title: ATAC-seq from activated CD4-positive, alpha-beta T cell (ENCLB990DDQ)

description:
https://www.encodeproject.org/experiments/ENCSR991PBP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR991PBP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB990DDQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS312MDQ at ENCODE; https://www.encodeproject.org/ENCBS312MDQ/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: Sample 5 Prostate Tumor

status: Public on Nov 04 2021

type: SRA

city: Happy Valley

first: Alex

middle: Daniel

last: Chitsazan

state: OR

address: 2720 S Moody Ave

country: USA

institute: Oregon Health and Science University

library_source: genomic

data_processing:
Reads were then aligned using snaptools aligned-paired-end command using all of the default parameters (bwa) to hg19
 Reads were than preprocessed using the snaptools snap-pre command using the default parameters
a binned matrix where each counts were generated for each 5kb bin in the genome using the snaptools -- snap-add-bmat command
a peak matrix was made with the snapATAC command runMACS (MACS2  parameters: --nomodel --shift 100 --ext 200 --qval 5e-2 -B –SPMR.)
Downstream analysis down in R
Genome_build: hg19
Supplementary_files_format_and_content: peak matrix, binned matrix in triplicate spare file and meta data text file

molecule: genomic DNA

organism: Homo sapiens

source_name: Prostate adenocarcinoma

extract_protocol:
Nuclei Isolation Buffer (NIB) was used to extract nuclei from flash-frozen prostate tumors via dounce homogenizer.
Nuclei were tagmented with specific barcode sequences annealed to the Tn5 enzyme after being sorted to a 96-well plate. Tagmented nuclei were mixed and sorted to another 96-well plate. A second set of indices were introduced via PCR to generate sci-ATAC-seq libraries. Clean-up was done using Qiagen PCR purification kits, followed up by AMPure bead purification twice.
single-cell ATAC-seq

tag: gleason score


title: DNase-seq from head of caudate nucleus (ENCLB987ETT)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR483HUW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR483HUW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB987ETT
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

source_name: Homo sapiens female adult (90 or above years) with Alzheimer's disease; head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: 90 or above year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Rush University

tag: link

value: ENCBS344QIE at ENCODE; https://www.encodeproject.org/ENCBS344QIE/

value: Derived from ENCODE donor ENCDO637GUS; https://www.encodeproject.org/ENCDO637GUS/


title: polyA plus RNA-seq from CD14-positive monocyte (ENCLB635ELE)

description:
https://www.encodeproject.org/experiments/ENCSR992MUF/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD14-positive monocyte.
experiment encode accession: ENCSR992MUF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-10-12
lab: David Hafler, Yale
library encode accession: ENCLB635ELE
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens CD14-positive monocyte primary cell, preserved by cryopreservation

value: CD14-positive monocyte

tag: description

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

tag: health state

value: healthy

value: ENCBS549CYH at ENCODE; https://www.encodeproject.org/ENCBS549CYH/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: KYSE150_2_7

city: Dallas

first: Adwait Amod

last: Sathe

state: Texas

address: 5323 Harry Hines Blvd.

department: McDermott Center of Human Growth and Development

institute: UT Southwestern Medical Center

data_processing:
Paired-end 75 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to mouse genome using bowtie2 (v2.3.3.1)
Duplicates were marked using picard-tools (v2.2.1) and blacklist regions were removed using bedtools (v2.7.1)
TN5 shifting of bam files was performed using the open-source Perl script "ATAC_BAM_shiftrt_gappedAlign.pl"
peaks were called using MACS version 2.1.0.20160309 with the following setting: Q-value < 0.05 and using the random background
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using HOMER. Scores represent normalized counts per 10 million.

source_name: Esophageal squamous carcinoma cell line

growth_protocol: HET-1A cells were cultured in BEBM medium with all the additives as ATCC recommends. KYSE-30 and KYSE-150 cells were grown in RPMI/F12 + 5% FBS + 1% antibiotic-antimycotic.

extract_protocol:
ATAC-seq libraries were prepared using the ATAC-seq inventor’s original protocol. Cells were harvested for ATAC-seq by centrifugation and re-suspended in cold PBS. 50,000 cells were immediately lysed using cold lysis buffer, and isolated nuclei from the cells were incubated in the Tn5-mediated transposase reaction mix for 30 min at 37 °C.
Following purification, the fragmented DNA library from each cell line was barcoded by PCR using customized Illumina sequencing primers. After primer dimers were cleaned up with AMPure XP beads (Beckman Coulter, CA), libraries were validated by Bioanalyzer and quantified by qRT-PCR.

tag: tissue

value: esophagus

tag: cell line

value: esophageal squamous cell carcinoma (ESCC) cell line KYSE-150


title: BruUV-seq from A673 (ENCLB620UGS)

description:
https://www.encodeproject.org/experiments/ENCSR953XJY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR953XJY
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR912SRZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB620UGS
size range: 400-500

source_name: Homo sapiens A673 cell line

tag: line

value: cell line

value: female

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS603AOW at ENCODE; https://www.encodeproject.org/ENCBS603AOW/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: polyA plus RNA-seq from naive B cell (ENCLB126OGA)

description:
https://www.encodeproject.org/experiments/ENCSR783SSV/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive B cell with multiple sclerosis.
experiment encode accession: ENCSR783SSV
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB126OGA
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens naive B primary cell with multiple sclerosis, preserved by cryopreservation

value: naive B cell

value: primary cell

value: B naive CD3- CD14- CD19+ CD27- IgD+

value: not collected

value: multiple sclerosis

value: ENCBS743ZAV at ENCODE; https://www.encodeproject.org/ENCBS743ZAV/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: Bru-seq from Calu3 (ENCLB958GMA)

description:
https://www.encodeproject.org/experiments/ENCSR692DCF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR692DCF
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB958GMA
size range: 400-500

source_name: Homo sapiens Calu3 cell line

value: male

value: adult

value: 25 year

value: Lung adenocarcinoma

value: ENCBS673NGX at ENCODE; https://www.encodeproject.org/ENCBS673NGX/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: HET1A_2_2

source_name: Esophageal epithelial cell line

value: esophagus

value: non-cancerous cell line HET-1A


title: HET1A_2_1


title: ATAC-seq from naive B cell (ENCLB244ASN)

description:
https://www.encodeproject.org/experiments/ENCSR685OFR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR685OFR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB244ASN
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (39 years) naive B primary cell

value: female

value: 39 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS623YDK at ENCODE; https://www.encodeproject.org/ENCBS623YDK/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


title: DNase-seq from posterior cingulate gyrus (ENCLB261IXB)

description:
https://www.encodeproject.org/experiments/ENCSR955RQG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR955RQG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB261IXB
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Homo sapiens female adult (90 or above years) with Alzheimer's disease; posterior cingulate gyrus tissue

value: posterior cingulate gyrus

value: tissue

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS372ZWI at ENCODE; https://www.encodeproject.org/ENCBS372ZWI/

value: Derived from ENCODE donor ENCDO597SRH; https://www.encodeproject.org/ENCDO597SRH/


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB053CKB)

description:
https://www.encodeproject.org/experiments/ENCSR889ONK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR889ONK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB053CKB

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

value: primary cell

value: male

value: adult

value: 42 year

value: AllCells

value: ENCBS837ULW at ENCODE; https://www.encodeproject.org/ENCBS837ULW/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: KYSE30_2_6

value: esophagus

value: esophageal squamous cell carcinoma (ESCC) cell line KYSE-30


title: Histone ChIP-seq from motor neuron (ENCLB449YNP)

description:
https://www.encodeproject.org/experiments/ENCSR682BFG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR682BFG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR201VAH
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB449YNP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (47 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

tag: antibody

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: 47 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: Donor with Amyotrophic Lateral Sclerosis

value: ENCBS309GBV at ENCODE; https://www.encodeproject.org/ENCBS309GBV/

value: Derived from ENCODE donor ENCDO908CUN; https://www.encodeproject.org/ENCDO908CUN/


title: Histone ChIP-seq from motor neuron (ENCLB373NMO)

description:
https://www.encodeproject.org/experiments/ENCSR682BFG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR682BFG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR201VAH
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB373NMO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: ENCBS545YIS at ENCODE; https://www.encodeproject.org/ENCBS545YIS/


title: Control ChIP-seq from WTC11 (ENCLB768LMK)

description:
https://www.encodeproject.org/experiments/ENCSR979TXM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR979TXM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB768LMK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HMGA2

value: cell line

value: adult

value: 30 year

value: Kevin White

value: ENCBS882AWW at ENCODE; https://www.encodeproject.org/ENCBS882AWW/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: ATAC-seq from naive B cell (ENCLB063PXP)

description:
https://www.encodeproject.org/experiments/ENCSR685OFR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR685OFR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB063PXP
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: naive B cell

value: primary cell

value: female

value: 39 year

value: StemExpress

value: ENCBS721IPZ at ENCODE; https://www.encodeproject.org/ENCBS721IPZ/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


title: ATAC-seq from activated T-cell (ENCLB332YGV)

description:
https://www.encodeproject.org/experiments/ENCSR775KMA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR775KMA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB332YGV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (38 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours

value: activated T-cell

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:4; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour;

value: ENCBS092RUO at ENCODE; https://www.encodeproject.org/ENCBS092RUO/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: 2078T-M88N [WES_5]

city: Pamplona

first: Ibai

last: Goicoechea

state: Navarra

address: Centro de Investigación Médica Aplicada (CIMA) Avenida Pío XII, 55

country: Spain

institute: Universidad de Navarra

data_processing:
Demultiplexing, alignment and gene counts were performed with Cell Ranger Single-Cell Software Suite (v3.01, 10X Genomics).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: NOT PROVIDED

organism: Mus musculus

source_name: Thymus

extract_protocol:
For WES B cells were sorted and genomic DNA from viable cells was purified using the NucleoSpin® Tissue kit (Macherey-Nagel), according to the manufacturer’s instructions
SureSelectXT Target Enrichment System for Illumina  Paired-End Multiplexed Sequencing Library Version C2, Dec 2018
Exome capture libraries were prepared per the instructions of the SureSelectXT mouse all exon target enrichment system (Agilent Technologies)

tag: cell type

value: B cells

value: Thymus

tag: strain background

tag: genotype/variation


title: BruUV-seq from A673 (ENCLB081VEU)

description:
https://www.encodeproject.org/experiments/ENCSR953XJY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR953XJY
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR912SRZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB081VEU
size range: 400-500

value: cell line

tag: biosample encode accession

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS913WHA at ENCODE; https://www.encodeproject.org/ENCBS913WHA/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: BruUV-seq from endothelial cell of umbilical vein (ENCLB162JLZ)

description:
https://www.encodeproject.org/experiments/ENCSR936LBO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR936LBO
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR849FAX
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB162JLZ
size range: 400-500

source_name: Homo sapiens newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: primary cell

tag: Sex

value: not collected

value: newborn

value: Lonza

value: unknown

value: ENCBS603RCW at ENCODE; https://www.encodeproject.org/ENCBS603RCW/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: DNase-seq from posterior cingulate gyrus (ENCLB862VEP)

description:
https://www.encodeproject.org/experiments/ENCSR690CVL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR690CVL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB862VEP
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

value: posterior cingulate gyrus

value: tissue

value: female

tag: dev stage

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS520XHP at ENCODE; https://www.encodeproject.org/ENCBS520XHP/

value: Derived from ENCODE donor ENCDO865EMM; https://www.encodeproject.org/ENCDO865EMM/


title: polyA plus RNA-seq from CD14-positive monocyte (ENCLB207UXB)

description:
https://www.encodeproject.org/experiments/ENCSR467YDA/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD14-positive monocyte.
experiment encode accession: ENCSR467YDA
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB207UXB
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: healthy

tag: age

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS666ANY at ENCODE; https://www.encodeproject.org/ENCBS666ANY/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: DNase-seq from head of caudate nucleus (ENCLB024MFU)

description:
https://www.encodeproject.org/experiments/ENCSR885WWJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR885WWJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB024MFU
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens male adult (90 or above years) with Alzheimer's disease; head of caudate nucleus tissue

value: head of caudate nucleus

value: male

tag: lab

value: ENCBS376ZDA at ENCODE; https://www.encodeproject.org/ENCBS376ZDA/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: 4dpi-mouse_lung-human_immune_cells

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

description: digested lungs from SARS-CoV-2 infected MISTRG6-hACE2 mice

data_processing:
Initial data processing was performed using the Cell Ranger version 3.0 pipeline (10X Genomics)
Post-processing, including filtering by number of genes expressed per cell, was performed using the Seurat package.
Following clustering and visualization with t-Distributed Stochastic Neighbor Embedding (t-SNE).
Identification of cell clusters was performed on the final aligned object guided by marker genes.
Genome_build: hg19-mm10
Supplementary_files_format_and_content: "barcodes.tsv.gz" contains cell barcodes, "features.tsv.gz" contains metadata for genes, "matrix.mtx.gz" contains digital expression matrix

source_name: lung

growth_protocol: Newborn MISTRG6 mice were reconstitued with human CD34+ fetal liver cells.

extract_protocol:
Lungs from infected mice were collected and digested at 37°C for 20 min using digestion cocktail containing 1 mg/ml collagenase D (Sigma) and 30 µg/ml DNase I (Sigma-Aldrich) in RPMI.
Single-cell 3’ RNA-seq libraries were prepared using Chromium Single Cell V3 Reagent Kit and Controller (10X Genomics)

treatment_protocol: Immune-reconstituted MISTRG6 mice were injected with AAV9 encoding hACE2  (purchased from Vector Biolabs) intratracheally at 8 weeks post engraftment.  These mice were then infected with  SARS-CoV-2.

tag: strain

value: MISTRG6 in Balb/c

value: lung

tag: disease


title: KYSE30_2_4

value: esophagus

value: esophageal squamous cell carcinoma (ESCC) cell line KYSE-30


title: TF ChIP-seq from HepG2 (ENCLB837YBD)

description:
https://www.encodeproject.org/experiments/ENCSR681KXT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR681KXT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR555EMB
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB837YBD
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF329

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

tag: source

value: Richard Myers

tag: link

value: ENCBS937DRB at ENCODE; https://www.encodeproject.org/ENCBS937DRB/

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


title: BruUV-seq from endothelial cell of umbilical vein (ENCLB095ITN)

description:
https://www.encodeproject.org/experiments/ENCSR936LBO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR936LBO
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR849FAX
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB095ITN
size range: 400-500

value: endothelial cell of umbilical vein

value: primary cell

value: not collected

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

tag: health state

value: unknown

value: ENCBS682VMT at ENCODE; https://www.encodeproject.org/ENCBS682VMT/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: TF ChIP-seq from HepG2 (ENCLB813WLA)

description:
https://www.encodeproject.org/experiments/ENCSR681KXT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR681KXT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR555EMB
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB813WLA
fragmentation methods: sonication (generic)

value: cell line

value: male

value: ENCBS427WVZ at ENCODE; https://www.encodeproject.org/ENCBS427WVZ/


title: polyA plus RNA-seq from IgD-negative memory B cell (ENCLB370GQC)

description:
https://www.encodeproject.org/experiments/ENCSR975CMV/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of IgD-negative memory B cell with multiple sclerosis.
experiment encode accession: ENCSR975CMV
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB370GQC
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens IgD-negative memory B primary cell with multiple sclerosis

value: IgD-negative memory B cell

tag: description

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS720RJK at ENCODE; https://www.encodeproject.org/ENCBS720RJK/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: polyA plus RNA-seq from immature natural killer cell (ENCLB517MCJ)

description:
https://www.encodeproject.org/experiments/ENCSR972TMF/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of immature natural killer cell.
experiment encode accession: ENCSR972TMF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB517MCJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: primary cell

value: not collected

value: healthy

value: ENCBS142IVK at ENCODE; https://www.encodeproject.org/ENCBS142IVK/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: TF ChIP-seq from HepG2 (ENCLB409BAQ)

description:
https://www.encodeproject.org/experiments/ENCSR567IOQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR567IOQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB409BAQ
fragmentation methods: sonication (generic)

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

value: GLMP

tag: line

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS396YAT at ENCODE; https://www.encodeproject.org/ENCBS396YAT/

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


title: Sample_1894-uninfected

description: Humanized mouse

data_processing:
For RNA-seq raw data processing, trimming was performed using cutadapt.
Alignment was performed using STAR (version 2.5.3) and raw read counts were generated using HTSeq.
Differential analysis was performed using DESeq2 R package.
Genome_build: hg19-mm10-covid
Supplementary_files_format_and_content: Txt file including gene count for each sample separately

source_name: homogenized lung tissue from humanized MISTRG6 mice

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen) per the manufacturer’s protocol.
Libraries were prepared with an Illumina rRNA depletion kit and sequenced on a NovaSeq.

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

tag: genotype

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Sample_1925-4dpi

description: Humanized mouse


title: ATAC-seq from CD8-positive, alpha-beta T cell (ENCLB729ABU)

description:
https://www.encodeproject.org/experiments/ENCSR476VJY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR476VJY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB729ABU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: male

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS484RJL at ENCODE; https://www.encodeproject.org/ENCBS484RJL/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: Sample_1905-7dpi

description: Humanized mouse


title: polyA plus RNA-seq from CD14-positive monocyte (ENCLB814KWX)

description:
https://www.encodeproject.org/experiments/ENCSR968ACN/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD14-positive monocyte with multiple sclerosis.
experiment encode accession: ENCSR968ACN
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB814KWX
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens CD14-positive monocyte primary cell with multiple sclerosis, preserved by cryopreservation

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS929PLQ at ENCODE; https://www.encodeproject.org/ENCBS929PLQ/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Histone ChIP-seq from motor neuron (ENCLB243INW)

description:
https://www.encodeproject.org/experiments/ENCSR489LNU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR489LNU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR744SMV
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB243INW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens female adult with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

tag: antibody

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: female

value: Healthy donor

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS733MQS at ENCODE; https://www.encodeproject.org/ENCBS733MQS/

value: Derived from ENCODE donor ENCDO689YDN; https://www.encodeproject.org/ENCDO689YDN/


title: Patient376

type: RNA

city: MIAMI

first: Xi

last: CHEN

state: FL

address: 1120 NW 14th Street

institute: University of Miami

data_processing: We normalized the raw data at the gene level using Robust MultiChip Averaging (RMA) algorithm as implemented in the Affymetrix® Expression ConsoleTM Software 1.3.

label: biotin

source_name: Human Colorectal cancer tissue

label_protocol:
According to the GeneChip™ Human Transcriptome Array 2. 0 (Affymetrix, Santa Clara, CA) protocol.
The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin

extract_protocol:
Archived CRC FFPE samples used in this study were stored at room temperature until sectioned for RNA extraction. The first 10µm of the tissue was discarded before cutting sections for RNA extraction. Five-micron sections were mounted on uncharged glass slides. Separate tissue sections from the top and bottom of the serial sections used for RNA extraction were stained with H&E for quality control from each tissue block. RNA was purified from 5µm thick tissue sections containing greater than 80% tumor using High Pure FFPE RNA Micro Kit (Roche) according to manufacturer’s instructions. A minimum of 4 sections per sample were required.
At least 20% of the RNA sample contain fragments of 300 base pairs or longer in length

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: DOD


title: Sample_1901-2dpi

description: Humanized mouse

tag: strain

value: MISTRG6 in Balb/c

value: Lung

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Histone ChIP-seq from motor neuron (ENCLB756JKW)

description:
https://www.encodeproject.org/experiments/ENCSR489LNU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR489LNU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR744SMV
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB756JKW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: biosample encode accession

tag: Sex

tag: dev stage

value: adult

tag: age

value: not collected

tag: lab

value: ENCBS152AIM at ENCODE; https://www.encodeproject.org/ENCBS152AIM/


title: polyA plus RNA-seq from immature natural killer cell (ENCLB964ZIE)

description:
https://www.encodeproject.org/experiments/ENCSR766TSI/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of immature natural killer cell with multiple sclerosis.
experiment encode accession: ENCSR766TSI
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB964ZIE
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens immature natural killer primary cell with multiple sclerosis

value: immature natural killer cell

value: primary cell

tag: description

value: supplied by Hafler lab as part of Encode4 project starting July2017

tag: health state

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

value: ENCBS745FCE at ENCODE; https://www.encodeproject.org/ENCBS745FCE/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Sample_1900-2dpi

description: Humanized mouse

tag: tissue

tag: genotype


title: Control ChIP-seq from WTC11 (ENCLB551SUF)

description:
https://www.encodeproject.org/experiments/ENCSR922EQL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR922EQL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-22
lab: Richard Myers, HAIB
library encode accession: ENCLB551SUF
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line

tag: line

value: cell line

value: male

value: 30 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS381DYL at ENCODE; https://www.encodeproject.org/ENCBS381DYL/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: polyA plus RNA-seq from CD8-positive, alpha-beta memory T cell (ENCLB313SVD)

description:
https://www.encodeproject.org/experiments/ENCSR764EGD/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD8-positive, alpha-beta memory T cell with multiple sclerosis.
experiment encode accession: ENCSR764EGD
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-10-12
lab: David Hafler, Yale
library encode accession: ENCLB313SVD
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell with multiple sclerosis, preserved by cryopreservation

value: CD8-positive, alpha-beta memory T cell

value: CD8+ memory CD3+ CD4- CD8+ CD45RA- CD45RO+

value: not collected

value: ENCBS229YZM at ENCODE; https://www.encodeproject.org/ENCBS229YZM/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: Sample_1904-7dpi

description: Humanized mouse

value: MISTRG6 in Balb/c

value: Lung

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Patient374

hyb_protocol: According to the GeneChip™ Human Transcriptome Array 2. 0 (Affymetrix, Santa Clara, CA) protocol.

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: No

tag: recurrence

tag: disease free survival (days)

value: DOD


title: Patient371

scan_protocol: According to the GeneChip™ Human Transcriptome Array 2. 0 (Affymetrix, Santa Clara, CA) protocol.

tag: death

tag: overall survival (days)

tag: disease status

value: NED


title: Sample_1926-4dpi

description: Humanized mouse

tag: strain


title: Patient372

value: FOLFOX


title: TF ChIP-seq from HepG2 (ENCLB757MLY)

description:
https://www.encodeproject.org/experiments/ENCSR567IOQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR567IOQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB757MLY
fragmentation methods: sonication (generic)

tag: antibody

value: GLMP

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: child

tag: age

value: 15 year

value: Richard Myers, HAIB

value: hepatocellular carcinoma

value: ENCBS126BIX at ENCODE; https://www.encodeproject.org/ENCBS126BIX/

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


title: Patient370

value: Unknown


title: Patient369

value: DOC


title: polyA plus RNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB525BFO)

description:
https://www.encodeproject.org/experiments/ENCSR969XWI/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, alpha-beta memory T cell with multiple sclerosis.
experiment encode accession: ENCSR969XWI
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB525BFO
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell with multiple sclerosis, preserved by cryopreservation

value: CD4-positive, alpha-beta memory T cell

value: primary cell

tag: description

value: CD4+ memory CD3+ CD4+ CD8- CD45RA- CD45RO+ nonTreg

value: not collected

tag: health state

value: multiple sclerosis

value: unknown

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

value: ENCBS812ZCI at ENCODE; https://www.encodeproject.org/ENCBS812ZCI/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: Patient375

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: No

value: NED


title: Patient367

value: FOLFOX

tag: recurrence

tag: disease free survival (days)


title: Patient373

tag: death

tag: overall survival (days)


title: Sample_2020-28dpi

description: Humanized mouse

tag: strain

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

tag: genotype

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: ATAC-seq from motor neuron (ENCLB098CDZ)

description:
https://www.encodeproject.org/experiments/ENCSR913OWV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR913OWV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB098CDZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (55 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

tag: biosample encode accession

tag: Sex

value: male

value: adult

value: 55 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: Healthy donor

value: ENCBS346LNG at ENCODE; https://www.encodeproject.org/ENCBS346LNG/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: Patient366

value: colorectal cancer (CRC) patient

value: No

tag: disease status


title: TF ChIP-seq from K562 (ENCLB943YJU)

description:
https://www.encodeproject.org/experiments/ENCSR763FNU/
***************
biological replicate number: 1
technical replicate number: 1
description: CGGBP1 ChIP-seq on human K562
experiment encode accession: ENCSR763FNU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR334KTB
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB943YJU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens CGGBP1

tag: antibody

tag: line

value: cell line

value: female

tag: dev stage

tag: age

value: 53 year

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS486RMP at ENCODE; https://www.encodeproject.org/ENCBS486RMP/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: polyA plus RNA-seq from immature natural killer cell (ENCLB780BLQ)

description:
https://www.encodeproject.org/experiments/ENCSR963EVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of immature natural killer cell.
experiment encode accession: ENCSR963EVZ
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB780BLQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

value: immature natural killer cell

value: primary cell

tag: description

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

tag: health state

value: healthy

value: unknown

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

value: ENCBS620QTW at ENCODE; https://www.encodeproject.org/ENCBS620QTW/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: Patient368

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: No

tag: recurrence

tag: disease free survival (days)

tag: death

value: NED


title: ATAC-seq from motor neuron (ENCLB127MFI)

description:
https://www.encodeproject.org/experiments/ENCSR913OWV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR913OWV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB127MFI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

tag: biosample encode accession

value: male

value: adult

value: 55 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: Healthy donor

value: ENCBS259EPB at ENCODE; https://www.encodeproject.org/ENCBS259EPB/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: Bru-seq from endothelial cell of umbilical vein (ENCLB374OQY)

description:
https://www.encodeproject.org/experiments/ENCSR849FAX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR849FAX
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB374OQY
size range: 400-500

source_name: Homo sapiens newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: primary cell

tag: Sex

value: not collected

value: unknown

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS903KNC at ENCODE; https://www.encodeproject.org/ENCBS903KNC/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: Sample_2021-28dpi

description: Humanized mouse

tag: strain

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

tag: genotype

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Sample_1761-4dpi

description: Humanized mouse


title: Patient363

value: colorectal cancer (CRC) patient

tag: overall survival (days)

tag: disease status

value: DOD


title: Bru-seq from A673 (ENCLB776OZU)

description:
https://www.encodeproject.org/experiments/ENCSR912SRZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR912SRZ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB776OZU
size range: 400-500

source_name: Homo sapiens A673 cell line

tag: line

value: cell line

value: female

tag: dev stage

value: child

tag: age

value: 15 year

value: ATCC

value: ENCBS236UZS at ENCODE; https://www.encodeproject.org/ENCBS236UZS/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: ATAC-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB089GEX)

description:
https://www.encodeproject.org/experiments/ENCSR915MTG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR915MTG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB089GEX
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads , 10 ng/mL Interleukin-2 nuclear fraction

value: primary cell

value: male

value: adult

value: 30 year

tag: lab

value: Yijun Ruan, JAX

tag: source

value: AllCells

tag: treatments

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

tag: subcellular fraction term name

value: nucleus

value: ENCBS603PFY at ENCODE; https://www.encodeproject.org/ENCBS603PFY/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: Bru-seq from A673 (ENCLB556DQX)

description:
https://www.encodeproject.org/experiments/ENCSR912SRZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR912SRZ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB556DQX
size range: 400-500

value: cell line

value: Mats Ljungman, UMichigan

tag: link

value: ENCBS143CJI at ENCODE; https://www.encodeproject.org/ENCBS143CJI/


title: Sample_1765-4dpi

description: Humanized mouse

value: MISTRG6 in Balb/c

value: Lung

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Bru-seq from endothelial cell of umbilical vein (ENCLB663KRM)

description:
https://www.encodeproject.org/experiments/ENCSR849FAX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR849FAX
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB663KRM
size range: 400-500

value: endothelial cell of umbilical vein

value: not collected

tag: health state

value: unknown

value: newborn

value: Lonza

value: ENCBS884VDH at ENCODE; https://www.encodeproject.org/ENCBS884VDH/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: TF ChIP-seq from WTC11 (ENCLB452HEL)

description:
https://www.encodeproject.org/experiments/ENCSR905MSY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR905MSY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR922EQL
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB452HEL
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXJ3

tag: antibody

value: male

value: adult

value: 30 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS284UUT at ENCODE; https://www.encodeproject.org/ENCBS284UUT/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from K562 (ENCLB865HXO)

description:
https://www.encodeproject.org/experiments/ENCSR763FNU/
***************
biological replicate number: 2
technical replicate number: 1
description: CGGBP1 ChIP-seq on human K562
experiment encode accession: ENCSR763FNU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR334KTB
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB865HXO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS899THP at ENCODE; https://www.encodeproject.org/ENCBS899THP/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Patient361

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

value: DOD


title: Sample_1892-14dpi

description: Humanized mouse

tag: strain

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

tag: genotype

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Sample_1766-4dpi

description: Humanized mouse


title: ATAC-seq from activated B cell (ENCLB227HYD)

description:
https://www.encodeproject.org/experiments/ENCSR659SFK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR659SFK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB227HYD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: activated B cell

value: primary cell

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS582QTR at ENCODE; https://www.encodeproject.org/ENCBS582QTR/

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


title: Patient362

tag: overall survival (days)

tag: disease status


title: Sample_1906-uninfected

description: Humanized mouse


title: Sample_1893-14dpi

description: Humanized mouse


title: TF ChIP-seq from WTC11 (ENCLB866FYK)

description:
https://www.encodeproject.org/experiments/ENCSR905MSY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR905MSY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR922EQL
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB866FYK
fragmentation methods: sonication (generic)

tag: line

value: cell line

value: 30 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

tag: link

value: ENCBS725WVN at ENCODE; https://www.encodeproject.org/ENCBS725WVN/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: polyA plus RNA-seq from IgD-negative memory B cell (ENCLB144ACP)

description:
https://www.encodeproject.org/experiments/ENCSR713DXI/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of IgD-negative memory B cell.
experiment encode accession: ENCSR713DXI
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB144ACP
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens IgD-negative memory B primary cell

value: IgD-negative memory B cell

tag: description

value: Sample from Hafler lab as part of Encode4 project

tag: biosample encode accession

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

tag: health state

value: multiple sclerosis

value: ENCBS093OKK at ENCODE; https://www.encodeproject.org/ENCBS093OKK/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: Sample_2025-uninfected

description: Humanized mouse

source_name: homogenized lung tissue from humanized MISTRG6 mice

value: MISTRG6 in Balb/c

value: Lung

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: ATAC-seq from naive B cell (ENCLB686RZZ)

description:
https://www.encodeproject.org/experiments/ENCSR903WVU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR903WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB686RZZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (40 years) naive B primary cell

value: naive B cell

value: primary cell

value: male

value: adult

value: 40 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS229WUM at ENCODE; https://www.encodeproject.org/ENCBS229WUM/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: Patient360

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

value: DOD


title: polyA plus RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB032ZBW)

description:
https://www.encodeproject.org/experiments/ENCSR761ZWF/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, CD25-positive, alpha-beta regulatory T cell with multiple sclerosis.
experiment encode accession: ENCSR761ZWF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB032ZBW
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens with multiple sclerosis; CD4-positive, CD25-positive, alpha-beta regulatory T primary cell, preserved by cryopreservation

value: Treg CD3+ CD4+ CD8- CD25+ CD127-

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS781DHR at ENCODE; https://www.encodeproject.org/ENCBS781DHR/


title: Patient359

tag: death

value: NED


title: ATAC-seq from naive B cell (ENCLB312ILG)

description:
https://www.encodeproject.org/experiments/ENCSR903WVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR903WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB312ILG
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: naive B cell

value: primary cell

tag: Sex

value: male

value: ENCBS437OQI at ENCODE; https://www.encodeproject.org/ENCBS437OQI/


title: Patient358

value: DOC


title: Patient357


title: DNase-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB428MUV)

description:
https://www.encodeproject.org/experiments/ENCSR572HUG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR572HUG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB428MUV

source_name: Homo sapiens male adult (42 years) activated CD8-positive, naive alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

tag: dev stage

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS718TWO at ENCODE; https://www.encodeproject.org/ENCBS718TWO/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: Sample_1740-14dpi

description: Humanized mouse

tag: strain

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

tag: genotype

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Sample_1739-14dpi

description: Humanized mouse


title: ATAC-seq from activated CD8-positive, alpha-beta T cell (ENCLB535ADB)

description:
https://www.encodeproject.org/experiments/ENCSR718HWW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR718HWW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB535ADB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

tag: age

value: 21 year

tag: lab

value: Yijun Ruan, JAX

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS908MHG at ENCODE; https://www.encodeproject.org/ENCBS908MHG/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: ATAC-seq from activated T-cell (ENCLB215DAT)

description:
https://www.encodeproject.org/experiments/ENCSR830ALP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR830ALP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB215DAT
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (43 years) activated T-cell primary cell

value: activated T-cell

value: primary cell

value: male

value: 43 year

value: Michael Snyder, Stanford

tag: source

value: StemExpress

tag: link

value: ENCBS283LLW at ENCODE; https://www.encodeproject.org/ENCBS283LLW/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: Sample_1738-4dpi

description: Humanized mouse


title: Patient356

source_name: Human Colorectal cancer tissue

value: colorectal cancer (CRC) patient

value: FOLFOX and AVASTIN (started 7/13 due to mass per CT,  not clear if mass is CRC or Pancreas Primary)

tag: overall survival (days)

tag: disease status

value: AWD


title: Histone ChIP-seq from motor neuron (ENCLB592ROF)

description:
https://www.encodeproject.org/experiments/ENCSR745TRI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR745TRI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR255MIG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB592ROF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

tag: biosample encode accession

value: adult

value: 55 year

value: Cooper-Knock lab, University of Sheffield, UK

tag: health state

value: Healthy donor

value: ENCBS259EPB at ENCODE; https://www.encodeproject.org/ENCBS259EPB/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: Control ChIP-seq from WTC11 (ENCLB422HGL)

description:
https://www.encodeproject.org/experiments/ENCSR654GXW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR654GXW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB422HGL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line

tag: line

value: cell line

value: male

value: 30 year

value: Richard Myers

value: ENCBS922HRW at ENCODE; https://www.encodeproject.org/ENCBS922HRW/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: Sample_1737-4dpi

description: Humanized mouse

value: MISTRG6 in Balb/c

value: Lung

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Sample_1736-7dpi

description: Humanized mouse


title: Histone ChIP-seq from motor neuron (ENCLB696XYM)

description:
https://www.encodeproject.org/experiments/ENCSR745TRI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR745TRI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR255MIG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB696XYM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: motor neuron

value: in vitro differentiated cells

tag: Sex

value: Michael Snyder, Stanford

value: ENCBS346LNG at ENCODE; https://www.encodeproject.org/ENCBS346LNG/


title: ATAC-seq from activated T-cell (ENCLB932HND)

description:
https://www.encodeproject.org/experiments/ENCSR830ALP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR830ALP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB932HND
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: activated T-cell

value: primary cell

tag: dev stage

value: adult

value: 43 year

value: StemExpress

value: ENCBS322HVV at ENCODE; https://www.encodeproject.org/ENCBS322HVV/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: Sample_1735-4dpi

description: Humanized mouse


title: ATAC-seq from HCT116 (ENCLB744PLW)

description:
https://www.encodeproject.org/experiments/ENCSR816PPJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR816PPJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB744PLW
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: male

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: colorectal carcinoma

value: ENCBS047AWE at ENCODE; https://www.encodeproject.org/ENCBS047AWE/

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


title: Patient365

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: No

tag: recurrence

tag: disease free survival (days)

tag: death

value: NED


title: Sample_1734-4dpi

description: Humanized mouse

tag: strain

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

tag: genotype

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Control ChIP-seq from K562 (ENCLB151SSJ)

description:
https://www.encodeproject.org/experiments/ENCSR957RYA/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-NFXL1 fusion protein.
experiment encode accession: ENCSR957RYA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-08-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB151SSJ
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NFXL1

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NFXL1.

value: female

value: adult

tag: age

value: 53 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Kevin White

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS094GEA at ENCODE; https://www.encodeproject.org/ENCBS094GEA/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Patient364

tag: overall survival (days)

tag: disease status

value: DOD


title: Patient355

value: AWD


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB200BYO)

description:
https://www.encodeproject.org/experiments/ENCSR755ARW/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD4-positive, alpha-beta T cell.
experiment encode accession: ENCSR755ARW
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB200BYO
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell, preserved by cryopreservation

value: primary cell

tag: description

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS677DRS at ENCODE; https://www.encodeproject.org/ENCBS677DRS/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: Patient7_2

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: Adjuvant FOLFOX

value: NED


title: ATAC-seq from HCT116 (ENCLB397TIL)

description:
https://www.encodeproject.org/experiments/ENCSR816PPJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR816PPJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB397TIL
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

tag: line

value: cell line

value: male

tag: dev stage

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: colorectal carcinoma

value: ENCBS512GOU at ENCODE; https://www.encodeproject.org/ENCBS512GOU/

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


title: Sample_1733-2dpi

description: Humanized mouse

tag: strain

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: Sample_1732-2dpi

description: Humanized mouse

tag: genotype


title: Patient353

tag: recurrence

tag: disease free survival (days)

tag: death


title: ATAC-seq from motor neuron (ENCLB562HZY)

description:
https://www.encodeproject.org/experiments/ENCSR812ZKP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR812ZKP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB562HZY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (49 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iNPC-derived motor neuron

value: Donor with Amyotrophic Lateral Sclerosis

tag: age

value: 49 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Cooper-Knock lab, University of Sheffield, UK

tag: link

value: ENCBS919RDK at ENCODE; https://www.encodeproject.org/ENCBS919RDK/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: Patient71

value: colorectal cancer (CRC) patient

value: Adjuvant FOLFOX x 11

tag: overall survival (days)

tag: disease status

value: NED


title: Patient354

tag: subject status

value: FOLFOX


title: DNase-seq from head of caudate nucleus (ENCLB550QDV)

description:
https://www.encodeproject.org/experiments/ENCSR639VTO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639VTO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB550QDV
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens female adult (81 years) with Cognitive impairment; head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

tag: biosample encode accession

tag: Sex

value: female

value: adult

value: 81 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS284MTX at ENCODE; https://www.encodeproject.org/ENCBS284MTX/

value: Derived from ENCODE donor ENCDO077CCP; https://www.encodeproject.org/ENCDO077CCP/


title: Patient6_2

tag: clinical stage

value: DOD


title: Patient69

value: Adjuvant FOLFOX


title: ATAC-seq from motor neuron (ENCLB942DBM)

description:
https://www.encodeproject.org/experiments/ENCSR812ZKP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR812ZKP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB942DBM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iNPC-derived motor neuron

value: male

tag: health state

value: Donor with Amyotrophic Lateral Sclerosis

tag: dev stage

value: 49 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS827VAK at ENCODE; https://www.encodeproject.org/ENCBS827VAK/


title: polyA plus RNA-seq from immature natural killer cell (ENCLB147VXF)

description:
https://www.encodeproject.org/experiments/ENCSR701JXD/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of immature natural killer cell with multiple sclerosis.
experiment encode accession: ENCSR701JXD
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB147VXF
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens immature natural killer primary cell with multiple sclerosis

value: immature natural killer cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS255ELL at ENCODE; https://www.encodeproject.org/ENCBS255ELL/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: TF ChIP-seq from HepG2 (ENCLB353MRH)

description:
https://www.encodeproject.org/experiments/ENCSR741TTE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR741TTE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB353MRH
fragmentation methods: sonication (generic)

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

tag: antibody

value: JRK

tag: line

value: cell line

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS362IUX at ENCODE; https://www.encodeproject.org/ENCBS362IUX/

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


title: Sample_1720-uninfected

description: Humanized mouse

tag: strain

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

tag: genotype

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: polyA plus RNA-seq from CD14-positive monocyte (ENCLB077NWQ)

description:
https://www.encodeproject.org/experiments/ENCSR638OAH/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD14-positive monocyte with multiple sclerosis.
experiment encode accession: ENCSR638OAH
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB077NWQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens CD14-positive monocyte primary cell with multiple sclerosis, preserved by cryopreservation

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

value: unknown

tag: age

tag: lab

value: ENCBS522LRV at ENCODE; https://www.encodeproject.org/ENCBS522LRV/


title: TF ChIP-seq from HepG2 (ENCLB974SFG)

description:
https://www.encodeproject.org/experiments/ENCSR741TTE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR741TTE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB974SFG
fragmentation methods: sonication (generic)

value: JRK

value: cell line

value: male

value: child

tag: source

tag: link

value: ENCBS919OVF at ENCODE; https://www.encodeproject.org/ENCBS919OVF/


title: DNase-seq from head of caudate nucleus (ENCLB632NLO)

description:
https://www.encodeproject.org/experiments/ENCSR637ZLM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR637ZLM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB632NLO

source_name: Homo sapiens female adult (90 or above years) head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

value: female

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS910SCN at ENCODE; https://www.encodeproject.org/ENCBS910SCN/

value: Derived from ENCODE donor ENCDO250PFZ; https://www.encodeproject.org/ENCDO250PFZ/


title: ACTD DNA-DNA SPRITE 16

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

institute: Princeton University

description:
genomic DNA
Female ES cells (pSM44 ES cell line) derived from a 129 × castaneous F1 mouse cross. These cells express Xist from the endogenous locus under control of a tetracycline-inducible promoter. The dox-inducible Xist gene is on the 129 allele, enabling allele-specific analysis of Xist induction and X chromosome silencing
ACTD.DSPRITE.clusters
DMSO.DSPRITE.clusters

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trim Galore! v0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and assessed with Fastqc v0.11.9. Subsequently, the DPM (GATCGGAAGAG) and RPM (ATCAGCACTTA) sequences are trimmed using Cutadapt v2.5 from the 5’ end of Read 1 along with the 3’ end DPM sequences that result from short reads being read through into the barcode (GGTGGTCTTT, GCCTCTTGTT, CCAGGTATTT, TAAGAGAGTT, TTCTCCTCTT, ACCCTCGATT). The additional trimming helps improve read mapping in the end-to-end alignment mode. The SPRITE barcodes of trimmed reads are identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline) and the ligation efficiency is assessed. Reads with an RPM or a DPM barcode are split into two separate files, to process RNA and DNA reads individually downstream, respectively.
For RNA-DNA SPRITE experiments, RNA reads were aligned to GRCm38.p6 with the Ensembl GRCm38 v95 gene model annotation using Hisat2 v2.1.01 with a high penalty for soft-clipping --sp 1000,1000. Unmapped and reads with a low MapQ score (samtools view -bq 20) were filtered out for downstream realignment. Mapped reads were annotated for gene exons and introns with the featureCounts tool from the subread package v1.6.4 using the Gencode release M25 annotations for GRCm38.p6 and the Repeat and Transposable element annotation from the Hammel lab. Filtered reads were subsequently realigned to our custom collection of repeat sequences using Bowtie v2.3.5, only keeping mapped and primary alignment reads.
For RNA-DNA or DNA-DNA SPRITE experiments, DNA reads were aligned to GRCm38.p6 using Bowtie2 v2.3.5, filtering out unmapped and reads with a low MapQ score (samtools view -bq 20).  RepeatMasker defined regions with milliDev <= 140 along with blacklisted v2 regions were filtered out using Bedtools v2.29.0.
A cluster file for each sample was generated from the processed reads. For RNA-DNA SPRITE experiments, the DNA and RNA reads were merged. MultiQC v1.6 was used to aggregate all reports.
Clusters corresponding to each treatment condition (ActD or DMSO) were identified from the cluster barcode. For RNA-DNA SPRITE experiments, the treatment condition was encoded in the first ODD barcode tag. For DNA-DNA SPRITE experiments, the treatment condition was encoded in the DPM barcode tag.
For each treatment condition, clusters from the different library preparations were merged into a single cluster file.
Genome_build: mm10
Supplementary_files_format_and_content: Each cluster occupies one line of the .clusters text file. A cluster corresponds to all reads with a shared series of tags and is identified by the barcode name and genomic alignments of contained reads.

source_name: Mouse Embryonic Stem cells

growth_protocol: All mouse ES cell lines were cultured in serum-free 2i/LIF medium

extract_protocol:
Cells were lifted using trypsinization and were crosslinked in suspension at room temperature with 2mM disuccinimidyl glutarate (DSG) for 45 minutes followed by 3% Formaldehyde for 10 minutes to preserve RNA and DNA interactions in situ.
After lysis of cells, nuclei were lightly sonicated. DNA was DNAse digested to an average size of approximately 150-1000 bp in length. Crosslinked complexes of interacting DNA, RNA, and protein were isolated on NHS beads, RNA and DNA ends were repaired, DNA was dA-tailed to generate a protruding 3’ A-base for ligation of barcodes, RNA was ligated with a partially ssRNA-dsDNA adaptor for ligation of barcodes, and were then split-pool tagged with a series of barcodes over multiple rounds of split-and-pool tagging. A distinct RNA adaptor was ligated to RNA to flag a molecule as RNA rather than DNA. This adaptor contains a shared overhang that allows for simultaneous tagging of RNA and DNA during the split-and-pool tagging process. Reverse transcription was performed to convert RNA into cDNA. After split-and-pool tagging, crosslinks were reversed, the DNA/RNA was isolated, was amplified 8-12 cycles using standard Illumina library prep (dual index), and purified using SPRI beads and gel cut. Libraries were sequenced on a NovaSeq S4 chip (150x150 read length).

treatment_protocol: Cells were treated with 25ul of 1mg/mL Actinomycin D or 25uL of DMSO per 1mL culture medium for 4 hours prior to harvest and crosslinking.

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: DNA-DNA SPRITE

tag: treatment

value: 4hr Actinomycin D or DMSO


title: ATAC-seq from natural killer cell (ENCLB115BKZ)

description:
https://www.encodeproject.org/experiments/ENCSR808HWS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR808HWS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB115BKZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (41 years) natural killer primary cell

value: natural killer cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: 41 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS920ZOR at ENCODE; https://www.encodeproject.org/ENCBS920ZOR/

value: Derived from ENCODE donor ENCDO911LCI; https://www.encodeproject.org/ENCDO911LCI/


title: ATAC-seq from natural killer cell (ENCLB243VNF)

description:
https://www.encodeproject.org/experiments/ENCSR808HWS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR808HWS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB243VNF
fragmentation methods: sonication (Bioruptor Pico)
size range: 150-1000

value: female

value: ENCBS592CJF at ENCODE; https://www.encodeproject.org/ENCBS592CJF/


title: Patient352

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: No

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: DOC


title: Patient351

value: NED


title: Patient349

value: Adjuvant chemotherapy (unknown type)


title: DNase-seq from naive B cell (ENCLB909XIV)

description:
https://www.encodeproject.org/experiments/ENCSR739VKY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR739VKY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB909XIV

source_name: Homo sapiens female adult (39 years) naive B primary cell

value: naive B cell

tag: dev stage

value: adult

tag: age

value: 39 year

value: John Stamatoyannopoulos, UW

value: ENCBS773HGU at ENCODE; https://www.encodeproject.org/ENCBS773HGU/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


title: Patient350

value: DOD


title: Patient348


title: Patient68


title: TF ChIP-seq from K562 (ENCLB825VBT)

description:
https://www.encodeproject.org/experiments/ENCSR805SIA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR805SIA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR758JMV
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB825VBT
fragmentation methods: sonication (generic)

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

tag: antibody

value: PURB

tag: line

value: cell line

value: 53 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS647NOE at ENCODE; https://www.encodeproject.org/ENCBS647NOE/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from WTC11 (ENCLB461JCC)

description:
https://www.encodeproject.org/experiments/ENCSR615YWF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR615YWF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB461JCC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

tag: link

value: ENCBS464LBW at ENCODE; https://www.encodeproject.org/ENCBS464LBW/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: ACTD DNA-DNA SPRITE 12

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: DNA-DNA SPRITE

tag: treatment

value: 4hr Actinomycin D or DMSO


title: ACTD DNA-DNA SPRITE 13


title: TF ChIP-seq from K562 (ENCLB394ASX)

description:
https://www.encodeproject.org/experiments/ENCSR805SIA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR805SIA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR758JMV
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB394ASX
fragmentation methods: sonication (generic)

value: PURB

tag: biosample encode accession

tag: Sex

value: female

value: adult

value: ENCBS997UML at ENCODE; https://www.encodeproject.org/ENCBS997UML/


title: ACTD DNA-DNA SPRITE 11


title: DNase-seq from middle frontal area 46 (ENCLB494IQT)

description:
https://www.encodeproject.org/experiments/ENCSR805RJA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR805RJA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB494IQT

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS234JZB at ENCODE; https://www.encodeproject.org/ENCBS234JZB/

value: Derived from ENCODE donor ENCDO258GJF; https://www.encodeproject.org/ENCDO258GJF/


title: DNase-seq from head of caudate nucleus (ENCLB995WFW)

description:
https://www.encodeproject.org/experiments/ENCSR635GDW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR635GDW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB995WFW

source_name: Homo sapiens female adult (79 years) head of caudate nucleus tissue

value: head of caudate nucleus

value: 79 year

value: ENCBS199DCJ at ENCODE; https://www.encodeproject.org/ENCBS199DCJ/

value: Derived from ENCODE donor ENCDO609ZOG; https://www.encodeproject.org/ENCDO609ZOG/


title: ATAC-seq from WTC11 (ENCLB621FEI)

description:
https://www.encodeproject.org/experiments/ENCSR541KFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541KFY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB621FEI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: cell line

value: male

value: 30 year

value: Michael Snyder, Stanford

value: Yin Shen

value: ENCBS732JEF at ENCODE; https://www.encodeproject.org/ENCBS732JEF/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: Patient347

source_name: Human Colorectal cancer tissue

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

value: NED


title: polyA plus RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB343PGR)

description:
https://www.encodeproject.org/experiments/ENCSR435WIF/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, CD25-positive, alpha-beta regulatory T cell with multiple sclerosis.
experiment encode accession: ENCSR435WIF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB343PGR
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens with multiple sclerosis; CD4-positive, CD25-positive, alpha-beta regulatory T primary cell, preserved by cryopreservation

value: primary cell

tag: description

value: Treg CD3+ CD4+ CD8- CD25+ CD127-

value: not collected

tag: dev stage

value: unknown

tag: age

value: Bradley Bernstein, Broad

value: David Hafler

value: multiple sclerosis

value: ENCBS595ZYR at ENCODE; https://www.encodeproject.org/ENCBS595ZYR/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: ACTD DNA-DNA SPRITE 15

value: Female ES cells

value: DNA-DNA SPRITE

value: 4hr Actinomycin D or DMSO


title: DNase-seq from posterior cingulate gyrus (ENCLB049FCU)

description:
https://www.encodeproject.org/experiments/ENCSR822GDF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR822GDF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB049FCU

source_name: Homo sapiens female adult (90 or above years) posterior cingulate gyrus tissue

value: posterior cingulate gyrus

value: tissue

value: female

value: adult

value: 90 or above year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Rush University

value: ENCBS277QGW at ENCODE; https://www.encodeproject.org/ENCBS277QGW/

value: Derived from ENCODE donor ENCDO101GPB; https://www.encodeproject.org/ENCDO101GPB/


title: ACTD DNA-DNA SPRITE 14


title: Sample_1721-uninfected

description: Humanized mouse

source_name: homogenized lung tissue from humanized MISTRG6 mice

tag: strain

value: MISTRG6 in Balb/c

tag: tissue

value: Lung

tag: genotype

value: MCSF(h/h),IL/GMCSF(h/h),THPO(h/h), SIRP(h/m), Rag2-/-IL2rg-/- IL6(h/h) (h=human; m=mouse)


title: ACTD DNA-DNA SPRITE 10

tag: cell line

tag: cell type

tag: protocol


title: Patient345

value: colorectal cancer (CRC) patient

value: FOLFOX

tag: overall survival (days)

tag: disease status

value: NED


title: Patient346

tag: subject status

tag: clinical stage

value: DOD


title: ACTD DNA-DNA SPRITE 09

value: Female ES cells

value: DNA-DNA SPRITE

tag: treatment

value: 4hr Actinomycin D or DMSO


title: Patient344

tag: recurrence

tag: disease free survival (days)

tag: death


title: Patient343

value: ChemoRT (5FU)


title: BruUV-seq from PC-9 (ENCLB500ZFB)

description:
https://www.encodeproject.org/experiments/ENCSR794QYB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR794QYB
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR223GHJ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB500ZFB
size range: 400-500

source_name: Homo sapiens PC-9 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: unknown

tag: age

value: Mats Ljungman, UMichigan

value: Sigma

tag: link

value: ENCBS071KQL at ENCODE; https://www.encodeproject.org/ENCBS071KQL/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: ATAC-seq from WTC11 (ENCLB715JYV)

description:
https://www.encodeproject.org/experiments/ENCSR541KFY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR541KFY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB715JYV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens WTC11 cell line

value: male

value: adult

value: 30 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yin Shen

value: ENCBS503FBI at ENCODE; https://www.encodeproject.org/ENCBS503FBI/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: ACTD DNA-DNA SPRITE 08

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: DNA-DNA SPRITE


title: ACTD DNA-DNA SPRITE 07

value: 4hr Actinomycin D or DMSO


title: BruUV-seq from PC-9 (ENCLB146TRE)

description:
https://www.encodeproject.org/experiments/ENCSR794QYB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR794QYB
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR223GHJ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB146TRE
size range: 400-500

value: cell line

value: ENCBS838HHQ at ENCODE; https://www.encodeproject.org/ENCBS838HHQ/


title: ATAC-seq from HCT116 (ENCLB131TIF)

description:
https://www.encodeproject.org/experiments/ENCSR998BBI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR998BBI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB131TIF
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: health state

value: colorectal carcinoma

value: ENCBS389MAM at ENCODE; https://www.encodeproject.org/ENCBS389MAM/

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


title: Patient342

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: overall survival (days)

tag: disease status

value: NED


title: ACTD DNA-DNA SPRITE 06

tag: treatment


title: DNase-seq from endothelial cell (ENCLB571ADE)

description:
https://www.encodeproject.org/experiments/ENCSR541IET/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR541IET
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB571ADE

source_name: Homo sapiens male adult (53 years) endothelial in vitro differentiated cells

value: endothelial cell

value: in vitro differentiated cells

tag: biosample encode accession

value: male

value: adult

value: 53 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS080VXQ at ENCODE; https://www.encodeproject.org/ENCBS080VXQ/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: DNase-seq from endothelial cell (ENCLB531PZG)

description:
https://www.encodeproject.org/experiments/ENCSR541IET/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541IET
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB531PZG

tag: Sex

value: ENCBS280HOU at ENCODE; https://www.encodeproject.org/ENCBS280HOU/


title: ATAC-seq from B cell (ENCLB998GZP)

description:
https://www.encodeproject.org/experiments/ENCSR603LVR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR603LVR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB998GZP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (22 years) B primary cell

value: B cell

value: primary cell

tag: dev stage

value: 22 year

value: Yijun Ruan, JAX

value: ENCBS832LJF at ENCODE; https://www.encodeproject.org/ENCBS832LJF/

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