title: HXR450_S_2

first: Yang

last: Hang

address: 1000 Jinqi Road, Fengxian District

institute: Shanghai Academy of Agricultural Sciences

description:
Library name: HXR450_S_2
L1EHF2500590--N14

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: IRGSP-1.0
Supplementary files format and content: xlsx files include FPKM value for each sample

organism: Oryza sativa Japonica Group

source_name: seedling

extract_protocol:
Total RNA was extracted from seedlings using TRIzol® Reagent, following the manufacturer's instructions. The quality of the RNA was determined using a 5300 Bioanalyser (Agilent), and the concentration was determined using an ND-2000 (NanoDrop Technologies).
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: seedling

tag: cultivar


title: PBMC, Day 84, ATAC-seq, Individual 39

status: Public on Mar 06 2026

type: SRA

city: Olsztyn

first: Maciej

last: Rybiński

state: Warmian-Masurian Voivodeship

address: Trylińskiego 18

country: Poland

institute: Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences.

description: Library name: Ind39

library_source: genomic

data_processing:
ATAC-seq: Paired-end reads were aligned using the STAR aligner. ENCODE-identified blacklisted regions and reads with mapping quality score < 2 were filtered out. Duplicates were identified and marked with samtools markdup. Peak calling done with MACS3 (version 3.0.1) utilizing callpeak function with the parameters --f BAMPE --verbose 3 --shift 0 -g hs -q 0.01 -B Consensus peak summits matrix generated with DiffBind utilizing dba.count function with summits parameter set to 75.
Assembly: GRCh38.p14
Supplementary files format and content: Consensus_ATAC-seq_Day 84.csv

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
ATAC-seq: nuclei were isolated from 100,000 PBMCs by incubation in 50 µl lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20; 0.1% IGEPAL CA-630; 0.01% digitonin). After 3 minutes on ice, 1 ml wash buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20) was added. Nuclei were pelleted and subjected to transposition using a Tn5 transposase reaction mix (Illumina), supplemented with 0.01% digitonin and 0.1% Tween-20. The transposition reaction was carried out at 37 °C for 30 minutes in a thermomixer. Transposed DNA was purified using the DNA Clean & Concentrator-5 Kit (Zymo Research), followed by PCR amplification, purification, and size selection with SPRISelect beads (Beckman Coulter). Library quality was assessed using an Agilent TapeStation. Indexed libraries were quantified, pooled, and prepared for sequencing.
ATAC-seq  libraries were sequenced on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).

treatment_protocol: Peripheral blood samples were obtained from a single healthy male participant (age 59) enrolled in the VitDHiD trial (ClinicalTrials.gov Identifier: NCT03537027). The study was approved by the Ethics Committee of the Northern Savo Hospital District (Approval No. 515/2018).

tag: tissue

value: peripheral blood

tag: cell line

value: PBMC

tag: cell type

value: monocytes, T and B cells


title: HXR450_S_1

city: Shanghai

country: China

description:
Library name: HXR450_S_1
L1EHF2500589--N13

library_source: transcriptomic

molecule: total RNA


title: DNase-seq from putamen (ENCLB707ASB)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR046FVG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR046FVG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB707ASB

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

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: tissue

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: unknown

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS945PZA at ENCODE; https://www.encodeproject.org/ENCBS945PZA/


title: AML JH5205, WGBS

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

description: Library name: JH5205_WGBS

data_processing:
Following DNA sequencing, fastq files were trimmed using TrimGalore. Trimmed reads were aligned to the hg19 genome using Bismark. Samtools was used to merge, sort, and deduplicate bam files. Finally, the informME analysis pipeline was applied to quantify methylation stochasticity within individual samples and to compare methylation stochasticity between samples.
Assembly: hg19
Supplementary files format and content: bigwig format. Tracks include mean methylation level (MML), normalized methylation entropy (NME), and Jensen Shannon Distance (JSD) to measure methylation stochasticity between samples.
Supplementary files format and content: Processed data for AML samples and normal CD34+ and GMP controls includes comparison to WGBS data from a previously published LMPP sample (GSM4036933).

source_name: Primary acute myeloid leukemia

extract_protocol:
Primary AML samples were collected from peripheral blood or bone marrow.
WGBS libraries for CMP and MEP normal controls were generated using the IDT Methyl-Seq Kit. For primary AML samples, and CD34+ and GMP normal controls, WGBS libraries were generated using NEBNext Ultra DNA library Prep kit for Illumina according to the manufacturer's instructions with modifications. Input gDNA was spiked with 1% unmethylated Lambda DNA (Promega) to monitor bisulfite conversion efficiency. Size selection was performed using SPRIselect beads and insert sizes of 300-400bp were isolated. Samples were bisulfite converted after size selection using EZ DNA Methylation-Lightning Kit (Zymo). Libraries were sequenced on an Illumina HiSeq4000 or NovaSeq6000 instruments.

value: Primary acute myeloid leukemia

tag: genotype

value: DNMT3A mutation


title: AML JH5034, WGBS

description: Library name: JH5034_WGBS


title: PBMC, Day 84, ATAC-seq, Individual 43

description: Library name: Ind43


title: CS2022_S_3

description:
Library name: CS2022_S_3
L1EHF2500588--Y15


title: PBMC, Day 84, ATAC-seq, Individual 14

description: Library name: Ind14


title: CS2022_S_2

description:
Library name: CS2022_S_2
L1EHF2500587--Y14


title: DNase-seq from anterior cingulate cortex (ENCLB280GDT)

description:
https://www.encodeproject.org/experiments/ENCSR038VQB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR038VQB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB280GDT

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: male

value: ENCBS080GGO at ENCODE; https://www.encodeproject.org/ENCBS080GGO/


title: AML JH4639, WGBS

description: Library name: JH4639_WGBS


title: PBMC, Day 84, ATAC-seq, Individual 06

description: Library name: Ind06


title: PBMC, Day 84, ATAC-seq, Individual 11

description: Library name: Ind11


title: DNase-seq from caudate nucleus (ENCLB190HWH)

description:
https://www.encodeproject.org/experiments/ENCSR034SGT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR034SGT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB190HWH

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: ENCBS738DGS at ENCODE; https://www.encodeproject.org/ENCBS738DGS/


title: AML JH4316, WGBS

description: Library name: JH4316_WGBS

value: TET2 mutation


title: DNase-seq from substantia nigra (ENCLB123BGV)

description:
https://www.encodeproject.org/experiments/ENCSR039BAA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR039BAA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB123BGV

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: ENCBS306MVT at ENCODE; https://www.encodeproject.org/ENCBS306MVT/


title: CS2022_S_1

description:
Library name: CS2022_S_1
L1EHF2500586--Y13

value: seedling


title: DNase-seq from substantia nigra (ENCLB495WPF)

description:
https://www.encodeproject.org/experiments/ENCSR043OJZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR043OJZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB495WPF

source_name: Homo sapiens male adult substantia nigra tissue

value: tissue

value: ENCBS065WOM at ENCODE; https://www.encodeproject.org/ENCBS065WOM/


title: DNase-seq from amygdala (ENCLB998JKS)

description:
https://www.encodeproject.org/experiments/ENCSR034PUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR034PUJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB998JKS

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: adult

value: unknown

value: ENCBS084IDG at ENCODE; https://www.encodeproject.org/ENCBS084IDG/


title: PBMC, Day 84, ATAC-seq, Individual 17

description: Library name: Ind17

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: pt4_CoronaryHealthy

city: Palo Alto

first: Paul

last: CHENG

address: 870 QUARRY RD EXT, PALO ALTO

institute: Stanford University

description: Library name: P4RCA

library_source: transcriptomic single cell

data_processing:
Data alignment, quality control and cell type annotation (scRNA-seq) Raw FASTQ files were aligned to the GRCh38 reference genome (v) using Cell Ranger (10x Genomics, v6.1). Subsequent quality control (QC), normalization, dimensional reduction, and clustering was performed with Seurat v4.0. Cells were filtered using the following thresholds: 500 < nFeature_RNA < 7000; nCount_RNA < 30,000; percent mitochondrial reads < 10. Raw RNA counts from cells that met these criteria were normalized and scaled using SCTransform regressing out percent mitochondrial reads and nCount_RNA. Principal component analysis (PCA) was performed on the normalized RNA counts, and the number of PCs used for downstream clustering was dependent on the following criteria: PCs cumulatively explain > 99% of the variation present in the data and percent variation associated with the PCs is less than 1%. Weighted nearest neighbor clustering (WNN) was performed with the significant RNA PCs directly without PCA as previously outlined with the FindMultiModalNeighbors function in Seurat. Subsequently, a uniform manifold approximation (UMAP) embedding was constructed and FindClusters was used to cluster cells using the Smart Local Moving modularity optimization algorithm in an unbiased manner.
Assembly: hg38
Supplementary files format and content: rds file, aggregated scRNA file

source_name: whole coronary artery

extract_protocol:
Artery digestion protocol: Immediately after collection, fresh coronary artery tissues were separated into equal 50mg pieces. These samples were then placed in a digestion solution comprising Liberase TM (10.4U/mL working concentration in HBSS, Sigma-Aldrich 05401127001) and elastase (8U/mL, Sigma E7885 in HBSS) followed by finely minced on ice using iris scissors. The resulting digested product was transferred to a 2.0ml Eppendorf tube and subjected to constant agitation at 650RPM in a heated Eppendorf Thermomixer (Model 5382). To enhance heat exchange, distilled water was added to the heating block. The digestion mixture was monitored at 30 and 45 minutes under the microscope to assess for single cell suspension, with vigorous pipetting (3 times) performed if undigested cell clumps were observed. After 60 minutes of digestion at 37°C, the digested products were vigorously pipetted 10 times and then filtered through a 70μm strainer. The filtered solution was centrifuged at 500g for 10 minutes in V-bottom plates to optimize cell collection. The resulting cell pellet was resuspended in fresh, cold HBSS. Finally, the samples underwent FACS (Fluorescence-Activated Cell Sorting) using Calcein green (ThermoFisher) for live/dead cell discrimination. The sorted cells were used immediately for single-cell capture and subsequent library preparation.
Single cell captures and library preparation were performed using chemistry version 3 (V3) according to 10x Genomics instructions. Cells were loaded into 10x Genomics microfluidics chip G for encapsulation with their proprietary barcoded gel beads in the 10x Genomics Chromium X controller. Single-cell libraries were contruscted according to manufacturer’s instructions with index labeling using the Dual Index Kit TT set A. This allows for library pooling into one lane for sequencing on the Illumina NovaSeq6000 platform with a targeted read depth of 75,000 reads per cell.

value: whole coronary artery


title: AML JH4198, WGBS

description: Library name: JH4189_WGBS

value: Primary acute myeloid leukemia

value: IDH1/2 mutation


title: pt4_CoronaryDiseased

description: Library name: P4RCAD


title: PBMC, Day 84, ATAC-seq, Individual 20

description: Library name: Ind20


title: apical-pellicle_WT_08

city: Suita

first: Yuta

last: Tachibana

state: Osaka

address: 3-1, Yamadaoka

department: Research Institute for Microbial Diseases (RIMD)

country: Japan

institute: Osaka University

description: Library name: apical-pellicle_WT_08

data_processing:
The gRNA sequencing reads were aligned to the gRNA library. The abundance of each gRNA was calculated and normalized to the total number of aligned reads.
Assembly: Apical-pellicle library for CRISPR screen
Supplementary files format and content: text file for each gRNA expresssion
Library strategy: CRISPR Screen

organism: Toxoplasma gondii

source_name: RH

extract_protocol:
Toxoplasma genomic DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen).
Integrated gRNA sequences were amplified and barcoded by PCR with KOD FX Neo (TOYOBO). Genomic DNA (1μg) was used for the template. The resulting libraries were sequenced on a DNBSEQ-G400RS (MGI).

value: RH

value: tachyzoite


title: PBMC, Day 84, ATAC-seq, Individual 24

description: Library name: Ind24


title: apical-pellicle_WT_07

description: Library name: apical-pellicle_WT_07


title: apical-pellicle_WT_09

description: Library name: apical-pellicle_WT_09


title: PBMC, Day 84, ATAC-seq, Individual 28

description: Library name: Ind28


title: vasculopathy2_LCX

description: Library name: V2LCX


title: DNase-seq from anterior cingulate cortex (ENCLB824DQH)

description:
https://www.encodeproject.org/experiments/ENCSR034ILY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR034ILY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB824DQH

source_name: Homo sapiens female adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: female

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS676YDU at ENCODE; https://www.encodeproject.org/ENCBS676YDU/


title: DNase-seq from nucleus accumbens (ENCLB412LKP)

description:
https://www.encodeproject.org/experiments/ENCSR033QXT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR033QXT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB412LKP

source_name: Homo sapiens male adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: male

value: ENCBS779RFV at ENCODE; https://www.encodeproject.org/ENCBS779RFV/


title: apical-pellicle_WT_06

description: Library name: apical-pellicle_WT_06


title: PBMC, Day 84, ATAC-seq, Individual 32

description: Library name: Ind32

value: peripheral blood


title: Pt8_CoronaryDiseased

description: Library name: P8LADCAD


title: DNase-seq from nucleus accumbens (ENCLB896YIO)

description:
https://www.encodeproject.org/experiments/ENCSR034HPF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR034HPF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB896YIO

value: adult

value: unknown

value: ENCBS493KUJ at ENCODE; https://www.encodeproject.org/ENCBS493KUJ/


title: DNase-seq from anterior cingulate cortex (ENCLB425UKH)

description:
https://www.encodeproject.org/experiments/ENCSR034ILY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR034ILY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB425UKH

value: ENCBS245QGL at ENCODE; https://www.encodeproject.org/ENCBS245QGL/


title: apical-pellicle_WT_05

description: Library name: apical-pellicle_WT_05


title: PBMC, Day 84, ATAC-seq, Individual 35

description: Library name: Ind35

value: PBMC

value: monocytes, T and B cells


title: pt6_RCA

description: Library name: P6RCA

value: whole coronary artery


title: pt5_RCA

description: Library name: P5RCA


title: apical-pellicle_WT_04

description: Library name: apical-pellicle_WT_04

value: RH

value: tachyzoite


title: DNase-seq from nucleus accumbens (ENCLB209SBV)

description:
https://www.encodeproject.org/experiments/ENCSR033QXT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR033QXT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB209SBV

value: John Stamatoyannopoulos, UW

value: ENCBS340RMV at ENCODE; https://www.encodeproject.org/ENCBS340RMV/


title: DNase-seq from putamen (ENCLB089GSZ)

description:
https://www.encodeproject.org/experiments/ENCSR031KAI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR031KAI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB089GSZ

source_name: Homo sapiens male adult putamen tissue

value: putamen

value: Kristin Ardlie

value: ENCBS763UFF at ENCODE; https://www.encodeproject.org/ENCBS763UFF/


title: PBMC, Day 84, ATAC-seq, Individual 37

description: Library name: Ind37


title: DNase-seq from putamen (ENCLB473XJW)

description:
https://www.encodeproject.org/experiments/ENCSR031KAI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR031KAI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB473XJW

value: tissue

value: male

value: ENCBS370GAP at ENCODE; https://www.encodeproject.org/ENCBS370GAP/


title: apical-pellicle_WT_03

description: Library name: apical-pellicle_WT_03


title: pt3_RCA

description: Library name: P3RCA


title: pt2_RCA

description: Library name: P2RCA


title: vasculopathy2_RCA

description: Library name: V2RCA


title: apical-pellicle_WT_02

description: Library name: apical-pellicle_WT_02


title: PBMC, Day 84, ATAC-seq, Individual 44

description: Library name: Ind44

value: peripheral blood


title: pt1_RCA2

description: Library name: P1RCA2


title: apical-pellicle_P4

description: Library name: apical-pellicle_P4


title: PBMC, Day 84, ATAC-seq, Individual 40

description: Library name: Ind40


title: DNase-seq from putamen (ENCLB421HSL)

description:
https://www.encodeproject.org/experiments/ENCSR024URI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR024URI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB421HSL

value: female

value: adult

value: unknown

value: ENCBS313IQW at ENCODE; https://www.encodeproject.org/ENCBS313IQW/


title: DNase-seq from amygdala (ENCLB106EUQ)

description:
https://www.encodeproject.org/experiments/ENCSR023UNS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR023UNS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB106EUQ

value: amygdala

value: ENCBS879MGI at ENCODE; https://www.encodeproject.org/ENCBS879MGI/


title: PBMC, Day 84, ATAC-seq, Individual 41

description: Library name: Ind41

value: PBMC

value: monocytes, T and B cells


title: PBMC, Day 84, ATAC-seq, Individual 05

description: Library name: Ind05


title: apical-pellicle_lib

description: Library name: apical-pellicle_lib

value: RH

value: tachyzoite


title: PBMC, Day 84, ATAC-seq, Individual 08

description: Library name: Ind08


title: pt1_RCA

description: Library name: P1RCA1

value: whole coronary artery


title: apical-pellicle_WT_01

description: Library name: apical-pellicle_WT_01


title: DNase-seq from caudate nucleus (ENCLB458CSC)

description:
https://www.encodeproject.org/experiments/ENCSR025TQQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR025TQQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB458CSC

value: caudate nucleus

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS681OOK at ENCODE; https://www.encodeproject.org/ENCBS681OOK/


title: DNase-seq from amygdala (ENCLB935LLP)

description:
https://www.encodeproject.org/experiments/ENCSR023AEW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR023AEW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB935LLP

value: tissue

value: male

value: ENCBS393AZO at ENCODE; https://www.encodeproject.org/ENCBS393AZO/


title: vasculopathy1_RCA

description: Library name: V1RCA


title: Male mouse colon, AND-1 T819A (TA), Normal

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I St NW

department: Biochemistry and Molecular Medicine

institute: George Washington University

description:
Library name: Sample 4
10X Genomics

data_processing:
Quality control was performed using fastqc. Mapping, demultiplexing, and gene quantification to generate matrix and barcode files for each sample was performed with cellranger and the mm10 reference genome. The fastq files and filtered barcode matrix .h5 files are provided in this submission.
Assembly: mm10
Supplementary files format and content: .h5 files, filtered

molecule: polyA RNA

organism: Mus musculus

source_name: Distal Colon, Normal tissue

extract_protocol:
Colon samples were minced with scissors and digested in a liberase digestion solution. Cells were immediately processed for single-cell RNA sequencing library preparation.
Library preparation was performed using the Chromium Next GEM Single Cell 3' Kit v3.1 with the 10X Genomics Dual Index Kit TT Set A according to manufacturer instructions.

value: Distal Colon, Normal tissue

value: Mixed colon cells

value: AND-1 T819A

tag: treatment

value: 38 weeks

tag: batch

value: Male


title: DNase-seq from Ammon's horn (ENCLB081OFQ)

description:
https://www.encodeproject.org/experiments/ENCSR022NUX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR022NUX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB081OFQ

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: adult

value: unknown

value: ENCBS419JBP at ENCODE; https://www.encodeproject.org/ENCBS419JBP/


title: PBMC, Day 84, ATAC-seq, Individual 10

description: Library name: Ind10

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: Male mouse colon, wild type (WT), Normal

description:
Library name: Sample 3
10X Genomics

value: wild type


title: DNase-seq from Ammon's horn (ENCLB298QFO)

description:
https://www.encodeproject.org/experiments/ENCSR022NUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR022NUX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB298QFO

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS084WGQ at ENCODE; https://www.encodeproject.org/ENCBS084WGQ/


title: PBMC, Day 84, ATAC-seq, Individual 18

description: Library name: Ind18


title: PBMC, Day 84, ATAC-seq, Individual 19

description: Library name: Ind19


title: DNase-seq from Ammon's horn (ENCLB891EHJ)

description:
https://www.encodeproject.org/experiments/ENCSR022NUX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR022NUX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB891EHJ

value: tissue

value: male

value: ENCBS185GCR at ENCODE; https://www.encodeproject.org/ENCBS185GCR/


title: PBMC, Day 84, ATAC-seq, Individual 21

description: Library name: Ind21


title: Visium FFPE, S15

city: Saint Louis

first: Haewon

last: Shin

state: MO

address: 660 S Euclid

institute: Washington University School of Medicine in St. Louis

description: Library name: SR002895_S15

data_processing:
Single-cell captures and library preparation were performed using chemistry version 3 (V3) according to 10x Genomics instructions. Cells were loaded into 10x Genomics microfluidics chip G for encapsulation with their proprietary barcoded gel beads in the 10x Genomics Chromium X controller. Single-cell libraries were constructed according to manufacturer’s instructions with index labeling using the Dual Index Kit TT set A. This allows for library pooling into one lane for sequencing on the Illumina NovaSeq6000 platform with a targeted read depth of 75,000 reads per cell.
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg: Images of the Visium capture area with markers used to register and align the tissue image to the spatial barcode grid.  Matrix.mtx.gz - Gene × cell UMI count matrix in Matrix Market format, filtered for high-quality cells. Rows are genes, columns are cells, values are UMI counts. Barcodes.tsv.gz - List of cell barcodes corresponding to the columns of the filtered UMI count matrix. One barcode per line. Features.tsv.gz - Gene annotation file corresponding to the rows of the filtered UMI count matrix. Columns are: gene ID, gene symbol, and optionally feature type. rds objects were created in Seurat with count matrices derived from Matrix.mtx, Barcodes.tsv, and Features.tsv. Counts were normalized, scaled, and variable features found using SCTransform.
Library strategy: Spatial Transcriptomics

source_name: human coronary artery

extract_protocol:
Visium FFPE: Fresh coronary tissue was fixed in 4% PFA overnight, washed with PBS, and embedded in FFPE blocks. FFPE blocks were sectioned onto Visium slides and underwent H&E staining before imaging. Libraries were generated using the Visium FFPE v2 kit and sequenced on a NextSeq2000 according to manufacturer's recommendations. Libraries were sequenced on a NovaSeq 6000.
Visium FFPE: Fresh coronary tissue was fixed in 4% PFA overnight, washed with PBS, and embedded in FFPE blocks. FFPE blocks were sectioned onto Visium slides and underwent H&E staining before imaging. Libraries were generated using the Visium FFPE v2 kit and sequenced on a NextSeq2000 according to manufacturer's recommendations. Libraries were sequenced on a NovaSeq 6000.

value: human coronary artery


title: Female mouse colon, wild type (WT), Normal

description:
Library name: Sample 1
10X Genomics

data_processing:
Quality control was performed using fastqc. Mapping, demultiplexing, and gene quantification to generate matrix and barcode files for each sample was performed with cellranger and the mm10 reference genome. The fastq files and filtered barcode matrix .h5 files are provided in this submission.
Assembly: mm10
Supplementary files format and content: .fastqs and .h5 files

value: Distal Colon, Normal tissue

tag: strain

value: Mixed colon cells

value: 38 weeks

value: Female


title: vasculopathy1_LCX

description: Library name: V1Lcx

value: whole coronary artery


title: Visium FFPE, T1176

description: Library name: SR002895_T1176


title: DNase-seq from putamen (ENCLB179LFC)

description:
https://www.encodeproject.org/experiments/ENCSR018YAL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR018YAL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB179LFC

value: putamen

value: adult

value: unknown

value: ENCBS861MKZ at ENCODE; https://www.encodeproject.org/ENCBS861MKZ/


title: DNase-seq from putamen (ENCLB400LCN)

description:
https://www.encodeproject.org/experiments/ENCSR018YAL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR018YAL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB400LCN

value: ENCBS589BGK at ENCODE; https://www.encodeproject.org/ENCBS589BGK/


title: Visium FFPE, S12

description: Library name: SR002895_S12


title: DNase-seq from amygdala (ENCLB424YXI)

description:
https://www.encodeproject.org/experiments/ENCSR018LPY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR018LPY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB424YXI

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: female

value: John Stamatoyannopoulos, UW

value: ENCBS384APY at ENCODE; https://www.encodeproject.org/ENCBS384APY/


title: PBMC, Day 84, ATAC-seq, Individual 23

description: Library name: Ind23

source_name: peripheral blood

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: Female mouse colon, AND-1 T819A (TA), Normal

description:
Library name: Sample 2
10X Genomics

value: Distal Colon, Normal tissue

value: AND-1 T819A


title: Visium FFPE, T1171_LM

description: Library name: T1171_LM

value: human coronary artery


title: Visium FFPE, T1170_LAD

description: Library name: T1170_LAD


title: PBMC, Day 84, ATAC-seq, Individual 27

description: Library name: Ind27


title: Visium FFPE, RK_LCX

description: Library name: SR002895_RK_LCX


title: DNase-seq from anterior cingulate cortex (ENCLB915MRD)

description:
https://www.encodeproject.org/experiments/ENCSR016KLL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR016KLL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB915MRD

value: anterior cingulate cortex

value: tissue

value: male

value: Kristin Ardlie

value: ENCBS549GWB at ENCODE; https://www.encodeproject.org/ENCBS549GWB/


title: Visium FFPE, T1186_RCA

description: Library name: T1186_RCA


title: PBMC, Day 84, ATAC-seq, Individual 34

description: Library name: Ind34


title: DNase-seq from anterior cingulate cortex (ENCLB256XSZ)

description:
https://www.encodeproject.org/experiments/ENCSR016KLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR016KLL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB256XSZ

value: adult

value: unknown

value: ENCBS594GXK at ENCODE; https://www.encodeproject.org/ENCBS594GXK/


title: DNase-seq from caudate nucleus (ENCLB619RNP)

description:
https://www.encodeproject.org/experiments/ENCSR015WAR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR015WAR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB619RNP

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: ENCBS065EOF at ENCODE; https://www.encodeproject.org/ENCBS065EOF/


title: Activity_Uncut_Rep3

first: Charles

middle: J

last: Lenihan

address: 8 S Durham St

description: Library name: Activity_Uncut_Rep3

library_source: other

data_processing:
Samples were processed by extracting sequences containing a protospacer, extracting their proximal three-letter sequence, then sorting and counting these three-letter sequences.
Assembly: Synthetic Construct (dsDNA oligonucleotides (IDT) containing protospacer 8.3 flanked by NNN were restriction enzyme cloned into pHAT4 using NcoI and XhoI. All enzymes were purchased from NEB. enzyme cloned into pHAT4 using NcoI and XhoI. All enzymes were purchased from NEB. For biochemical assays, targets (388 bp) were amplified using primers that anneal to the T7 promoter and terminator. All targets were gel purified before use. To facilitate imaging, the T7 promoter primer, which generates the target strand, was labeled with a Cy5 fluorophore.!Sample_data_processing = Supplementary files format and content: Processed data files are two-column tab-delimited .txt files. The first column specifies the three-base PAM sequence, and the second column specifies the number of counts of that PAM sequence.

molecule: other

organism: Thermotoga maritima MSB8

source_name: bacterial cell

extract_protocol: DNA was extracted from agarose gels with GeneJET Gel Extraction Kit (Thermo Scientific). Extracted DNA served as template for PCR amplification using NEBNext® Ultra™ II Q5® Master Mix (NEB). Primers were designed to add Illumina sequencing handles external to the amplicon.

treatment_protocol: For samples labelled "EMSA:" Cascade DNA binding assays were performed in buffer containing 10 mM HEPES-NaOH, pH 7.5, 200 mM Potassium Acetate, 10 mM Magnesium Acetate, 20 uM Cobalt Acetate, 2 mM ATP, 0.1 mg/ml Bovine Serum Albumin, 250 ng/ul Salmon sperm DNA, and 1 mM TCEP. 10 nM Cascade was incubated at 80 °C with 4 nM target library DNA for 30 minutes. Bound DNA was separated from free DNA by electrophoresis through 2.0 % agarose gels and imaged on a Typhoon imager (Cy5 channel). DNA ladders were imaged following ethidium bromide staining with an Odyssey imager.  For samples labelled "Activity:" Reactions were performed in buffer containing 10 mM HEPES-NaOH, pH 7.5, 200 mM Potassium Acetate, 10 mM Magnesium Acetate, 20 uM Cobalt Acetate, 2 mM ATP, 0.1 mg/ml Bovine Serum Albumin, 250 ng/ul Salmon sperm DNA, and 1 mM TCEP. 10 nM Cascade was incubated with 4 nM target library DNA at 80 °C for 30 minutes. To start the reaction, Cas3 wasadded to the reaction to a final concentration of 250 nM. Reactions were allowed to proceed, at 80 °C, for the 32 minutes before termination by addition of EDTA to 50 mM and moving to ice. The targets were analyzed by electrophoresis through 2.0 % agarose gels and imaged as above.

value: bacterial cell

tag: group

value: Activity


title: Activity_Cut_Rep5

description: Library name: Activity_Cut_Rep5


title: DNase-seq from amygdala (ENCLB975GUI)

description:
https://www.encodeproject.org/experiments/ENCSR014SNN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR014SNN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB975GUI

value: amygdala

value: John Stamatoyannopoulos, UW

value: ENCBS881HHH at ENCODE; https://www.encodeproject.org/ENCBS881HHH/


title: Visium FFPE, T1071

description: Library name: T1071


title: DNase-seq from Ammon's horn (ENCLB249VQZ)

description:
https://www.encodeproject.org/experiments/ENCSR014QBR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR014QBR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB249VQZ

source_name: Homo sapiens female adult Ammon's horn tissue

value: Ammon's horn

value: female

value: ENCBS807DGG at ENCODE; https://www.encodeproject.org/ENCBS807DGG/


title: Activity_Cut_Rep2

description: Library name: Activity_Cut_Rep2


title: Visium FFPE, T1153R

description: Library name: T1153R

value: human coronary artery


title: Activity_Cut_Rep4

description: Library name: Activity_Cut_Rep4


title: Activity_Cut_Rep3

description: Library name: Activity_Cut_Rep3


title: Activity_Uncut_Rep2

description: Library name: Activity_Uncut_Rep2


title: Visium FFPE, T1077

description: Library name: T1077


title: PBMC, Day 84, ATAC-seq, Individual 42

description: Library name: Ind42

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: PBMC, Day 84, ATAC-seq, Individual 07

description: Library name: Ind07


title: DNase-seq from Ammon's horn (ENCLB984RKG)

description:
https://www.encodeproject.org/experiments/ENCSR014QBR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR014QBR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB984RKG

value: tissue

value: adult

value: Kristin Ardlie

value: ENCBS035NRZ at ENCODE; https://www.encodeproject.org/ENCBS035NRZ/


title: Activity_Uncut_Rep5

description: Library name: Activity_Uncut_Rep5


title: KRT5 negative SKOV3 cells, rep 2

city: Ithaca

first: Coulter

last: Ralston

state: NY

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

description: Library name: A7

data_processing:
De-multiplexed FASTQ files were inspected for quality using FASTQC. Reads were aligned to the GRCh38 human reference genome using the STAR two-pass method.
Assembly: GRCh38
Supplementary files format and content: csv file containing raw counts for all samples. Each column with represents a sample.

growth_protocol: SKOV3 cells cultured in McCoy’s 5A medium (VWR) supplemented with 10% FBS, L-Glutamine and 1 x penicillin-streptomycin. HEK293T cells were cultured in DMEM 1X medium supplemented with 10% FBS, Glutamine, sodium pyravate and 1 x penicillin-streptomycin. Cell lines were athenticated in the lab and tested for Mycoplasma contamination every 6 months. All cell line used in the study were used within 20 passages of thawing.

extract_protocol:
Total RNA was isolated using TRIzol reagent according to manufacture’s instructions (Invitrogen). RNA integrity and concentrations were determined using Nanodrop and only the purified RNA samples were used for further analysis. ERCC Spike in in Mix 1 (Thermo Fisher) was added to samples prior to library creation according to manufacturer’s recommendation.
3' mRNA-seq libraries were created using QuantSeq 3’ mRNA-Seq library prep kit according to the manufacturer's instructions using 10ng total RNA.

treatment_protocol: Lentiviral packaging and transduction was performed on SKOV3 cells. Briefly, Transfection was performed using a transfection mix containing psPAX2 packaging plasmid (Addgene #12260), pMD2.G envelope plasmid (Addgene #12259) and human KRT5 promoter clone (GeneCopoeia #HPRM15909-LvPM02)  that drive the expression of mCherry in Opti-MEM medium. To differentiate between KRT5+ and KRT5- cells populations, another aliqout of transfection mixture containing ubiquitous promoter that drives the eGFP expression was also prepared. Lipofectamine 2000 (Invitrogen) was used as a transfection reagent and manufacturer’s instructions were followed to perform transfection. The transfection mixture containing KRT5 promoter plasmid and ubiquitous promoter were added to two culture plates containing at least 3 x 105 HEK293T cells. The culture plates were allowed to incubate overnight and additional 1ml of antibiotic-free DMEM medium was added. After 48 hrs of incubation, the supernatent was harvested and Lentiviral particles were concentrated using centrifugal filters (Amicon Ultra -15 #UFC903024). Freshly prepared Lentiviral particles were used to transduce SKOV3 cells. After 4 days of transduction, SKOV3 cell culture containing both KRT5+ (mCherry+eGFP+) and KRT5- (mCherry-eGFP+) were selected using puromycin. For detection of KRT5 expression, the transduced SKOV3 cells were placed in Fluorescence-activated cell sorting buffer. Cell sorting and subsequent data analysis were perfomred on a FACS Aria II sorter that is equipped with the FACS DiVa software (BD Bioscience). Dead cells were excluded with Cytox Red and untransduced SKOV3 cells served as controls. The brighest KRT5+ (mCherry+eGFP+) and KRT5- (mCherry-eGFP+) were identified and gated electronically based on their characteristic light-scattering properties on the mCherry and eGFP channel emission pattern. The two populations were collecetd in two different tubes containing FACS buffer and used for downstream applications.

value: KRT5- Cell Sort


title: PBMC, Day 84, ATAC-seq, Individual 25

description: Library name: Ind25


title: siSF3B1a Phospho-Mimic SF3B1 C

city: Rochester

first: Clara

last: Kielkopf

state: New York

address: 601 Elmwood Ave

department: Biochemistry & Biophysics

institute: University of Rochester

description: Library name: siSF3B1a_epSF3B1_C

data_processing:
Performed by URGRC: raw reads were trimmed and filtered with fastp 0.23.1 (--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r). Reads were then aligned using STAR 2.7.9a (--twopassMode Basic --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical).
Read counts quantified by subread 2.0.3 (featureCounts -t exon -s 2 -p --countReadPairs -B -C).
Assembly: GRCh38 Primary Assembly
Supplementary files format and content: raw_counts.txt: Tab-delimited text file containing ENSEMBL gene IDs, gene symbols, and raw counts per gene for each sample.
Supplementary files format and content: *_SJ.out.tab (output from STAR): Tab-delimited text files for each sample containing splice junction counts. Column descriptions: 1. chromosome; 2. first base of junction (1-based); 3. last base of junction (1-based); 4. strand, 0 = undefined, 1 = +, 2 = -; 5. intron motif, 0 = noncanonical, 1 = GT/AG, 2 = CT/AC, 3 = GC/AG, 4 = CT/GC, 5 = AT/AC, 6 = GT/AT; 6. inclusion in annotation file, 0 = absent, 1 = present; 7. number of uniquely mapping reads spanning the junction; 8. number of multimapping reads spanning the junction; 9. maximum spliced alignment overhang.

source_name: HEK 293T

growth_protocol: Human embryonic kidney epithelial cells (HEK 293T, ATCC CRL-3216) were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNAs were extracted from transfected cells in biological triplicates using an RNeasy Mini kit (Qiagen) and further purified with an RNA Clean & Concentrator kit (Zymo Research).
The University of Rochester Genomics Research Center (URGRC) prepared polyA-selected libraries using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with nonspecific or SF3B1-targeting Stealth siRNAs (Thermo Fisher Sci.) and empty vector or plasmids containing wildtype, phospho-dead, or phospho-mimic SF3B1 constructs. Cells were harvested two days after transfection.

value: HEK 293T

value: siSF3B1a + FLAG-SF3B1-EP


title: Activity_Cut_Rep1

description: Library name: Activity_Cut_Rep1

value: bacterial cell

value: Activity


title: DNase-seq from substantia nigra (ENCLB413IUX)

description:
https://www.encodeproject.org/experiments/ENCSR014GCS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR014GCS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB413IUX

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS496YHX at ENCODE; https://www.encodeproject.org/ENCBS496YHX/


title: Activity_Uncut_Rep4

description: Library name: Activity_Uncut_Rep4


title: PBMC, Day 84, ATAC-seq, Individual 03

description: Library name: Ind03


title: KRT5 negative SKOV3 cells, rep 3

description: Library name: A6


title: siSF3B1a Phospho-Mimic SF3B1 B

description: Library name: siSF3B1a_epSF3B1_B


title: Activity_Uncut_Rep1

description: Library name: Activity_Uncut_Rep1


title: siSF3B1a Phospho-Mimic SF3B1 A

description: Library name: siSF3B1a_epSF3B1_A


title: siSF3B1a Phospho-Dead SF3B1 C

description: Library name: siSF3B1a_apSF3B1_C

value: siSF3B1a + FLAG-SF3B1-AP


title: KRT5 negative SKOV3 cells, rep 1

description: Library name: A5


title: KRT5 positive SKOV3 cells, rep 3

description: Library name: A4

value: KRT5+ Cell Sort


title: EMSA_Unbound_Rep4

description: Library name: EMSA_Unbound_Rep4

value: EMSA


title: DNase-seq from cerebellum (ENCLB491CDC)

description:
https://www.encodeproject.org/experiments/ENCSR010CKD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR010CKD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB491CDC

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: female

value: ENCBS493LJE at ENCODE; https://www.encodeproject.org/ENCBS493LJE/


title: EMSA_Bound_Rep4

description: Library name: EMSA_Bound_Rep4


title: siSF3B1a Phospho-Dead SF3B1 B

description: Library name: siSF3B1a_apSF3B1_B


title: EMSA_Bound_Rep3

description: Library name: EMSA_Bound_Rep3


title: DNase-seq from nucleus accumbens (ENCLB256HED)

description:
https://www.encodeproject.org/experiments/ENCSR010VHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR010VHC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB256HED

value: nucleus accumbens

value: tissue

value: male

value: adult

value: Kristin Ardlie

value: ENCBS474WSU at ENCODE; https://www.encodeproject.org/ENCBS474WSU/


title: EMSA_Unbound_Rep3

description: Library name: EMSA_Unbound_Rep3

value: bacterial cell


title: KRT5 positive SKOV3 cells, rep 2

description: Library name: A2


title: siSF3B1a Wildtype SF3B1 C

description: Library name: siSF3B1a_wtSF3B1_C

value: HEK 293T

value: siSF3B1a + FLAG-SF3B1-WT


title: DNase-seq from caudate nucleus (ENCLB792VLV)

description:
https://www.encodeproject.org/experiments/ENCSR010BRB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR010BRB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB792VLV

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS121PFW at ENCODE; https://www.encodeproject.org/ENCBS121PFW/


title: DNase-seq from Ammon's horn (ENCLB089BLH)

description:
https://www.encodeproject.org/experiments/ENCSR007GLQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR007GLQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB089BLH

value: Ammon's horn

value: ENCBS192SVZ at ENCODE; https://www.encodeproject.org/ENCBS192SVZ/


title: KRT5 positive SKOV3 cells, rep 1

description: Library name: A1

value: KRT5+ Cell Sort


title: EMSA_Bound_Rep2

description: Library name: EMSA_Bound_Rep2

value: EMSA


title: siSF3B1a Phospho-Dead SF3B1 A

description: Library name: siSF3B1a_apSF3B1_A

value: siSF3B1a + FLAG-SF3B1-AP


title: DNase-seq from NCI-H526 (ENCLB799BNQ)

description:
https://www.encodeproject.org/experiments/ENCSR945CAC/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR945CAC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB799BNQ

source_name: Homo sapiens NCI-H526 cell line

tag: line

value: cell line

value: 55 year

value: ATCC

value: ENCBS594BMY at ENCODE; https://www.encodeproject.org/ENCBS594BMY/


title: siSF3B1a Wildtype SF3B1 A

description: Library name: siSF3B1a_wtSF3B1_A


title: DNase-seq from NCI-H526 (ENCLB526UDU)

description:
https://www.encodeproject.org/experiments/ENCSR945CAC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR945CAC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB526UDU

value: male

value: adult

value: ENCBS510FQD at ENCODE; https://www.encodeproject.org/ENCBS510FQD/


title: EMSA_Unbound_Rep2

description: Library name: EMSA_Unbound_Rep2

value: bacterial cell


title: DNase-seq from Ammon's horn (ENCLB982WRP)

description:
https://www.encodeproject.org/experiments/ENCSR007GLQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR007GLQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB982WRP

value: tissue

value: female

value: Kristin Ardlie

value: ENCBS828SXA at ENCODE; https://www.encodeproject.org/ENCBS828SXA/


title: DNase-seq from NCI-H526 (ENCLB122VFI)

description:
https://www.encodeproject.org/experiments/ENCSR945CAC/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR945CAC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB122VFI

value: John Stamatoyannopoulos, UW

value: ENCBS832UJY at ENCODE; https://www.encodeproject.org/ENCBS832UJY/


title: EMSA_Bound_Rep1

description: Library name: EMSA_Bound_Rep1


title: DNase-seq from putamen (ENCLB099REC)

description:
https://www.encodeproject.org/experiments/ENCSR005ZWB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR005ZWB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB099REC

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: unknown

value: ENCBS092WNY at ENCODE; https://www.encodeproject.org/ENCBS092WNY/


title: siSF3B1a Wildtype SF3B1 B

description: Library name: siSF3B1a_wtSF3B1_B

value: HEK 293T

value: siSF3B1a + FLAG-SF3B1-WT


title: siSF3B1a C

description: Library name: siSF3B1a_C

value: siSF3B1a + empty vector


title: DNase-seq from anterior cingulate cortex (ENCLB071MFO)

description:
https://www.encodeproject.org/experiments/ENCSR008EPU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR008EPU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB071MFO

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: ENCBS534KDJ at ENCODE; https://www.encodeproject.org/ENCBS534KDJ/


title: DNase-seq from NCI-H526 (ENCLB655HCQ)

description:
https://www.encodeproject.org/experiments/ENCSR945CAC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR945CAC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB655HCQ

value: cell line

value: male

value: adult

value: 55 year

value: ATCC

value: ENCBS610CFL at ENCODE; https://www.encodeproject.org/ENCBS610CFL/


title: DNase-seq from nucleus accumbens (ENCLB957WEY)

description:
https://www.encodeproject.org/experiments/ENCSR006NRS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR006NRS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB957WEY

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: female

value: Kristin Ardlie

value: ENCBS804XVJ at ENCODE; https://www.encodeproject.org/ENCBS804XVJ/


title: siSF3B1a B

description: Library name: siSF3B1a_B


title: EMSA_Unbound_Rep1

description: Library name: EMSA_Unbound_Rep1

value: bacterial cell

value: EMSA


title: DNase-seq from cerebellum (ENCLB938PHL)

description:
https://www.encodeproject.org/experiments/ENCSR005HBB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR005HBB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB938PHL

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS828QSY at ENCODE; https://www.encodeproject.org/ENCBS828QSY/


title: DNase-seq from layer of hippocampus (ENCLB970QEQ)

description:
https://www.encodeproject.org/experiments/ENCSR460GLK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR460GLK
assay title: DNase-seq
assembly: mm10
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB970QEQ

source_name: Mus musculus strain B6CASTF1/J female (18-20 months) layer of hippocampus tissue

value: layer of hippocampus

tag: description

value: B6Cast F1 18 - 20 month female Hippocampus

value: not collected

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS557IAD at ENCODE; https://www.encodeproject.org/ENCBS557IAD/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: DNase-seq from NCI-H69 (ENCLB168NAJ)

description:
https://www.encodeproject.org/experiments/ENCSR925BVJ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR925BVJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB168NAJ
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens NCI-H69 cell line

value: cell line

value: male

value: adult

value: 55 year

value: ATCC

value: ENCBS272DMV at ENCODE; https://www.encodeproject.org/ENCBS272DMV/


title: DNase-seq from caudate nucleus (ENCLB292IJX)

description:
https://www.encodeproject.org/experiments/ENCSR004WWN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR004WWN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB292IJX

value: caudate nucleus

value: tissue

value: unknown

value: Kristin Ardlie

value: ENCBS038PEU at ENCODE; https://www.encodeproject.org/ENCBS038PEU/


title: siSF3B1a A

description: Library name: siSF3B1a_A

tag: cell line

value: HEK 293T

value: siSF3B1a + empty vector


title: DNase-seq from layer of hippocampus (ENCLB328QGK)

description:
https://www.encodeproject.org/experiments/ENCSR443DYB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR443DYB
assay title: DNase-seq
assembly: mm10
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB328QGK

source_name: Mus musculus strain B6CASTF1/J male (25 days) layer of hippocampus tissue

value: layer of hippocampus

value: B6Cast F1 PND25 male Hippocampus

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: ENCBS226OKY at ENCODE; https://www.encodeproject.org/ENCBS226OKY/


title: DNase-seq from putamen (ENCLB155NCB)

description:
https://www.encodeproject.org/experiments/ENCSR004BCA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR004BCA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB155NCB

value: putamen

value: female

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS280PMZ at ENCODE; https://www.encodeproject.org/ENCBS280PMZ/


title: DNase-seq from NCI-H2107 (ENCLB272LMJ)

description:
https://www.encodeproject.org/experiments/ENCSR802JQY/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR802JQY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB272LMJ

source_name: Homo sapiens NCI-H2107 cell line

value: cell line

value: male

value: 36 year

value: ATCC

value: ENCBS588VBS at ENCODE; https://www.encodeproject.org/ENCBS588VBS/


title: DNase-seq from NCI-H82 (ENCLB178WRO)

description:
https://www.encodeproject.org/experiments/ENCSR725CSF/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR725CSF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB178WRO
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens NCI-H82 cell line

value: 40 year

value: ENCBS282BOV at ENCODE; https://www.encodeproject.org/ENCBS282BOV/


title: DNase-seq from kidney (ENCLB085NNC)

description:
https://www.encodeproject.org/experiments/ENCSR142NDV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR142NDV
assay title: DNase-seq
assembly: mm10
encode release date: 2025-10-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB085NNC

source_name: Mus musculus strain B6CASTF1/J female postnatal (8-10 months) kidney tissue

value: kidney

value: tissue

value: postnatal

value: 8-10 month

value: The Jackson Laboratory

value: ENCBS692TFI at ENCODE; https://www.encodeproject.org/ENCBS692TFI/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Neonatal sample large

city: Duarte

first: Sangeeta

last: Dhawan

address: 1500 E Duarte Rd

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: 48719

data_processing:
Raw fastq reads from the in-house neonatal murine samples were aligned to the mouse genome (mm10) followed by gene level quantification (CellRanger V7.0 (31)), filtering of doublets, ambient RNA correction and removal of low quality cells (Seurat V4.0(32)).
The in-house and published adult murine datasets were jointly integrated using Harmony V1.2.4(33), followed by normalization, UMAP projection, clustering (Seurat V4.0(32)) and cell type identification using known marker genes
Assembly: mm10
Supplementary files format and content: Seurat object in R RDS format containing normalized counts, cell type annotations and UMAP coordinates

source_name: Pancreatic islet

extract_protocol:
Cells were captured using the Chromium X system and Next GEM Single Cell 3’ Reagent Kits v3. (10x Genomics), per manufacturer’s protocol, yielding ~5,800 and ~18,000 cells from the small and large neonatal islet samples respectively.
Final sequencing libraries were assessed using the Agilent High Sensitivity DNA Chip and quantified with the Qubit High Sensitivity DNA Assay Kit (Thermo Fisher). Libraries were sequenced on an Illumina NovaSeq 6000 platform with the S4 Reagent Kit v1.5 (Illumina) at TGen, using a paired end read sequencing of 28 cycles for Read 1, 101 cycles for Read 2, and 10 cycles each for i7 and i5 index reads. Image analysis was performed with Real-time analysis (RTA) v3.4.4 software.

tag: tissue

value: Pancreatic islet


title: DNase-seq from immature natural killer cell (ENCLB624RMW)

description:
https://www.encodeproject.org/experiments/ENCSR978XCX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR978XCX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB624RMW

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

value: immature natural killer cell

value: primary cell

tag: biosample encode accession

value: adult

value: 30 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS691TMN at ENCODE; https://www.encodeproject.org/ENCBS691TMN/


title: DNase-seq from immature natural killer cell (ENCLB065QLU)

description:
https://www.encodeproject.org/experiments/ENCSR978XCX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR978XCX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB065QLU

tag: encode accession

value: male

value: ENCBS566YCZ at ENCODE; https://www.encodeproject.org/ENCBS566YCZ/


title: siControl C

description: Library name: siControl_C

source_name: HEK 293T

value: HEK 293T

value: siControl + empty vector


title: siSF3B1b B

description: Library name: siSF3B1b_B

value: siSF3B1b + empty vector


title: siControl B

description: Library name: siControl_B


title: DNase-seq from NCI-H82 (ENCLB908HQE)

description:
https://www.encodeproject.org/experiments/ENCSR725CSF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR725CSF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB908HQE
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: cell line

tag: Sex

value: 40 year

value: ATCC

value: ENCBS426DPZ at ENCODE; https://www.encodeproject.org/ENCBS426DPZ/


title: siSF3B1b A

description: Library name: siSF3B1b_A


title: Neonatal sample small

description: Library name: 48718

value: Pancreatic islet


title: DNase-seq from NCI-H1417 (ENCLB205WYJ)

description:
https://www.encodeproject.org/experiments/ENCSR605EUP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR605EUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB205WYJ

source_name: Homo sapiens NCI-H1417 cell line

value: female

tag: dev stage

value: 61 year

value: ENCBS658CEW at ENCODE; https://www.encodeproject.org/ENCBS658CEW/


title: Experiment3_D14_WT_multiome_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 18
10X genomics - scMultiome (RNA + ATAC)

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: nuclear RNA

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).

value: Spleen

tag: cell type

value: WT

value: NP-CGG + Alum + LPS

tag: library type

value: mRNA


title: DNase-seq from K562 (ENCLB636JVO)

description:
https://www.encodeproject.org/experiments/ENCSR970WFK/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR970WFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB636JVO

source_name: Homo sapiens K562 cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

tag: age

value: 53 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: ENCBS375NFW at ENCODE; https://www.encodeproject.org/ENCBS375NFW/


title: DNase-seq from NCI-H2107 (ENCLB781OHX)

description:
https://www.encodeproject.org/experiments/ENCSR802JQY/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR802JQY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB781OHX
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: cell line

value: male

value: 36 year

tag: link

value: ENCBS135SCT at ENCODE; https://www.encodeproject.org/ENCBS135SCT/


title: Experiment3_D14_Prdm1cKO_multiome_GEX

description:
Library name: Sample 16
10X genomics - scMultiome (RNA + ATAC)

tag: genotype

value: Prdm1 cKO

tag: treatment


title: siControl A

description: Library name: siControl_A

value: HEK 293T

value: siControl + empty vector


title: DNase-seq from NCI-H774 (ENCLB937JAX)

description:
https://www.encodeproject.org/experiments/ENCSR539QGM/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR539QGM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB937JAX
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens NCI-H774 cell line

tag: line

value: ATCC

value: ENCBS544YGC at ENCODE; https://www.encodeproject.org/ENCBS544YGC/


title: siSF3B1b C

description: Library name: siSF3B1b_C

value: siSF3B1b + empty vector


title: DNase-seq from caudate nucleus (ENCLB120OOO)

description:
https://www.encodeproject.org/experiments/ENCSR004WWN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR004WWN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB120OOO

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: tissue

value: unknown

value: Kristin Ardlie

value: ENCBS190CIW at ENCODE; https://www.encodeproject.org/ENCBS190CIW/


title: DNase-seq from suppressor macrophage (ENCLB462KYF)

description:
https://www.encodeproject.org/experiments/ENCSR361JSG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR361JSG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB462KYF

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

value: suppressor macrophage

value: primary cell

value: adult

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

tag: treatments

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

value: ENCBS661NMY at ENCODE; https://www.encodeproject.org/ENCBS661NMY/


title: DNase-seq from K562 (ENCLB197PVO)

description:
https://www.encodeproject.org/experiments/ENCSR970WFK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR970WFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB197PVO

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS223YPB at ENCODE; https://www.encodeproject.org/ENCBS223YPB/


title: AT2.MDA453_C

city: Aurora

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description: Library name: AT2.MDA453_C

data_processing:
Illumina adapters were removed using bbduk and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl human transcriptome (GRCh38.p12, release 96)
Assembly: hg38
Supplementary files format and content: Text file containing STAR gene counts

source_name: iAT2 + MDA-MB-453

growth_protocol: iAT2 cells were cultured in SAGM media (small airway epithelial cell growth medium; Lonza Walkersville, No. CC-3118) supplemented with 1% FBS. SUM159PT and MDA-MB-453 cells were cultured in DMEM with 10% FBS.

extract_protocol:
QIAshredder columns (Qiagen, No. 79654) were used to prepare cell lysates and the RNeasy Plus Kit (Qiagen, No. 74136) was used to isolate RNA.
Illumina HiSeq libraries were prepared and sequenced by the Genomics and Microarray Core Facility at CU Anschutz (Aurora, CO).

treatment_protocol: Cells were no contact co-cultured in SAGM media with 1% FBS for 5 days.

tag: cell line

value: iAT2 + MDA-MB-453

value: lung epithelial & TNBC

value: No contact co-culture


title: DNase-seq from K562 (ENCLB605RBQ)

description:
https://www.encodeproject.org/experiments/ENCSR970WFK/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR970WFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB605RBQ

value: ATCC

value: ENCBS247OFO at ENCODE; https://www.encodeproject.org/ENCBS247OFO/


title: Experiment3_D14_Prdm1cKO_multiome_ATAC

description:
Library name: Sample 15
10X genomics - scMultiome (RNA + ATAC)

library_source: genomic single cell

tag: tissue

value: Spleen

value: Prdm1 cKO

value: NP-CGG + Alum + LPS

value: ATAC


title: Experiment3_D14_WT_multiome_ATAC

description:
Library name: Sample 17
10X genomics - scMultiome (RNA + ATAC)

value: WT


title: DNase-seq from K562 (ENCLB286EMS)

description:
https://www.encodeproject.org/experiments/ENCSR970WFK/
***************
biological replicate number: 8
technical replicate number: 1
description:
experiment encode accession: ENCSR970WFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB286EMS

tag: biosample encode accession

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS000SIY at ENCODE; https://www.encodeproject.org/ENCBS000SIY/


title: AT2.MDA453_B

description: Library name: AT2.MDA453_B


title: DNase-seq from K562 (ENCLB105SIJ)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 23
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: ENCLB105SIJ
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: cell line

tag: encode accession

value: female

value: ENCBS601MFP at ENCODE; https://www.encodeproject.org/ENCBS601MFP/


title: DNase-seq from K562 (ENCLB880UOW)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 24
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: ENCLB880UOW
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

tag: Sex

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS055PMS at ENCODE; https://www.encodeproject.org/ENCBS055PMS/


title: Experiment2_D14_WT_FBHTO

description:
Library name: Sample 13
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: CITE-seq

molecule: cytoplasmic RNA

value: HTO


title: AT2.MDA453_A

description: Library name: AT2.MDA453_A

value: iAT2 + MDA-MB-453

value: lung epithelial & TNBC

value: No contact co-culture


title: DNase-seq from NCI-H510A (ENCLB945KII)

description:
https://www.encodeproject.org/experiments/ENCSR295UEC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR295UEC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB945KII

source_name: Homo sapiens NCI-H510A cell line

value: male

tag: dev stage

value: 56 year

value: ATCC

value: ENCBS291ZRS at ENCODE; https://www.encodeproject.org/ENCBS291ZRS/


title: DNase-seq from K562 (ENCLB285PJY)

description:
https://www.encodeproject.org/experiments/ENCSR970WFK/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR970WFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB285PJY

value: adult

value: ENCBS681BOC at ENCODE; https://www.encodeproject.org/ENCBS681BOC/


title: DNase-seq from NCI-H510A (ENCLB303BMG)

description:
https://www.encodeproject.org/experiments/ENCSR295UEC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR295UEC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB303BMG

value: John Stamatoyannopoulos, UW

value: ENCBS573KCC at ENCODE; https://www.encodeproject.org/ENCBS573KCC/


title: AT2.SUM_A

description: Library name: AT2.SUM_A

source_name: iAT2 + SUM159PT

value: iAT2 + SUM159PT

tag: cell type


title: AT2.SUM_C

description: Library name: AT2.SUM_C


title: DNase-seq from K562 (ENCLB781XDB)

description:
https://www.encodeproject.org/experiments/ENCSR970WFK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR970WFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB781XDB

value: cell line

value: female

value: ENCBS565AHW at ENCODE; https://www.encodeproject.org/ENCBS565AHW/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB764YTO)

description:
https://www.encodeproject.org/experiments/ENCSR853IHW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR853IHW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB764YTO

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 48 hours

value: primary cell

value: 38 year

value: AllCells

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

value: ENCBS280VRZ at ENCODE; https://www.encodeproject.org/ENCBS280VRZ/


title: Experiment2_D14_Prdm1cKO_GEX

description:
Library name: Sample 11
10X genomics - 5Prime - V2

value: Spleen

value: Prdm1 cKO

value: NP-CGG + Alum + LPS

tag: library type

value: mRNA


title: Experiment2_D14_WT_BCR

description:
Library name: Sample 12
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

value: WT


title: AT2_C

description: Library name: AT2_C

value: lung epithelial

value: Cultured alone


title: DNase-seq from inflammatory macrophage (ENCLB632PXL)

description:
https://www.encodeproject.org/experiments/ENCSR168WGF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR168WGF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB632PXL
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500,Illumina HiSeq 4000

source_name: Homo sapiens male adult (40 years) inflammatory macrophage primary cell

value: inflammatory macrophage

value: male

value: adult

value: 40 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS808WTA at ENCODE; https://www.encodeproject.org/ENCBS808WTA/


title: Experiment2_D14_WT_GEX

description:
Library name: Sample 14
10X genomics - 5Prime - V2


title: DNase-seq from NCI-H510A (ENCLB198WHP)

description:
https://www.encodeproject.org/experiments/ENCSR295UEC/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR295UEC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB198WHP

value: cell line

value: 56 year

value: ATCC

value: ENCBS421GAD at ENCODE; https://www.encodeproject.org/ENCBS421GAD/


title: Experiment2_D14_Prdm1cKO_FBHTO

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

value: Spleen

value: Prdm1 cKO

value: HTO


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB575HJJ)

description:
https://www.encodeproject.org/experiments/ENCSR853IHW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR853IHW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB575HJJ

value: primary cell

value: 38 year

value: AllCells

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

value: ENCBS623JBC at ENCODE; https://www.encodeproject.org/ENCBS623JBC/


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB544JXM)

description:
https://www.encodeproject.org/experiments/ENCSR915DCW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR915DCW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB544JXM

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 1 hour, 100 ng/mL Interleukin-2 for 1 hour

value: male

value: adult

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS103SLK at ENCODE; https://www.encodeproject.org/ENCBS103SLK/


title: DNase-seq from suppressor macrophage (ENCLB280QMU)

description:
https://www.encodeproject.org/experiments/ENCSR166BXN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR166BXN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB280QMU

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

value: suppressor macrophage

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS524CDB at ENCODE; https://www.encodeproject.org/ENCBS524CDB/


title: Experiment2_D14_Prdm1cKO_BCR

description:
Library name: Sample 9
10X genomics - 5Prime - V2

value: Spleen

value: Prdm1 cKO

value: NP-CGG + Alum + LPS

value: mRNA


title: DNase-seq from NCI-H345 (ENCLB264JAN)

description:
https://www.encodeproject.org/experiments/ENCSR163MZZ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR163MZZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB264JAN
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens NCI-H345 cell line

value: cell line

value: 64 year

value: ATCC

value: ENCBS146SXF at ENCODE; https://www.encodeproject.org/ENCBS146SXF/


title: MPRA from MIN6 (ENCLB963BPS)

description:
https://www.encodeproject.org/experiments/ENCSR981ILP/
***************
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: ENCSR981ILP
assay title: MPRA
possible controls: ENCSR361QPQ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB963BPS
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: ENCBS155VLH at ENCODE; https://www.encodeproject.org/ENCBS155VLH/


title: DNase-seq from K562 (ENCLB682IGF)

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 10
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: ENCLB682IGF

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS581ZES at ENCODE; https://www.encodeproject.org/ENCBS581ZES/


title: Experiment1_D7_WT_GEX

description:
Library name: Sample 8
10X genomics - 5Prime - V2

value: Spleen

value: WT


title: AT2.SUM_B

description: Library name: AT2.SUM_B

value: iAT2 + SUM159PT

value: lung epithelial & TNBC

value: No contact co-culture


title: AT2_B

description: Library name: AT2_B

value: lung epithelial

value: Cultured alone


title: AT2_A

description: Library name: AT2_A


title: DNase-seq from K562 (ENCLB785QOO)

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 6
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: ENCLB785QOO

value: cell line

tag: age

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS982NXC at ENCODE; https://www.encodeproject.org/ENCBS982NXC/


title: DNase-seq from K562 (ENCLB094TPV)

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 9
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: ENCLB094TPV

tag: lab

value: ENCBS915BAO at ENCODE; https://www.encodeproject.org/ENCBS915BAO/


title: Experiment1_D7_WT_BCR

description:
Library name: Sample 7
10X genomics - 5Prime - V2

value: NP-CGG + Alum + LPS

value: mRNA