mouse from 10x Genomics. Cell barcode associations from CellRanger VDJ and linked gene expression were used for coupling the BCR and transcriptomes, respectively. Cells that did not contain both the BCR and gene expression features were excluded for all downstream clonal analyses. The somatic hypermutation rate and affinity maturation were determined for these cells as described previously7. Clones were identified based on cells that have identical V(D)J rearrangements in their heavy and light chain loci (kappa or lambda) for cells bearing IGHV1-72*01 gene
For all multiome data analysis, Prdm1 cKO and WT FASTQ files were processed separately with Cell Ranger ARC (v2.0.2) using the GRCh38 (2020) reference genome for alignment. Outputs from individual GEM wells were aggregated using the ‘aggr’ function. Cell and gene filtering were performed in Scanpy (1.11.4), retaining cells with >2000 detected genes and <10% mitochondrial reads, and genes expressed in at least 20 cells. Cell cycle effects were regressed out using the ‘regress_out’ function in SCANPY with established G1/S and G2/M gene sets. MIRA was used for gene expression and chromatin accessibility topic modeling. A joint embedding space was then constructed by integrating transformed expression and accessibility topic models. Scanpy used for dimentionality reduction using umap function and clustering the cells using leiden function. Clusters were annotated using the gene signature score transferred from ICGS2 of the scRNA-seq. Peaks were called using MACS2 (version 3.0.3).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: cytoplasmic RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Splenocytes were washed and prepared as single-cell suspensions in FACS buffer (Catalog # - 10010; pH 7.4; Gibco 1x PBS without calcium and magnesium plus 2% FBS and 2 mM EDTA;). Erythrocytes were depleted using 3 mL of ACK lysis buffer (Thermo Fisher Scientific) for 5 minutes, then quenched and washed with FACS staining buffer. After pelleting, the cells were resuspended in plain PBS and pelleted again to remove any residual protein before live/dead staining. Cells were counted using a BD cell counter or manually with a hemocytometer and Trypan Blue (Sigma Aldrich). For the isolation of NP+B220+ subset by flow cytometry, splenocytes were isolated from Prdm1 cKO and WT mice immunized with NP-CGG, alum and LPS on 7- and 14-days post-immunization (d.p.i.). Splenocytes were washed and prepared as single-cell suspensions as before and and labeled with viability dye eFluor 780 (eF780), PE-Dazzle Red 594 B220 (RA3-6B2) and PE  NP138 for 20 minutes at 4˚C and were sorted as NP+B220+ subset using FACSAria II (BD) with 70 μm nozzle at 4˚C.
For scRNA-seq and BCR-seq, flow sorted NP+B220+ splenocytes subsets were suspended in 5% FBS and loaded along with oil and beads containing unique barcodes onto the Chromium controller (10x Genomics) to form an emulsion. Single cells contained in oil droplets were then lysed and mRNA was captured by the beads and subjected to reverse transcription and cDNA amplification to generate libraries for sequencing, according to the manufacturer’s Chromium Single Cell 5’V2 protocol, as described previously1. From the cDNA libraries, one aliquot was used for fragmentation and preparation for transcriptome profiling, and another for amplification of VDJ regions using the BCR kit. Samples were then sequenced using a NovaSeq 6000 (Illumina) in which 30,000 and 5,000 reads were generated with the mRNA and BCR libraries respectively. For multiome-seq, low sorted NP+B220+ splenocytes were washed twice with PBS containing 0.04% BSA and lysed in 100 μL of chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20, 0.1% IGEPAL, 0.01% digitonin, 1% BSA, 1 mM DTT, 1 U/μL RNase inhibitor [Protector, Sigma]). Cells were mixed by pipetting and incubated on ice for 3 min. Lysis was quenched with 1 mL of chilled wash buffer (same composition as lysis buffer excluding digitonin) and mixed gently. Nuclei were washed three times with wash buffer and resuspended in diluted nuclei buffer (10x Genomics) supplemented with 1 mM DTT and 1 U/μL RNase inhibitor. Nuclei were counted, resuspended in chilled PBS (750–1,000 nuclei/μL), and aliquoted (180 μL per sample). Labeling reactions were quenched with 2% BSA in PBS, followed by centrifugation at 500 × g for 4 min at 4 °C. After pooling and washing, nuclei were resuspended in diluted nuclei buffer and processed according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (10x Genomics) through the pre-amplification PCR step. Ten microliters of the pre-amplified product were fractionated using 0.6× SPRI bead cleanup to separate cDNA (gene expression) and gDNA (ATAC) products. Final libraries were prepared according to the manufacturer's protocol and sequenced on a NovaSeq 6000 (Illumina) in which 30,000 reads were generated with the mRNA and ATAC libraries separately.

treatment_protocol: Eight to ten week old Prdm1fl/flCd19cre/+ (Prdm1 cKO) and Prdm1+/+ Cd19cre/+ (WT) mice were immunized intraperitoneally with 50 μg NP(23)-CGG (Biosearch Technologies) mixed with 50% (v/v) imject alum (Thermo Fisher Scientific) and 1 μg LPS (Sigma).

tag: tissue

value: Spleen

value: Prdm1 cKO

tag: treatment

value: NP-CGG + Alum + LPS

tag: library type

value: mRNA


title: MPRA from MIN6 (ENCLB948MXQ)

description:
https://www.encodeproject.org/experiments/ENCSR981ILP/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TCF7L2 enhancer.
experiment encode accession: ENCSR981ILP
assay title: MPRA
possible controls: ENCSR361QPQ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB948MXQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Mus musculus MIN6 cell line genetically modified (insertion) using transient transfection

value: not collected

value: unknown

value: Nadav Ahituv, UCSF

value: ENCBS226BJQ at ENCODE; https://www.encodeproject.org/ENCBS226BJQ/


title: R-002-iA_C

description: Library name: Sample 24


title: MPRA from MIN6 (ENCLB957KRJ)

description:
https://www.encodeproject.org/experiments/ENCSR909OSG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZFAND3 enhancer.
experiment encode accession: ENCSR909OSG
assay title: MPRA
possible controls: ENCSR463MKA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB957KRJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: ENCBS078DWC at ENCODE; https://www.encodeproject.org/ENCBS078DWC/


title: Experiment1_D14_WT_GEX

description:
Library name: Sample 4
10X genomics - 5Prime - V2

value: WT


title: MPRA from MIN6 (ENCLB317DLQ)

description:
https://www.encodeproject.org/experiments/ENCSR909OSG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZFAND3 enhancer.
experiment encode accession: ENCSR909OSG
assay title: MPRA
possible controls: ENCSR463MKA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB317DLQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS771OVU at ENCODE; https://www.encodeproject.org/ENCBS771OVU/


title: R-002-iA_B

description: Library name: Sample 23


title: Experiment1_D14_WT_BCR

description:
Library name: Sample 3
10X genomics - 5Prime - V2

data_processing:
For all scRNA-Seq experiments, UMI counts were calculated using CellRanger (v.6.1.2) and reads were aligned using mm10 as the reference genome. CellRanger filtered feature sparse matrix counts files from the NP+B220+ splenocyte sample obtained on 14 d.p.i. (HDF5 format) were supplied for unsupervised cell-clustering analysis using the ICGS2 algorithm in the software AltAnalyze using default parameters2. ICGS2 delineates non-negative matrix factorization (NMF) clusters and unique marker genes. Cell-type/state labels were initially based on ICGS2 cluster-specific marker gene-set enrichment (GO-Elite) and then further refined with manual curation using literature-associated markers. A small proportion of non-B-lineage cells were identified based on their marker gene profiles and were excluded from the downstream analysis.
ICGS2 cell clusters for NP+B220+ splenocytes isolated from WT on 14 d.p.i. were used as the reference for all remaining single-cell RNA-seq  experiments presented (supervised classification). Label transfer was performed in the software cellHarmony using centroid-based classification and a minimum Pearson correlation coefficient of 0.7 on the log2 scaled gene expression counts, to exclude low-quality alignments.
Single-cell VDJ sequencing data were processed using Cellranger VDJ (v.6.1.2) reference for mouse from 10x Genomics. Cell barcode associations from CellRanger VDJ and linked gene expression were used for coupling the BCR and transcriptomes, respectively. Cells that did not contain both the BCR and gene expression features were excluded for all downstream clonal analyses. The somatic hypermutation rate and affinity maturation were determined for these cells as described previously7. Clones were identified based on cells that have identical V(D)J rearrangements in their heavy and light chain loci (kappa or lambda) for cells bearing IGHV1-72*01 gene
For all multiome data analysis, Prdm1 cKO and WT FASTQ files were processed separately with Cell Ranger ARC (v2.0.2) using the GRCh38 (2020) reference genome for alignment. Outputs from individual GEM wells were aggregated using the ‘aggr’ function. Cell and gene filtering were performed in Scanpy (1.11.4), retaining cells with >2000 detected genes and <10% mitochondrial reads, and genes expressed in at least 20 cells. Cell cycle effects were regressed out using the ‘regress_out’ function in SCANPY with established G1/S and G2/M gene sets. MIRA was used for gene expression and chromatin accessibility topic modeling. A joint embedding space was then constructed by integrating transformed expression and accessibility topic models. Scanpy used for dimentionality reduction using umap function and clustering the cells using leiden function. Clusters were annotated using the gene signature score transferred from ICGS2 of the scRNA-seq. Peaks were called using MACS2 (version 3.0.3).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: BCR-Seq


title: DNase-seq from K562 (ENCLB039CAD)

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR840YOF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB039CAD

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS474XMG at ENCODE; https://www.encodeproject.org/ENCBS474XMG/


title: R-003-iA_A

description: Library name: Sample 25

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: SSRI responder


title: MPRA from MIN6 (ENCLB794LPH)

description:
https://www.encodeproject.org/experiments/ENCSR909OSG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZFAND3 enhancer.
experiment encode accession: ENCSR909OSG
assay title: MPRA
possible controls: ENCSR463MKA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB794LPH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: not collected

value: unknown

value: ENCBS148ZFV at ENCODE; https://www.encodeproject.org/ENCBS148ZFV/


title: Experiment1_D14_Prdm1cKO_GEX

description:
Library name: Sample 2
10X genomics - 5Prime - V2

value: Spleen

value: Prdm1 cKO

value: NP-CGG + Alum + LPS

value: mRNA


title: Experiment1_D7_Prdm1cKO_BCR

description:
Library name: Sample 5
10X genomics - 5Prime - V2


title: DNase-seq from K562 (ENCLB560PPF)

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 7
technical replicate number: 1
description:
experiment encode accession: ENCSR840YOF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB560PPF

value: cell line

value: female

value: ENCBS053ACF at ENCODE; https://www.encodeproject.org/ENCBS053ACF/


title: R-002-iA_A

description: Library name: Sample 22


title: DNase-seq from K562 (ENCLB316LSJ)

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR840YOF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB316LSJ

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS600QDG at ENCODE; https://www.encodeproject.org/ENCBS600QDG/


title: MPRA from Neuro-2a (ENCLB454MUN)

description:
https://www.encodeproject.org/experiments/ENCSR642DFC/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ultra conserved element UC88.
experiment encode accession: ENCSR642DFC
assay title: MPRA
possible controls: ENCSR020AUG
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB454MUN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Mus musculus strain A albino mouse Neuro-2a cell line genetically modified (insertion) using transient transfection

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS831HYC at ENCODE; https://www.encodeproject.org/ENCBS831HYC/


title: MB49 tumor cells

city: St. Louis

first: Elise

last: Alspach

state: MO

address: 1100 South Grand Boulevard

department: MMI

institute: St. Louis University

description:
Library name: MB49
10x Genomics

data_processing:
Datasets were processed using Cell Ranger and the Seurat R toolkit (Version 5). Multiplets and low-quality cells were excluded from the data based on abnormal feature/unique molecular identifier count and a high percentage of mitochondrial gene expression, respectively. Samples were integrated using reciprocal principal component analysis. Cells were visualized using uniform manifold approximation and projection (UMAP) dimensional reduction, and UMAP figures were visualized using both the built-in Seurat visualization tools and the scCustomize package.
Assembly: Mouse mm10 (2020)
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: MB49 murine epithelial bladder carcinoma cells were purchased from Millipore Sigma. MB49 cells were grown in Dulbecco’s Modified Eagle Medium supplemented with 10% non-heat inactivated fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
MB49 cells in tissue culture were dissociated using 0.25% Trypsin/EDTA and passed through a 100-micron strainer to obtain a single cell suspension.
Single cell RNA libraries from 10,000-20,000 cells per sample were generated using a Chromium Controller and the GEM-X Single Cell 5’ kit from 10X Genomics. Library sequencing was performed by the Genome Technology Access Center at Washington University in St. Louis.

value: epithelial bladder cancer

value: tissue culture


title: Experiment1_D14_Prdm1cKO_BCR

description:
Library name: Sample 1
10X genomics - 5Prime - V2


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB973FNI)

description:
https://www.encodeproject.org/experiments/ENCSR840FLY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR840FLY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB973FNI

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

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS506IUK at ENCODE; https://www.encodeproject.org/ENCBS506IUK/


title: DNase-seq from K562 (ENCLB659FAC)

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 8
technical replicate number: 1
description:
experiment encode accession: ENCSR840YOF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB659FAC

value: cell line

value: female

value: ENCBS852LAT at ENCODE; https://www.encodeproject.org/ENCBS852LAT/


title: MPRA from Neuro-2a (ENCLB287RFF)

description:
https://www.encodeproject.org/experiments/ENCSR642DFC/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ultra conserved element UC88.
experiment encode accession: ENCSR642DFC
assay title: MPRA
possible controls: ENCSR020AUG
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB287RFF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: not collected

value: unknown

value: ENCBS761QWU at ENCODE; https://www.encodeproject.org/ENCBS761QWU/


title: R-001-iA_B

description: Library name: Sample 20

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: SSRI responder


title: Control MPRA from NIH3T3 (ENCLB898KMH)

description:
https://www.encodeproject.org/experiments/ENCSR517PBF/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR517PBF
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB898KMH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Mus musculus strain NIH3T3 NIH3T3 cell line genetically modified (insertion) using transient transfection

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS663DVO at ENCODE; https://www.encodeproject.org/ENCBS663DVO/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB539PNA)

description:
https://www.encodeproject.org/experiments/ENCSR792ZWJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR792ZWJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB539PNA

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-4 for 24 hours

value: primary cell

value: male

value: adult

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS572DHL at ENCODE; https://www.encodeproject.org/ENCBS572DHL/


title: male T cells

description:
Library name: male
10x Genomics

data_processing:
Datasets were processed using Cell Ranger and the Seurat R toolkit (Version 5). Multiplets and low-quality cells were excluded from the data based on abnormal feature/unique molecular identifier count and a high percentage of mitochondrial gene expression, respectively. Samples were integrated using reciprocal principal component analysis. Cells were visualized using uniform manifold approximation and projection (UMAP) dimensional reduction, and UMAP figures were visualized using both the built-in Seurat visualization tools and the scCustomize package.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MB49 tumors

extract_protocol:
Tumors were digested at 37°C using type IV collagenase (Stemcell Technologies, catalog number 07427), red blood cells were lysed using RBC lysis buffer (Thermo-Fisher Scientific, catalog number 00-4333-57), and homogenates were passed through 100-micron strainers to obtain a single cell suspension. Viable CD4+ T cells were isolated by fluorescence-activated cell sorting (FACS).
Single cell RNA libraries from 10,000-20,000 cells per sample were generated using a Chromium Controller and the GEM-X Single Cell 5’ kit (catalog number 1000707) from 10X Genomics. Library sequencing was performed by the Genome Technology Access Center at Washington University in St. Louis.

value: MB49 tumors

value: tumor infiltrating T cells

tag: time

value: day 14

value: 12-14 weeks

tag: strain


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB020UBN)

description:
https://www.encodeproject.org/experiments/ENCSR792ZWJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR792ZWJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB020UBN

tag: biosample encode accession

value: 38 year

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS592BVN at ENCODE; https://www.encodeproject.org/ENCBS592BVN/


title: Control MPRA from NIH3T3 (ENCLB482SUJ)

description:
https://www.encodeproject.org/experiments/ENCSR517PBF/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR517PBF
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB482SUJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

tag: line

value: cell line

tag: encode accession

tag: Sex

value: not collected

value: unknown

value: ENCBS151EIL at ENCODE; https://www.encodeproject.org/ENCBS151EIL/


title: NR-003-iA_C

description: Library name: Sample 18

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: SSRI non-responder


title: LLC-Thy1.1 P0 and P2 cancer cell lines, CMO

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
Library name: LLC-Thy1.1_CMO
CMO: read1 contains cell barcode and UMI; read2 contains  cell multiplexing oligonucleotide (CMO) sequence

library_source: other

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count or Cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Compressed .h5/tar.gz files containing UMI RNA/ADT/HTO/CMO counts per cell in Cellranger output format, and comma-delimited text files including metadata per cell,
Supplementary files format and content: as well as comma delimited files with information of the ADT/HTO/STREP antibodies or CMO hashes used.

molecule: other

extract_protocol: All methods listed in Bardet et al. Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq.

value: LLC-Thy1.1 P0 and P2 cancer cell lines


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB771LHQ)

description:
https://www.encodeproject.org/experiments/ENCSR834HNG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR834HNG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB771LHQ

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-15 for 24 hours

value: primary cell

value: male

tag: dev stage

value: adult

tag: age

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS486CZP at ENCODE; https://www.encodeproject.org/ENCBS486CZP/


title: MPRA from Neuro-2a (ENCLB042NRY)

description:
https://www.encodeproject.org/experiments/ENCSR642DFC/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ultra conserved element UC88.
experiment encode accession: ENCSR642DFC
assay title: MPRA
possible controls: ENCSR020AUG
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB042NRY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

tag: lab

value: Nadav Ahituv, UCSF

value: ATCC

tag: link

value: ENCBS247ZIH at ENCODE; https://www.encodeproject.org/ENCBS247ZIH/


title: DNase-seq from inflammatory macrophage (ENCLB004ILC)

description:
https://www.encodeproject.org/experiments/ENCSR773SWT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR773SWT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB004ILC

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

value: inflammatory macrophage

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS150GKO at ENCODE; https://www.encodeproject.org/ENCBS150GKO/


title: R-001-iA_C

description: Library name: Sample 21

tag: cell line

value: Patient-derived hiPSC

tag: cell type

value: SSRI responder


title: Control MPRA from MIN6 (ENCLB731QBN)

description:
https://www.encodeproject.org/experiments/ENCSR463MKA/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZFAND3 enhancer.
experiment encode accession: ENCSR463MKA
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB731QBN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: not collected

value: unknown

value: ENCBS078DWC at ENCODE; https://www.encodeproject.org/ENCBS078DWC/


title: Control MPRA from NIH3T3 (ENCLB891GRM)

description:
https://www.encodeproject.org/experiments/ENCSR517PBF/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR517PBF
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB891GRM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS749TUG at ENCODE; https://www.encodeproject.org/ENCBS749TUG/


title: NR-003-iA_A

description: Library name: Sample 16

value: hiPSC-derived astrocyte

tag: genotype

value: SSRI non-responder


title: Orthotopic HBSS-inoculated (mock) mouse lung tissue (ORTHO-M), ADT

description:
Library name: ORTHO-M_ADT
ADT, HTO and STREP: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag (ADT), Hashtag oligo (HTO) or streptavidin-conjugated oligo (STREP) sequence

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count or Cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Compressed .h5/tar.gz files containing UMI RNA/ADT/HTO/CMO counts per cell in Cellranger output format, and comma-delimited text files including metadata per cell,
Supplementary files format and content: as well as comma delimited files with information of the ADT/HTO/STREP antibodies or CMO hashes used.
Library strategy: CITE-seq

molecule: protein

source_name: Lung tissue

tag: tissue

value: Lung tissue

value: 14-AAD-CD45+Thy1.1- immune cells


title: NR-002-iA_C

description: Library name: Sample 15


title: Control MPRA from MIN6 (ENCLB684YWY)

description:
https://www.encodeproject.org/experiments/ENCSR463MKA/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZFAND3 enhancer.
experiment encode accession: ENCSR463MKA
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB684YWY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS771OVU at ENCODE; https://www.encodeproject.org/ENCBS771OVU/


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB246SYQ)

description:
https://www.encodeproject.org/experiments/ENCSR762ZVI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR762ZVI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB246SYQ

source_name: Homo sapiens male adult (38 years) stimulated activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

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

value: ENCBS352YNU at ENCODE; https://www.encodeproject.org/ENCBS352YNU/


title: NR-002-iA_B

description: Library name: Sample 14

value: Patient-derived hiPSC


title: LLC-Thy1.1 P0 and P2 cancer cell lines, cDNA

description:
Library name: LLC-Thy1.1_cDNA
3’ mRNA (Next GEM v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

molecule: polyA RNA

value: LLC-Thy1.1 P0 and P2 cancer cell lines


title: female T cells

description:
Library name: female
10x Genomics

value: MB49 tumors

value: female

value: tumor infiltrating T cells

value: day 14

value: 12-14 weeks


title: Control MPRA from MIN6 (ENCLB808PXG)

description:
https://www.encodeproject.org/experiments/ENCSR463MKA/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZFAND3 enhancer.
experiment encode accession: ENCSR463MKA
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB808PXG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: not collected

value: unknown

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS148ZFV at ENCODE; https://www.encodeproject.org/ENCBS148ZFV/


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB084IVG)

description:
https://www.encodeproject.org/experiments/ENCSR582SEN/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR582SEN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB084IVG

source_name: Homo sapiens male adult (38 years) stimulated activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour;

value: ENCBS144SSH at ENCODE; https://www.encodeproject.org/ENCBS144SSH/


title: LLC-Thy1.1 P0 and P2 cancer cell lines, HTO

description:
Library name: LLC-Thy1.1_HTO
HTO: read1 contains cell barcode and UMI; read2 contains Hashtag oligo (HTO) sequence

value: LLC-Thy1.1 P0 and P2 cancer cell lines


title: Orthotopic HBSS-inoculated (mock) mouse lung tissue (ORTHO-M), cDNA

description:
Library name: ORTHO-M_cDNA
5’ mRNA (Next GEM v2 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: Lung tissue

value: 13-AAD-CD45+Thy1.1- immune cells


title: R-001-iA_A

description: Library name: Sample 19

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: SSRI responder


title: NR-003-iA_B

description: Library name: Sample 17

value: SSRI non-responder


title: Orthotopic LLC-Thy1.1 P2 mouse LUAD adjacent lung tissue (ORTHO-A), ADT

description:
Library name: ORTHO-A_ADT
ADT, HTO and STREP: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag (ADT), Hashtag oligo (HTO) or streptavidin-conjugated oligo (STREP) sequence

value: 12-AAD-CD45+Thy1.1- immune cells


title: NR-002-iA_A

description: Library name: Sample 13


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB812YRV)

description:
https://www.encodeproject.org/experiments/ENCSR573JCI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR573JCI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB812YRV

source_name: Homo sapiens male adult (38 years) stimulated activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-15 for 24 hours

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS839OQO at ENCODE; https://www.encodeproject.org/ENCBS839OQO/


title: DNase-seq from mucosa of descending colon (ENCLB995RRF)

description:
https://www.encodeproject.org/experiments/ENCSR737MGZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR737MGZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB995RRF

source_name: Homo sapiens female adult (61 years) mucosa of descending colon tissue

value: mucosa of descending colon

value: tissue

value: female

tag: health state

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

value: 61 year

value: Shin Lin

value: ENCBS194NLI at ENCODE; https://www.encodeproject.org/ENCBS194NLI/


title: NR-001-iA_C

description: Library name: Sample 12


title: MPRA from NIH3T3 (ENCLB454RRB)

description:
https://www.encodeproject.org/experiments/ENCSR426MVD/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR426MVD
assay title: MPRA
possible controls: ENCSR517PBF
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB454RRB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: not collected

value: unknown

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS663DVO at ENCODE; https://www.encodeproject.org/ENCBS663DVO/


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB294BDE)

description:
https://www.encodeproject.org/experiments/ENCSR582SEN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR582SEN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB294BDE

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour;

value: ENCBS070NDO at ENCODE; https://www.encodeproject.org/ENCBS070NDO/


title: NR-001-iA_B

description: Library name: Sample 11

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: SSRI non-responder


title: Orthotopic LLC-Thy1.1 P2 mouse LUAD tumors (ORTHO-T), ADT

description:
Library name: ORTHO-T_ADT
ADT, HTO and STREP: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag (ADT), Hashtag oligo (HTO) or streptavidin-conjugated oligo (STREP) sequence

source_name: Lung tumour

value: Lung tumour

value: 10-AAD-CD45+Thy1.1- immune cells


title: NR-001-iA_A

description: Library name: Sample 10


title: DNase-seq from SW 1271 (ENCLB950WBP)

description:
https://www.encodeproject.org/experiments/ENCSR553PHO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR553PHO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB950WBP
instrument models: Illumina HiSeq 4000,Illumina NextSeq 500

source_name: Homo sapiens SW 1271 cell line

value: cell line

value: 69 year

value: ENCBS863MMW at ENCODE; https://www.encodeproject.org/ENCBS863MMW/


title: MPRA from NIH3T3 (ENCLB571AMB)

description:
https://www.encodeproject.org/experiments/ENCSR426MVD/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR426MVD
assay title: MPRA
possible controls: ENCSR517PBF
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB571AMB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: not collected

value: unknown

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS749TUG at ENCODE; https://www.encodeproject.org/ENCBS749TUG/


title: MPRA from Neuro-2a (ENCLB790ZZM)

description:
https://www.encodeproject.org/experiments/ENCSR397JKG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL3 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the RET enhancer.
experiment encode accession: ENCSR397JKG
assay title: MPRA
possible controls: ENCSR186OUG
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB790ZZM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS638JOH at ENCODE; https://www.encodeproject.org/ENCBS638JOH/


title: Orthotopic LLC-Thy1.1 P2 mouse LUAD tumors (ORTHO-T), cDNA

description:
Library name: ORTHO-T_cDNA
5’ mRNA (Next GEM v2 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: 9-AAD-CD45+Thy1.1- immune cells


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB591WOW)

description:
https://www.encodeproject.org/experiments/ENCSR552PGF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR552PGF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB591WOW

source_name: Homo sapiens male adult (38 years) stimulated activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

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

value: ENCBS924UBS at ENCODE; https://www.encodeproject.org/ENCBS924UBS/


title: MPRA from NIH3T3 (ENCLB117QTS)

description:
https://www.encodeproject.org/experiments/ENCSR426MVD/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR426MVD
assay title: MPRA
possible controls: ENCSR517PBF
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB117QTS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: ENCBS151EIL at ENCODE; https://www.encodeproject.org/ENCBS151EIL/


title: DNase-seq from GM12878 (ENCLB371NBV)

description:
https://www.encodeproject.org/experiments/ENCSR507IEF/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR507IEF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB371NBV

source_name: Homo sapiens GM12878 cell line

value: female

value: Coriell

value: ENCBS822LCD at ENCODE; https://www.encodeproject.org/ENCBS822LCD/


title: DNase-seq from GM12878 (ENCLB489PGR)

description:
https://www.encodeproject.org/experiments/ENCSR507IEF/
***************
biological replicate number: 8
technical replicate number: 1
description:
experiment encode accession: ENCSR507IEF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB489PGR

value: unknown

value: ENCBS168PZM at ENCODE; https://www.encodeproject.org/ENCBS168PZM/


title: MPRA from Neuro-2a (ENCLB602EPI)

description:
https://www.encodeproject.org/experiments/ENCSR397JKG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL3 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the RET enhancer.
experiment encode accession: ENCSR397JKG
assay title: MPRA
possible controls: ENCSR186OUG
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB602EPI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: not collected

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS469PBP at ENCODE; https://www.encodeproject.org/ENCBS469PBP/


title: Subcutaneous LLC-Thy1.1 P2 mouse tumors, cDNA

description:
Library name: SUBCUT_cDNA
5’ mRNA (Next GEM v2 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

source_name: Subcutaneous tumour

value: Subcutaneous tumour

value: 7-AAD-CD45+Thy1.1- immune cells


title: Subcutaneous LLC-Thy1.1 P2 mouse tumors, ADT

description:
Library name: SUBCUT_ADT
ADT, HTO and STREP: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag (ADT), Hashtag oligo (HTO) or streptavidin-conjugated oligo (STREP) sequence

value: 8-AAD-CD45+Thy1.1- immune cells


title: HC-003-iA_B

description: Library name: Sample 8

source_name: Patient-derived hiPSC

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: Healthy control


title: HC-003-iA_A

description: Library name: Sample 7


title: Orthotopic LLC-Thy1.1 P2 mouse LUAD adjacent lung tissue (ORTHO-A), cDNA

description:
Library name: ORTHO-A_cDNA
5’ mRNA (Next GEM v2 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: Lung tissue

value: 11-AAD-CD45+Thy1.1- immune cells


title: Control MPRA from NIH3T3 (ENCLB675KDN)

description:
https://www.encodeproject.org/experiments/ENCSR369JXL/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR369JXL
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB675KDN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: ENCBS971MTR at ENCODE; https://www.encodeproject.org/ENCBS971MTR/


title: MPRA from Neuro-2a (ENCLB095PTT)

description:
https://www.encodeproject.org/experiments/ENCSR397JKG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL3 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the RET enhancer.
experiment encode accession: ENCSR397JKG
assay title: MPRA
possible controls: ENCSR186OUG
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB095PTT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Mus musculus strain A albino mouse Neuro-2a cell line genetically modified (insertion) using transient transfection

value: ENCBS854QJA at ENCODE; https://www.encodeproject.org/ENCBS854QJA/


title: DNase-seq from GM12878 (ENCLB112OLA)

description:
https://www.encodeproject.org/experiments/ENCSR507IEF/
***************
biological replicate number: 7
technical replicate number: 1
description:
experiment encode accession: ENCSR507IEF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB112OLA

value: female

value: unknown

value: adult

value: John Stamatoyannopoulos, UW

value: Coriell

value: ENCBS382GWZ at ENCODE; https://www.encodeproject.org/ENCBS382GWZ/


title: Control MPRA from NIH3T3 (ENCLB262MHO)

description:
https://www.encodeproject.org/experiments/ENCSR369JXL/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR369JXL
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB262MHO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Mus musculus strain NIH3T3 NIH3T3 cell line genetically modified (insertion) using transient transfection

value: not collected

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS185MKD at ENCODE; https://www.encodeproject.org/ENCBS185MKD/


title: DNase-seq from GM12878 (ENCLB416FGM)

description:
https://www.encodeproject.org/experiments/ENCSR507IEF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR507IEF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB416FGM

value: ENCBS782JHT at ENCODE; https://www.encodeproject.org/ENCBS782JHT/


title: HC-002-iA_C

description: Library name: Sample 6

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: Healthy control


title: DNase-seq from T-helper 1 cell (ENCLB502UNV)

description:
https://www.encodeproject.org/experiments/ENCSR370YEN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR370YEN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB502UNV

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

value: T-helper 1 cell

value: primary cell

value: male

value: 24 year

value: AllCells

value: ENCBS274HOW at ENCODE; https://www.encodeproject.org/ENCBS274HOW/


title: HC-002-iA_B

description: Library name: Sample 5


title: T26 3

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

country: China

institute: Northwestern Polytechnical University

description: Library name: Sample 6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Murine Colon Adenocarcinoma Cells


title: T26 2

description: Library name: Sample 5


title: Control MPRA from NIH3T3 (ENCLB437QRM)

description:
https://www.encodeproject.org/experiments/ENCSR369JXL/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR369JXL
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB437QRM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: unknown

value: ENCBS297MWK at ENCODE; https://www.encodeproject.org/ENCBS297MWK/


title: DNase-seq from T-helper 1 cell (ENCLB297JME)

description:
https://www.encodeproject.org/experiments/ENCSR370YEN/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR370YEN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB297JME

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS123CUX at ENCODE; https://www.encodeproject.org/ENCBS123CUX/


title: Control MPRA from MIN6 (ENCLB944IDP)

description:
https://www.encodeproject.org/experiments/ENCSR361QPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TCF7L2 enhancer.
experiment encode accession: ENCSR361QPQ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB944IDP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Mus musculus MIN6 cell line genetically modified (insertion) using transient transfection

value: not collected

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS450ZQL at ENCODE; https://www.encodeproject.org/ENCBS450ZQL/


title: HC-003-iA_C

description: Library name: Sample 9

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: Healthy control


title: Con 3

description: Library name: Sample 3


title: HC-002-iA_A

description: Library name: Sample 4


title: HC-001-iA_C

description: Library name: Sample 3


title: T26 1

description: Library name: Sample 4


title: Control MPRA from MIN6 (ENCLB915ENT)

description:
https://www.encodeproject.org/experiments/ENCSR361QPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TCF7L2 enhancer.
experiment encode accession: ENCSR361QPQ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB915ENT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS226BJQ at ENCODE; https://www.encodeproject.org/ENCBS226BJQ/


title: Con 2

description: Library name: Sample 2


title: DNase-seq from T-helper 1 cell (ENCLB180GWN)

description:
https://www.encodeproject.org/experiments/ENCSR370YEN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR370YEN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB180GWN

value: T-helper 1 cell

value: primary cell

value: male

value: 24 year

value: AllCells

value: ENCBS360YJS at ENCODE; https://www.encodeproject.org/ENCBS360YJS/


title: Control MPRA from MIN6 (ENCLB316GDY)

description:
https://www.encodeproject.org/experiments/ENCSR361QPQ/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TCF7L2 enhancer.
experiment encode accession: ENCSR361QPQ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB316GDY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: unknown

value: ENCBS155VLH at ENCODE; https://www.encodeproject.org/ENCBS155VLH/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB971LBU)

description:
https://www.encodeproject.org/experiments/ENCSR361EAQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR361EAQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB971LBU

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-7 for 24 hours

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P13232; treatment_term_name:Interleukin-7; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS582AMI at ENCODE; https://www.encodeproject.org/ENCBS582AMI/


title: Con 1

description: Library name: Sample 1

value: Murine Colon Adenocarcinoma Cells


title: DNase-seq from K562 (ENCLB746WOK)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 28
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB746WOK

source_name: Homo sapiens K562 cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS518TEX at ENCODE; https://www.encodeproject.org/ENCBS518TEX/


title: Mature_4

description: Library name: Sample 7

source_name: Bone Marrow Derived Dendritic Cells

value: Bone Marrow Derived Dendritic Cells

tag: developmental stage

value: mature


title: Control MPRA from Neuro-2a (ENCLB700VKY)

description:
https://www.encodeproject.org/experiments/ENCSR186OUG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL3 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the RET enhancer.
experiment encode accession: ENCSR186OUG
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB700VKY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: not collected

value: Nadav Ahituv, UCSF

value: ENCBS469PBP at ENCODE; https://www.encodeproject.org/ENCBS469PBP/


title: Control MPRA from Neuro-2a (ENCLB138SPX)

description:
https://www.encodeproject.org/experiments/ENCSR186OUG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL3 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the RET enhancer.
experiment encode accession: ENCSR186OUG
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB138SPX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: unknown

value: ENCBS638JOH at ENCODE; https://www.encodeproject.org/ENCBS638JOH/


title: Mature_3

description: Library name: Sample 6


title: DNase-seq from inflammatory macrophage (ENCLB993LOK)

description:
https://www.encodeproject.org/experiments/ENCSR358FCI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR358FCI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB993LOK

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

value: inflammatory macrophage

value: primary cell

value: male

value: adult

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS146NIH at ENCODE; https://www.encodeproject.org/ENCBS146NIH/


title: Mature_2

description: Library name: Sample 5


title: CART19_VX800_D02

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

description: Library name: CART19_VX800_D02

data_processing:
Reads were mapped to the GRCh38 reference genome using CellRanger count (GRCh38)
Assembly: GRCh38
Supplementary files format and content: Cell barcodes are contained in files ending with barcodes.tsv.gz; feature names are contained in files ending with features.tsv.gz; expression counts matrices are contained in files ending with matrix.mtx.gz

source_name: Lymphocytes

growth_protocol: Cells were grown in culture for 13 days with complete RPMI with a 1:1 cell:bead ratio with anti-CD3/CD28 dynabeads and 500U/mL recombinant IL-2. Cells were incubated in a 5% CO2 incubator at 37.0°C.

extract_protocol:
RNA extraction
10,000 live cells were partitioned into droplets using the Chromium Next GEM Single-Cell 5’Kit v2 (10x Genomics, 1000263), quantified via the Qubit dsDNA HS Assay Kit, quality-checked for fragment sizes via High Sensitivity D5000 ScreenTapes, and sequenced.

treatment_protocol: Cells were treated with either 0.1% DMSO or 800nM venetoclax on days 2,5,6,7,8,9,10 of the growth period

value: Lymphocytes

value: CAR T-cells

tag: treatment

value: 800nM Venetoclax


title: CART19_VX800_D03

description: Library name: CART19_VX800_D03


title: DNase-seq from K562 (ENCLB465AWD)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 26
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB465AWD

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS001TDH at ENCODE; https://www.encodeproject.org/ENCBS001TDH/


title: CART19_VX800_D01

description: Library name: CART19_VX800_D01


title: Control MPRA from Neuro-2a (ENCLB215YZE)

description:
https://www.encodeproject.org/experiments/ENCSR186OUG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL3 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the RET enhancer.
experiment encode accession: ENCSR186OUG
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB215YZE
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: not collected

value: unknown

value: Nadav Ahituv, UCSF

tag: source

value: ENCBS854QJA at ENCODE; https://www.encodeproject.org/ENCBS854QJA/


title: HC-001-iA_B

description: Library name: Sample 2

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: Healthy control


title: CART19_DMSO_D03

description: Library name: CART19_DMSO_D03

value: 0.1% DMSO


title: MPRA from NIH3T3 (ENCLB317ISS)

description:
https://www.encodeproject.org/experiments/ENCSR035ODX/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR035ODX
assay title: MPRA
possible controls: ENCSR369JXL
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB317ISS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

tag: line

value: ENCBS971MTR at ENCODE; https://www.encodeproject.org/ENCBS971MTR/


title: DNase-seq from K562 (ENCLB924URO)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 29
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB924URO

tag: encode accession

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS777CQG at ENCODE; https://www.encodeproject.org/ENCBS777CQG/


title: DNase-seq from K562 (ENCLB001YFG)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 27
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB001YFG

tag: Sex

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS413ZPV at ENCODE; https://www.encodeproject.org/ENCBS413ZPV/


title: Immature_3

description: Library name: Sample 3

value: Bone Marrow Derived Dendritic Cells

value: immature


title: Immature_2

description: Library name: Sample 2


title: MPRA from NIH3T3 (ENCLB830JTS)

description:
https://www.encodeproject.org/experiments/ENCSR035ODX/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR035ODX
assay title: MPRA
possible controls: ENCSR369JXL
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB830JTS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: not collected

tag: dev stage

value: ATCC

value: ENCBS297MWK at ENCODE; https://www.encodeproject.org/ENCBS297MWK/


title: CART19_DMSO_D02

description: Library name: CART19_DMSO_D02

value: Lymphocytes

value: CAR T-cells


title: Immature_1

description: Library name: Sample 1


title: DNase-seq from K562 (ENCLB784NIK)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 30
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB784NIK

tag: age

value: 53 year

value: ENCBS033QRE at ENCODE; https://www.encodeproject.org/ENCBS033QRE/


title: HC-001-iA_A

description: Library name: Sample 1

value: Patient-derived hiPSC

value: hiPSC-derived astrocyte

value: Healthy control


title: CART19_DMSO_D01

description: Library name: CART19_DMSO_D01

value: 0.1% DMSO


title: H43

city: Borstel

first: Silke

last: Meiners

address: Parkallee 1-40

department: Leibniz Lung Center

country: Germany

institute: Research Center Borstel

description: Library name: MUC27203_S12

data_processing:
Following a final quality control step, the libraries were subjected to paired-end sequencing (2x150 bases) on the Novaseq6000 sequencer (Illumina), targeting a depth of at least 30 million paired reads per sample.
Initial processing (demultiplexing) of raw data to fastq files was performed using the bcl2fastq v2.20.0.422 program from Illumina.
Assembly: GRCm38.p6
Supplementary files format and content: Excel files include raw counts for each sample

growth_protocol: 1.5 million A549 cells and 1 million H1299 cells were cultured in 15 cm dishes and incubated for 48 hours.

extract_protocol:
Total RNA was isolated according to the manufacturer protocol (Total RNA kit from Peqlab, VWR). The RNA integrity number (RIN) was assessed using the Agilent 2100 Bioanalyzer system, and concentration was quantified using the Qubit 2.0 RNA BR assay (Invitrogen).
TruSeq stranded m-RNA Library Preparation kit (Illumina) with 1 μg of RNA used by following the kit's protocol.

value: PA200 KO


title: DNase-seq from immature natural killer cell (ENCLB083NUG)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 10
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB083NUG

source_name: Homo sapiens male adult (30 years) immature natural killer primary cell

value: immature natural killer cell

value: primary cell

value: male

value: adult

value: 30 year

tag: lab

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS096ERJ at ENCODE; https://www.encodeproject.org/ENCBS096ERJ/


title: DNase-seq from immature natural killer cell (ENCLB935DCU)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 11
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB935DCU

tag: link

value: ENCBS940QYA at ENCODE; https://www.encodeproject.org/ENCBS940QYA/


title: Mature_1

description: Library name: Sample 4

value: Bone Marrow Derived Dendritic Cells

value: mature


title: H5

description: Library name: MUC27202_S11

tag: cell line


title: DNase-seq from immature natural killer cell (ENCLB281ORJ)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB281ORJ

value: ENCBS973BMP at ENCODE; https://www.encodeproject.org/ENCBS973BMP/


title: OT-I cells electroporated with Luciferase (control) mRNA, replicate 3

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

description:
Library name: OT_I_Luc_5
OT_I_Luc_5

data_processing:
Trimming of sequences using Trimmomatic.
Alignment to reference genome mm39 (Mus musculus) using STAR software.
Uniquely mapped reads were counted using featureCounts.
Assembly: mm39
Supplementary files format and content: Raw counts matrix for all the samples in a txt file. Genes described with the Mus musculus ensembl references.

source_name: OT-I

growth_protocol: The electroporated cells were cultured in complete RPMI medium supplemented with 50 IU/ml rhIL-2 (proleukin, Novartis).

extract_protocol:
Total RNA was extracted from omentum samples via the RNeasy Mini Kit (Qiagen). RNA integrity was assessed via the Agilent 2200 TapeStation.
The samples were sent to Macrogen, Inc., for library preparation and sequencing on a NovaSeq 6000 (Illumina)

treatment_protocol: Activated OT.I and PMEL-1 T cells were resuspended in phenol red-free OPTI-MEM (Gibco) at 100 × 106 cells/ml. The cells (2 × 107) were electroporated with 20 μg of mRNA via the Gene Pulser Mx System (Bio-Rad, Hercules, CA, USA).

value: OT-I

tag: cell type

value: Lymphocites

value: Electroporation with Luciferase (control) mRNA


title: Control MPRA from Neuro-2a (ENCLB999KUB)

description:
https://www.encodeproject.org/experiments/ENCSR020AUG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ultra conserved element UC88.
experiment encode accession: ENCSR020AUG
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB999KUB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: not collected

value: unknown

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS831HYC at ENCODE; https://www.encodeproject.org/ENCBS831HYC/


title: H1

description: Library name: MUC27201_S10

tag: genotype

value: PA200 KO


title: OT-I cells electroporated with Luciferase (control) mRNA, replicate 2

description:
Library name: OT_I_Luc_3
OT_I_Luc_3


title: Control MPRA from Neuro-2a (ENCLB972LFA)

description:
https://www.encodeproject.org/experiments/ENCSR020AUG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ultra conserved element UC88.
experiment encode accession: ENCSR020AUG
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB972LFA
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS247ZIH at ENCODE; https://www.encodeproject.org/ENCBS247ZIH/


title: OT-I cells electroporated with Luciferase (control) mRNA, replicate 1

description:
Library name: OT_I_Luc_2
OT_I_Luc_2


title: MPRA from NIH3T3 (ENCLB023VEL)

description:
https://www.encodeproject.org/experiments/ENCSR035ODX/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4Z vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZRS enhancer.
experiment encode accession: ENCSR035ODX
assay title: MPRA
possible controls: ENCSR369JXL
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB023VEL
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS185MKD at ENCODE; https://www.encodeproject.org/ENCBS185MKD/


title: DNase-seq from immature natural killer cell (ENCLB639SSW)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB639SSW

value: immature natural killer cell

value: primary cell

value: male

value: adult

value: 30 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS342UMK at ENCODE; https://www.encodeproject.org/ENCBS342UMK/


title: H12

description: Library name: MUC27200_S9

value: WT


title: DNase-seq from immature natural killer cell (ENCLB125YLG)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB125YLG

value: ENCBS789NWW at ENCODE; https://www.encodeproject.org/ENCBS789NWW/


title: 7_4_8_S5

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: Library name: 7_4_8_S5

data_processing:
[1] Bushnell B, Rood J, Singer E (2017) BBMerge – Accurate paired shotgun read merging via overlap. PLoS ONE 12(10): e0185056. https://doi.org/10.1371/journal.pone.0185056
[2] Martin, M. (2011) Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads. EMBnet Journal, 17, 10-12. https://doi.org/10.14806/ej.17.1.200
[3] Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21. doi:10.1093/bioinformatics/bts635
[4] Li, B., Dewey, C.N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011). https://doi.org/10.1186/1471-2105-12-323
[5] Love MI, Huber W, Anders S (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: spleen

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini kit
Read adapters were detected using BBMerge (v37.02) [1] and subsequently removed with cutadapt (v1.8.1) [2]. Processed raw reads were then aligned to mouse genome mm10 using STAR (v2.7.7a)[3]. Gene expression was evaluated as read count at gene level with RSEM (v1.3.0) [4] and Gencode gene model vM21. Gene express data were then normalized and differential expression between experimental groups were evaluated using DEseq2 [5].

value: spleen


title: 7_4_7_S4

description: Library name: 7_4_7_S4


title: H8

description: Library name: MUC27199_S8


title: Control MPRA from Neuro-2a (ENCLB160WFR)

description:
https://www.encodeproject.org/experiments/ENCSR020AUG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ultra conserved element UC88.
experiment encode accession: ENCSR020AUG
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB160WFR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: not collected

value: unknown

value: Nadav Ahituv, UCSF

value: ENCBS761QWU at ENCODE; https://www.encodeproject.org/ENCBS761QWU/


title: OT-I cells electroporated with IL33 mRNA, replicate 2

description:
Library name: OT_I_IL33_2
OT_I_IL33_2

value: OT-I

value: Lymphocites

value: Electroporation with IL33 mRNA


title: 7_4_6_S3

description: Library name: 7_4_6_S3


title: DNase-seq from immature natural killer cell (ENCLB417XAR)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB417XAR

value: immature natural killer cell

value: primary cell

value: male

value: ENCBS548DBA at ENCODE; https://www.encodeproject.org/ENCBS548DBA/


title: 7_4_5_S2

description: Library name: 7_4_5_S2


title: DNase-seq from immature natural killer cell (ENCLB430GWI)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB430GWI

value: adult

value: 30 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS494DHT at ENCODE; https://www.encodeproject.org/ENCBS494DHT/


title: OT-I cells electroporated with IL33 mRNA, replicate 1

description:
Library name: OT_I_IL33_1
OT_I_IL33_1


title: 7_4_1_S1

description: Library name: 7_4_1_S1

value: spleen


title: OT-I cells electroporated with IL33 mRNA, replicate 3

description:
Library name: OT_I_IL33_3
OT_I_IL33_3


title: DNase-seq from immature natural killer cell (ENCLB428YSA)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 8
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB428YSA

value: ENCBS663PFZ at ENCODE; https://www.encodeproject.org/ENCBS663PFZ/


title: A76

description: Library name: MUC27197_S6

value: PA200 KO


title: DNase-seq from immature natural killer cell (ENCLB816BTK)

description:
https://www.encodeproject.org/experiments/ENCSR309XUP/
***************
biological replicate number: 7
technical replicate number: 1
description:
experiment encode accession: ENCSR309XUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB816BTK

value: ENCBS437LHS at ENCODE; https://www.encodeproject.org/ENCBS437LHS/


title: 6_6_8_S10

description: Library name: 6_6_8_S10


title: A17

description: Library name: MUC27196_S5


title: CD8, high fat diet fed mice, 6

city: Kyoto

first: Masaki

last: Tajima

address: Yoshidakonoe cho

country: Japan

institute: Kyoto University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: freshely isolated cells

extract_protocol:
RNA was isolated using ISOGEN with Spin Column kit according to the instruction provided by the manufacturer (Nippongene).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

treatment_protocol: cells isolated from mice treated with normal diet (12 weeks), high fat diet (12 weeks),  and switched diet (high fat diet for 6 weeks and then normal diet for 6 weeks)

tag: tissue

value: WT

value: high fat diet (12 weeks)


title: A13

description: Library name: MUC27195_S4


title: CD8, high fat diet fed mice, 5


title: CD8, high fat diet fed mice, 4


title: A48

description: Library name: MUC27193_S2


title: 6_6_3_S8

description: Library name: 6_6_3_S8


title: 6_6_2_S7

description: Library name: 6_6_2_S7


title: 6_6_6_S9

description: Library name: 6_6_6_S9


title: CD8, high fat diet fed mice, 3


title: A35

description: Library name: MUC27192_S1


title: CD8, high fat diet fed mice, 2


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB459FMG)

description:
https://www.encodeproject.org/experiments/ENCSR208RXB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR208RXB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB459FMG

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-12 subunit alpha for 4 hours

value: 38 year

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS589QPH at ENCODE; https://www.encodeproject.org/ENCBS589QPH/


title: 6_6_1_S6

description: Library name: 6_6_1_S6


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB701TAE)

description:
https://www.encodeproject.org/experiments/ENCSR208RXB/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR208RXB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB701TAE

value: primary cell

value: male

value: ENCBS888DWA at ENCODE; https://www.encodeproject.org/ENCBS888DWA/


title: AML SU758, scMultiome GEX

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

data_processing:
For each cell analyzed, paired-end reads were mapped to human genome hg38 using Cell Ranger (10x Genomics) for scRNA-seq or Cell Ranger Arc for single-cell multiomics.
For the single-omic scRNA-seq data, cells with number of non-zero genes larger than 1,000; number of reads less than 60,000; and percentage of mitochondria reads less than 25% were retained.
For the multi-omic data, cells were retained if: number of reads larger than 5,000 but smaller than 100,000 from the scATAC-seq data modality; number of reads larger than 1,000 but smaller than 100,000 from the scRNA-seq data modality; and the percentage of mitochondria reads less than 30%.
The gene expression data were then normalized and log-transformed using the R package Seurat.
Samples from different patients or technologies (single or multi-omics) were integrated using Harmony based on the gene expression data.
Assembly: hg38
Supplementary files format and content: Tab-separated files (tsv) containing log-normalized count data.
Library strategy: Single-cell Multiome

molecule: nuclear RNA

source_name: Primary acute myeloid leukemia

extract_protocol:
Cryopreserved samples were used to generate a single cell suspension (for scRNA-seq) or a single nuclei suspension (for single-cell Multiome, according to protocol Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing [10x Genomics]). Single cells (for scRNA-seq) or nuclei (for scMultiome ATAC+Gene Expression) were captured on a 10x Chromium Controller instrument according to manufacturer instructions.
Libraries were generated using Chromium NextGEM Single-cell 3’ Gene Expression reagents (for scRNA-seq) or using the Chromium Next GEM Single-cell Multiome ATAC + Gene Expression reagents (for scMultiome). Quality control on intermediate products and final libraries was performed using the Agilent Bioanalyzer High Sensitivity Kit. The final libraries were quantified via qPCR using KAPA Library Quantification Kits. A spike-in of 1% PhiX control library (Illumina) was used as the technical control.

value: Primary acute myeloid leukemia

value: CEBPA mutation


title: CD8, high fat diet fed mice, 1


title: H4

description: Library name: MUC27198_S7


title: AML SU504 Replicate 2, scMultiome GEX

description: SU504 was sequenced with scRNA-seq and single-cell multiome sequencing (Biological replicates). This record contains the gene expression portion of the single-cell multiomics data.


title: A77

description: Library name: MUC27194_S3


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB638MNM)

description:
https://www.encodeproject.org/experiments/ENCSR188VGU/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR188VGU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB638MNM

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours

value: adult

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour;

value: ENCBS686XVZ at ENCODE; https://www.encodeproject.org/ENCBS686XVZ/


title: GFP positive GC B cells 1

city: Toronto

first: Liam

middle: D

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description: Library name: 30-09-22_9_BP_S8-S9_S109

data_processing:
Reads were QC'ed using fastqc (v 0.11.5) and multiqc (v 1.7) aligned to the GRCm38 (mm10) mouse reference using STAR (v 2.5.2b).
Gene counts and transcripts per million (TPM) normalization were determined using RSEM (v 1.3.0).
Assembly: mm10
Supplementary files format and content: exprMtrx_expected_count.csv: comma-delimited file containing RSEM output expected gene counts for each sample
Supplementary files format and content: exprMtrx_TPM.csv:comma-delimited file containing RSEM output gene TPM values for each sample

extract_protocol:
Spleens from SRBC-injected ChAT-GFP-tg animals were harvested on day 8 after immunization. ChAT-GFP+ and ChAT-GFP- subsets of GC B cells (CD19+, CD95+, CD38lo) and TFH cells (CD3+, PD1+, Cxcr5+) were sorted from splenic single-cell suspensions. Each replicate consisted of pooled (combined using equal parts), equivalent cell subsets derived from the spleens of two mice to ensure sufficient input cell numbers for RNA isolation. Total RNA was extracted using TRIzol (Invitrogen) according to manufacturer instructions.
Library preparation was performed using the NeoPrep Library System (Illumina) following the manufacturer’s instructions.

treatment_protocol: SRBC immunization as outlined in this study.

value: spleen

value: GC B cells

tag: chat-gfp

value: GFP positive


title: DNase-seq from inflammatory macrophage (ENCLB971QLW)

description:
https://www.encodeproject.org/experiments/ENCSR227ODJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR227ODJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB971QLW

source_name: Homo sapiens male adult (24 years) inflammatory macrophage primary cell treated with 100 ng/mL lipopolysaccharide for 4 hours

value: inflammatory macrophage

value: 24 year

value: Shelly Heimfeld

tag: treatments

value: treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS936BJS at ENCODE; https://www.encodeproject.org/ENCBS936BJS/


title: CD8, switched diet fed mice, 6

value: WT

value: switched diet (12 weeks)


title: GFP negative Tfh cells 4

description: Library name: 30-09-22_7_TN_S5-S7_S107

value: Tfh cells

value: GFP negative


title: AML SU494, scMultiome GEX

value: Primary acute myeloid leukemia

value: CEBPA mutation