title: ATAC-seq from motor neuron (ENCLB857RZX)

description:
https://www.encodeproject.org/experiments/ENCSR709QRD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR709QRD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB857RZX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: female

value: Michael Snyder, Stanford

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

value: Healthy donor

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

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


title: TF ChIP-seq from HepG2 (ENCLB546VHZ)

status: Public on Nov 04 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR756CJS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR756CJS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR356LLA
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB546VHZ
fragmentation methods: sonication (generic)

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF850

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

tag: health state

value: hepatocellular carcinoma

tag: link

value: ENCBS469GQH at ENCODE; https://www.encodeproject.org/ENCBS469GQH/

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


title: polyA plus RNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB133RPW)

description:
https://www.encodeproject.org/experiments/ENCSR266LHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR266LHQ
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB133RPW
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell, 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

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS802GRA at ENCODE; https://www.encodeproject.org/ENCBS802GRA/

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


title: RNA-DNA SPRITE 122

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

institute: Princeton University

description:
RNA and 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
HL522DSXX.all.20190924.clusters.gz

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.
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 Ensembl GRCm38 v95 gene model annotation 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.
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). Data generated in F1 hybrid cells (pSM33: C57BL/6 × 129SV-Jae or pSM44: 129 × castaneous) were assigned the allele of origin using SNPsplit v0.3.4. RepeatMasker defined regions with milliDev <= 140 along with blacklisted v2 regions were filtered out using Bedtools v2.29.0.
RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. MultiQC v1.6 was used to aggregate all reports.
Genome_build: mm10
Supplementary_files_format_and_content: RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. Each cluster, containing all reads with a shared series of tags, occupies one line of the resulting text file and contains the barcode name and genomic alignments.

organism: Mus musculus

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).

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 120


title: RNA-DNA SPRITE 121


title: Patient23_234

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

value: Yes, unknown type

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: DOD


title: Patient25_193

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

value: NED


title: BruUV-seq from Panc1 (ENCLB278IYP)

description:
https://www.encodeproject.org/experiments/ENCSR571PAZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR571PAZ
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR639ZOU
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB278IYP
size range: 400-500

source_name: Homo sapiens Panc1 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

value: pancreatic carcinoma

tag: dev stage

value: adult

tag: age

value: 56 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS730FTG at ENCODE; https://www.encodeproject.org/ENCBS730FTG/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/


title: RNA-DNA SPRITE 119


title: BruUV-seq from Panc1 (ENCLB108RES)

description:
https://www.encodeproject.org/experiments/ENCSR571PAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR571PAZ
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR639ZOU
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB108RES
size range: 400-500

tag: lab

tag: source

tag: health state

tag: link

value: ENCBS051QRV at ENCODE; https://www.encodeproject.org/ENCBS051QRV/


title: ATAC-seq from activated naive B cell (ENCLB942SAU)

description:
https://www.encodeproject.org/experiments/ENCSR653VSR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR653VSR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB942SAU
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: activated naive B cell

value: primary cell

value: female

value: 39 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS197VUB at ENCODE; https://www.encodeproject.org/ENCBS197VUB/

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


title: RNA-DNA SPRITE 118

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: Patient24_336

scan_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: Xeloda

tag: recurrence

tag: disease free survival (days)

value: AWD


title: RNA-DNA SPRITE 117


title: ATAC-seq from activated naive B cell (ENCLB653MLT)

description:
https://www.encodeproject.org/experiments/ENCSR653VSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR653VSR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB653MLT
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: adult

value: ENCBS255HZX at ENCODE; https://www.encodeproject.org/ENCBS255HZX/


title: Patient21_232

value: No

tag: death

tag: overall survival (days)

tag: disease status

value: DOD


title: Patient18_550


title: RNA-DNA SPRITE 116


title: RNA-DNA SPRITE 115


title: Patient19_147

value: Unknown


title: polyA plus RNA-seq from CD8-positive, alpha-beta memory T cell (ENCLB258DEM)

description:
https://www.encodeproject.org/experiments/ENCSR338WIW/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD8-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR338WIW
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB258DEM
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

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

value: primary cell

tag: description

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

tag: biosample encode accession

tag: Sex

value: not collected

value: healthy

tag: dev stage

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS274KKV at ENCODE; https://www.encodeproject.org/ENCBS274KKV/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Patient15_333

value: colorectal cancer (CRC) patient

value: ChemoRT (5FU)


title: Patient20_275


title: polyA plus RNA-seq from CD14-positive monocyte (ENCLB216JFL)

description:
https://www.encodeproject.org/experiments/ENCSR264LON/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD14-positive monocyte with multiple sclerosis.
experiment encode accession: ENCSR264LON
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB216JFL
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: Monocyte CD3- CD14+ CD19-

tag: health state

value: multiple sclerosis

tag: age

tag: lab

tag: source

value: ENCBS080GJD at ENCODE; https://www.encodeproject.org/ENCBS080GJD/

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


title: Patient22_326

value: No

value: DOD


title: Patient14_133

value: FOLFOX


title: Patient17_281

value: NED


title: ATAC-seq from T-cell (ENCLB486DVK)

description:
https://www.encodeproject.org/experiments/ENCSR258RSH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR258RSH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB486DVK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: T-cell

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS995ZBK at ENCODE; https://www.encodeproject.org/ENCBS995ZBK/

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


title: ATAC-seq from HCT116 (ENCLB441CJJ)

description:
https://www.encodeproject.org/experiments/ENCSR445VYQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR445VYQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB441CJJ
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 POLR2A

tag: line

value: cell line

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: colorectal carcinoma

value: ENCBS089MRW at ENCODE; https://www.encodeproject.org/ENCBS089MRW/

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


title: DNase-seq from brain (ENCLB196KIF)

description:
https://www.encodeproject.org/experiments/ENCSR049SVH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR049SVH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB196KIF
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens male adult (53 years) brain organoid, 180 days post differentiation, preserved by cryopreservation

value: brain

value: organoid

value: PGP1 derived brain organoid 180 days

value: 53 year

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS871LYY at ENCODE; https://www.encodeproject.org/ENCBS871LYY/

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


title: RNA-DNA SPRITE 113

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: Histone ChIP-seq from motor neuron (ENCLB574SMO)

description:
https://www.encodeproject.org/experiments/ENCSR754DRC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR754DRC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR124KQG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB574SMO
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: male

value: adult

value: 47 year

value: Michael Snyder, Stanford

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

value: Donor with Amyotrophic Lateral Sclerosis

value: ENCBS238JUI at ENCODE; https://www.encodeproject.org/ENCBS238JUI/

value: Derived from ENCODE donor ENCDO565NIZ; https://www.encodeproject.org/ENCDO565NIZ/


title: Histone ChIP-seq from motor neuron (ENCLB800UES)

description:
https://www.encodeproject.org/experiments/ENCSR754DRC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR754DRC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR124KQG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB800UES
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ENCBS038RNY at ENCODE; https://www.encodeproject.org/ENCBS038RNY/


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB581WOB)

description:
https://www.encodeproject.org/experiments/ENCSR042SVA/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD4-positive, alpha-beta T cell with multiple sclerosis.
experiment encode accession: ENCSR042SVA
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB581WOB
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS321BAK at ENCODE; https://www.encodeproject.org/ENCBS321BAK/

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


title: RNA-DNA SPRITE 112

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 114


title: ATAC-seq from HCT116 (ENCLB199GXO)

description:
https://www.encodeproject.org/experiments/ENCSR445VYQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR445VYQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB199GXO
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: cell line

value: male

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: colorectal carcinoma

value: ENCBS084QBE at ENCODE; https://www.encodeproject.org/ENCBS084QBE/

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


title: Patient12_194

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

value: NED


title: polyA plus RNA-seq from immature natural killer cell (ENCLB789KZR)

description:
https://www.encodeproject.org/experiments/ENCSR039JPA/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of immature natural killer cell with multiple sclerosis.
experiment encode accession: ENCSR039JPA
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB789KZR
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: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: multiple sclerosis

tag: dev stage

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS911UEN at ENCODE; https://www.encodeproject.org/ENCBS911UEN/

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


title: DNase-seq from head of caudate nucleus (ENCLB580MJB)

description:
https://www.encodeproject.org/experiments/ENCSR862SQC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR862SQC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB580MJB
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Homo sapiens male adult (84 years) head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

value: male

value: adult

tag: age

value: 84 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Rush University

tag: link

value: ENCBS046TKS at ENCODE; https://www.encodeproject.org/ENCBS046TKS/

value: Derived from ENCODE donor ENCDO999WDR; https://www.encodeproject.org/ENCDO999WDR/


title: RNA-DNA SPRITE 111

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: ATAC-seq from motor neuron (ENCLB613AAP)

description:
https://www.encodeproject.org/experiments/ENCSR709QRD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR709QRD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB613AAP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: female

value: Healthy donor

value: unknown

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: RNA-DNA SPRITE 110

description:
RNA and 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
HL522DSXX.all.20190924.clusters.gz


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB804TXW)

description:
https://www.encodeproject.org/experiments/ENCSR038QZA/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD4-positive, alpha-beta T cell with multiple sclerosis.
experiment encode accession: ENCSR038QZA
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB804TXW
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell with multiple sclerosis

value: primary cell

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

value: not collected

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS040CMJ at ENCODE; https://www.encodeproject.org/ENCBS040CMJ/

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


title: Patient272

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: FOLFOX

tag: recurrence

tag: disease status

value: NED


title: RNA-DNA SPRITE 109

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: Histone ChIP-seq from motor neuron (ENCLB246HMJ)

description:
https://www.encodeproject.org/experiments/ENCSR571HAY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR571HAY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR201VAH
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB246HMJ
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

value: male

value: adult

value: 47 year

value: Michael Snyder, Stanford

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

value: Donor with Amyotrophic Lateral Sclerosis

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

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


title: TF ChIP-seq from SK-N-SH (ENCLB792ISQ)

description:
https://www.encodeproject.org/experiments/ENCSR036THH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-BACH2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR036THH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR456LEZ, ENCSR072QAK
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB792ISQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens BACH2 treated with 6 μM all-trans-retinoic acid for 48 hours

tag: line

value: SK-N-SH

value: cell line

tag: biosample encode accession

tag: Sex

value: female

value: child

value: 4 year

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: Metastatic neuroblastoma from bone marrow

value: ENCBS130REU at ENCODE; https://www.encodeproject.org/ENCBS130REU/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: Histone ChIP-seq from motor neuron (ENCLB251LOT)

description:
https://www.encodeproject.org/experiments/ENCSR571HAY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR571HAY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR201VAH
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB251LOT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: male

tag: dev stage

value: adult

tag: age

tag: lab

tag: health state

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


title: RNA-DNA SPRITE 108

tag: cell line

tag: cell type

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: TF ChIP-seq from SK-N-SH (ENCLB689YRS)

description:
https://www.encodeproject.org/experiments/ENCSR036THH/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-BACH2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR036THH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR456LEZ, ENCSR072QAK
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB689YRS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: SK-N-SH

value: cell line

value: female

value: Michael Snyder, Stanford

tag: source

tag: link

value: ENCBS649WQR at ENCODE; https://www.encodeproject.org/ENCBS649WQR/


title: RNA-DNA SPRITE 107

tag: protocol

tag: treatment


title: Patient238

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: NED


title: DNase-seq from head of caudate nucleus (ENCLB032GPJ)

description:
https://www.encodeproject.org/experiments/ENCSR233DFT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR233DFT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB032GPJ
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens male adult (83 years) head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

tag: biosample encode accession

tag: Sex

tag: dev stage

value: 83 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS181WVI at ENCODE; https://www.encodeproject.org/ENCBS181WVI/

value: Derived from ENCODE donor ENCDO592ZWW; https://www.encodeproject.org/ENCDO592ZWW/


title: Bru-seq from MCF 10A (ENCLB721BAN)

description:
https://www.encodeproject.org/experiments/ENCSR444JTC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR444JTC
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB721BAN
size range: 400-500

source_name: Homo sapiens MCF 10A cell line

tag: line

value: MCF 10A

value: adult

tag: age

value: 36 year

tag: lab

value: Mats Ljungman, UMichigan

value: ATCC

tag: health state

value: fibrocystic disease

value: ENCBS258MZF at ENCODE; https://www.encodeproject.org/ENCBS258MZF/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: Patient231

value: colorectal cancer (CRC) patient

value: ChemoRT (5FU)


title: RNA-DNA SPRITE 106

source_name: Mouse Embryonic Stem cells

tag: cell line

tag: cell type

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: Patient283

source_name: Human Colorectal cancer tissue

value: FOLFOX

value: NED


title: Bru-seq from MCF 10A (ENCLB162GNS)

description:
https://www.encodeproject.org/experiments/ENCSR444JTC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR444JTC
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB162GNS
size range: 400-500

value: cell line

value: female

tag: source

tag: link

value: ENCBS398OEY at ENCODE; https://www.encodeproject.org/ENCBS398OEY/


title: DNase-seq from posterior cingulate gyrus (ENCLB006XLQ)

description:
https://www.encodeproject.org/experiments/ENCSR709PZI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR709PZI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB006XLQ

source_name: Homo sapiens female adult (88 years) with Alzheimer's disease; posterior cingulate gyrus tissue

value: posterior cingulate gyrus

value: tissue

value: adult

value: 88 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS723SKE at ENCODE; https://www.encodeproject.org/ENCBS723SKE/

value: Derived from ENCODE donor ENCDO070VNS; https://www.encodeproject.org/ENCDO070VNS/


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB508DSM)

description:
https://www.encodeproject.org/experiments/ENCSR445QDZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR445QDZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB508DSM

source_name: Homo sapiens male adult (36 years) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: male

value: 36 year

value: StemExpress

value: ENCBS393QBE at ENCODE; https://www.encodeproject.org/ENCBS393QBE/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: Patient216

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: ChemoRT (5FU)

value: DOC


title: Patient218

tag: recurrence

tag: disease free survival (days)

value: NED


title: Patient230

tag: death

tag: overall survival (days)


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB181JKP)

description:
https://www.encodeproject.org/experiments/ENCSR159UIB/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD8-positive, alpha-beta T cell with multiple sclerosis.
experiment encode accession: ENCSR159UIB
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB181JKP
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell with multiple sclerosis

tag: description

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

tag: biosample encode accession

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS771DND at ENCODE; https://www.encodeproject.org/ENCBS771DND/

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


title: RNA-DNA SPRITE 104

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: DNase-seq from head of caudate nucleus (ENCLB992YIA)

description:
https://www.encodeproject.org/experiments/ENCSR161ZGA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR161ZGA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB992YIA
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: head of caudate nucleus

value: tissue

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS279JIS at ENCODE; https://www.encodeproject.org/ENCBS279JIS/

value: Derived from ENCODE donor ENCDO754RFQ; https://www.encodeproject.org/ENCDO754RFQ/


title: TF ChIP-seq from HepG2 (ENCLB238DYC)

description:
https://www.encodeproject.org/experiments/ENCSR707WZK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR707WZK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR479INP
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB238DYC
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NCOA1

tag: antibody

tag: line

value: cell line

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

tag: lab

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS842JRL at ENCODE; https://www.encodeproject.org/ENCBS842JRL/

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


title: Patient214

tag: subject status

value: colorectal cancer (CRC) patient

tag: disease status

value: NED


title: TF ChIP-seq from HepG2 (ENCLB885PNV)

description:
https://www.encodeproject.org/experiments/ENCSR707WZK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR707WZK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR479INP
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB885PNV
fragmentation methods: sonication (generic)

tag: source

tag: link

value: ENCBS305WNM at ENCODE; https://www.encodeproject.org/ENCBS305WNM/


title: RNA-DNA SPRITE 103

tag: cell line

tag: cell type

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: ATAC-seq from natural killer cell (ENCLB842MIY)

description:
https://www.encodeproject.org/experiments/ENCSR854TTM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR854TTM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB842MIY
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (47 years) natural killer primary cell

value: natural killer cell

value: primary cell

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS734IHH at ENCODE; https://www.encodeproject.org/ENCBS734IHH/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: RNA-DNA SPRITE 105


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB309FPY)

description:
https://www.encodeproject.org/experiments/ENCSR152BBF/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD8-positive, alpha-beta T cell.
experiment encode accession: ENCSR152BBF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB309FPY
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell, preserved by cryopreservation

tag: description

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS044FCF at ENCODE; https://www.encodeproject.org/ENCBS044FCF/

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


title: Patient213

value: colorectal cancer (CRC) patient

tag: clinical stage

value: No

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

value: DOC


title: Patient208

value: DOD


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB721TDX)

description:
https://www.encodeproject.org/experiments/ENCSR230KVL/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD8-positive, alpha-beta T cell.
experiment encode accession: ENCSR230KVL
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-10-12
lab: David Hafler, Yale
library encode accession: ENCLB721TDX
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell

value: primary cell

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

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: age

value: ENCBS135XFB at ENCODE; https://www.encodeproject.org/ENCBS135XFB/

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


title: ATAC-seq from natural killer cell (ENCLB662OAK)

description:
https://www.encodeproject.org/experiments/ENCSR854TTM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR854TTM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB662OAK
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: natural killer cell

value: male

value: adult

value: 47 year

tag: lab

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS282OCK at ENCODE; https://www.encodeproject.org/ENCBS282OCK/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: ATAC-seq from motor neuron (ENCLB231UBZ)

description:
https://www.encodeproject.org/experiments/ENCSR704VZY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR704VZY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB231UBZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male child (6 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: child

value: 6 year

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

tag: health state

value: Healthy donor

value: ENCBS409BIE at ENCODE; https://www.encodeproject.org/ENCBS409BIE/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: RNA-DNA SPRITE 101

description:
RNA and 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
HL522DSXX.all.20190924.clusters.gz

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: TF ChIP-seq from SK-N-SH (ENCLB842FWM)

description:
https://www.encodeproject.org/experiments/ENCSR219GUP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZC3H10 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR219GUP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR411BTN, ENCSR209FGM
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB842FWM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZC3H10 treated with 6 uM all-trans-retinoic acid for 48 hours

tag: antibody

tag: line

value: SK-N-SH

value: cell line

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 year

tag: source

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

tag: link

value: ENCBS735PWL at ENCODE; https://www.encodeproject.org/ENCBS735PWL/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: RNA-DNA SPRITE 100

tag: cell line

tag: cell type


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB892OQK)

description:
https://www.encodeproject.org/experiments/ENCSR167NUS/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD8-positive, alpha-beta T cell.
experiment encode accession: ENCSR167NUS
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB892OQK
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

value: primary cell

tag: description

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS872QPK at ENCODE; https://www.encodeproject.org/ENCBS872QPK/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: RNA-DNA SPRITE 099

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 098


title: TF ChIP-seq from SK-N-SH (ENCLB347QTW)

description:
https://www.encodeproject.org/experiments/ENCSR219GUP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZC3H10 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR219GUP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR411BTN, ENCSR209FGM
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB347QTW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZC3H10 treated with 6 μM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: cell line

value: female

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Metastatic neuroblastoma from bone marrow

value: ENCBS557DZR at ENCODE; https://www.encodeproject.org/ENCBS557DZR/


title: ATAC-seq from motor neuron (ENCLB730OXX)

description:
https://www.encodeproject.org/experiments/ENCSR704VZY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR704VZY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB730OXX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: male

value: 6 year

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

value: Healthy donor

value: ENCBS182GDQ at ENCODE; https://www.encodeproject.org/ENCBS182GDQ/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB031XFT)

description:
https://www.encodeproject.org/experiments/ENCSR703VGI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR703VGI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB031XFT

source_name: Homo sapiens male adult (33 years) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS689LKA at ENCODE; https://www.encodeproject.org/ENCBS689LKA/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: Patient167

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: Patient203

value: FOLFOX, 5FU/RT

value: NED


title: DNase-seq from head of caudate nucleus (ENCLB527DHK)

description:
https://www.encodeproject.org/experiments/ENCSR010SZN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR010SZN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB527DHK
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

tag: age

value: 90 or above year

tag: lab

value: Rush University

value: ENCBS215MDS at ENCODE; https://www.encodeproject.org/ENCBS215MDS/

value: Derived from ENCODE donor ENCDO093CLS; https://www.encodeproject.org/ENCDO093CLS/


title: Histone ChIP-seq from motor neuron (ENCLB347SQJ)

description:
https://www.encodeproject.org/experiments/ENCSR564EFE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR564EFE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR124KQG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB347SQJ
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: male

value: adult

value: 47 year

value: Michael Snyder, Stanford

tag: source

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

tag: health state

value: Donor with Amyotrophic Lateral Sclerosis

value: ENCBS238JUI at ENCODE; https://www.encodeproject.org/ENCBS238JUI/

value: Derived from ENCODE donor ENCDO565NIZ; https://www.encodeproject.org/ENCDO565NIZ/


title: RNA-DNA SPRITE 102

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: polyA plus RNA-seq from CD8-positive, alpha-beta memory T cell (ENCLB104NYU)

description:
https://www.encodeproject.org/experiments/ENCSR007OKF/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD8-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR007OKF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB104NYU
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

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

value: primary cell

tag: description

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

tag: link

value: ENCBS235RVH at ENCODE; https://www.encodeproject.org/ENCBS235RVH/

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


title: RNA-DNA SPRITE 097

source_name: Mouse Embryonic Stem cells


title: Histone ChIP-seq from motor neuron (ENCLB009SXC)

description:
https://www.encodeproject.org/experiments/ENCSR564EFE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR564EFE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR124KQG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB009SXC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: male

value: adult

value: 47 year

value: Michael Snyder, Stanford

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

value: ENCBS038RNY at ENCODE; https://www.encodeproject.org/ENCBS038RNY/


title: RNA-DNA SPRITE 095

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 096


title: ATAC-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB993RAZ)

description:
https://www.encodeproject.org/experiments/ENCSR637OPZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR637OPZ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB993RAZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (36 years) activated CD8-positive, naive alpha-beta T primary cell

value: primary cell

value: 36 year

value: StemExpress

value: ENCBS006TYP at ENCODE; https://www.encodeproject.org/ENCBS006TYP/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: polyA plus RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB042TJR)

description:
https://www.encodeproject.org/experiments/ENCSR214NBT/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, CD25-positive, alpha-beta regulatory T cell.
experiment encode accession: ENCSR214NBT
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB042TJR
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS681GZX at ENCODE; https://www.encodeproject.org/ENCBS681GZX/

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


title: Patient168

source_name: Human Colorectal cancer tissue

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: FOLFOX/bev

tag: recurrence

tag: disease free survival (days)

tag: death

value: NED


title: ATAC-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB578TCJ)

description:
https://www.encodeproject.org/experiments/ENCSR637OPZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR637OPZ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB578TCJ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: Michael Snyder, Stanford

value: ENCBS780KMU at ENCODE; https://www.encodeproject.org/ENCBS780KMU/


title: Patient166

value: ChemoRT

tag: overall survival (days)

tag: disease status


title: RNA-DNA SPRITE 094

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 093


title: Patient155

value: No


title: DNase-seq from head of caudate nucleus (ENCLB332LRI)

description:
https://www.encodeproject.org/experiments/ENCSR002IHL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR002IHL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB332LRI

source_name: Homo sapiens male adult (83 years) head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

tag: age

value: 83 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Rush University

value: ENCBS138ZUG at ENCODE; https://www.encodeproject.org/ENCBS138ZUG/

value: Derived from ENCODE donor ENCDO161NAR; https://www.encodeproject.org/ENCDO161NAR/


title: Patient142

value: colorectal cancer (CRC) patient

value: NED


title: Histone ChIP-seq from motor neuron (ENCLB036RFS)

description:
https://www.encodeproject.org/experiments/ENCSR698HPK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR698HPK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR255MIG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB036RFS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (55 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: male

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: Histone ChIP-seq from motor neuron (ENCLB014GJW)

description:
https://www.encodeproject.org/experiments/ENCSR698HPK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR698HPK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR255MIG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB014GJW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: description

value: Michael Snyder, Stanford

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


title: Patient122

value: FOLFOX

value: DOC


title: DNase-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB652PEX)

description:
https://www.encodeproject.org/experiments/ENCSR114XWV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR114XWV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB652PEX

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, 100 ng/mL Interleukin-15 for 24 hours

value: primary cell

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; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:24; duration_units:hour;

tag: link

value: ENCBS442TID at ENCODE; https://www.encodeproject.org/ENCBS442TID/

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


title: RNA-DNA SPRITE 092

description:
RNA and 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
HL522DSXX.all.20190924.clusters.gz

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: Patient121

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

value: NED


title: DNase-seq from central memory CD8-positive, alpha-beta T cell (ENCLB364RVS)

description:
https://www.encodeproject.org/experiments/ENCSR560UTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR560UTV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB364RVS

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

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 33 year

value: StemExpress

value: ENCBS566MSX at ENCODE; https://www.encodeproject.org/ENCBS566MSX/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: RNA-DNA SPRITE 091


title: RNA-DNA SPRITE 090


title: radioresistant, 18

city: Changzhou

first: You

last: Zhou

state: Jiangsu

address: Juqian Rd No.185

country: China

institute: The Third Affiliated Hospital of Soochow University

description:
Expression_lncRNA.txt
All_Differentially_Expressed_lncRNAs.txt

data_processing:
Solexa pipeline version 1.8 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using Hisat2 with default parameters.
Fragments Per Kilobase of gene/transcript model per Million mapped reads (FPKM) were calculated using Ballgown. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CRC

extract_protocol:
Total RNA was extracted using Trizol reagent. Illumina KAPA Stranded RNA-Seq Library Prep Kit was used with 1 ug of purified RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: CRC

tag: phenotype

value: radioresistant


title: Patient289

tag: overall survival (days)

tag: disease status

value: DOD


title: Patient157

value: No


title: radioresistant, 17


title: Patient239


title: Patient552


title: Patient236


title: Patient235


title: ATAC-seq from activated T-cell (ENCLB853RXW)

description:
https://www.encodeproject.org/experiments/ENCSR558ZSN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR558ZSN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB853RXW
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (21 years) activated T-cell primary cell

value: activated T-cell

value: primary cell

value: female

value: 21 year

tag: lab

value: Michael Snyder, Stanford

tag: source

tag: link

value: ENCBS595NCI at ENCODE; https://www.encodeproject.org/ENCBS595NCI/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: Patient233

value: colorectal cancer (CRC) patient


title: radiosensitive, 16

value: radiosensitive


title: RNA-DNA SPRITE 089

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: ATAC-seq from motor neuron (ENCLB663GMQ)

description:
https://www.encodeproject.org/experiments/ENCSR634WYX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR634WYX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB663GMQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

value: male

value: adult

value: 47 year

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

tag: health state

value: Donor with Amyotrophic Lateral Sclerosis

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

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


title: radioresistant, 14

value: CRC

value: radioresistant


title: radiosensitive, 15


title: RNA-DNA SPRITE 086


title: Patient228_2

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

value: DOD


title: ATAC-seq from motor neuron (ENCLB252NND)

description:
https://www.encodeproject.org/experiments/ENCSR634WYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR634WYX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB252NND
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: age

value: Michael Snyder, Stanford

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


title: RNA-DNA SPRITE 087

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: Control ChIP-seq from K562 (ENCLB029CWQ)

description:
https://www.encodeproject.org/experiments/ENCSR758JMV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR758JMV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-22
lab: Richard Myers, HAIB
library encode accession: ENCLB029CWQ
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

value: female

value: 53 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

value: chronic myelogenous leukemia (CML)

value: ENCBS044YQM at ENCODE; https://www.encodeproject.org/ENCBS044YQM/

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


title: Patient226

tag: overall survival (days)

tag: disease status


title: RNA-DNA SPRITE 085

tag: cell line

tag: cell type

tag: protocol

tag: treatment


title: BruUV-seq from HepG2 (ENCLB941AFB)

description:
https://www.encodeproject.org/experiments/ENCSR555WGR/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR555WGR
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR974AQD
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB941AFB
size range: 400-500

source_name: Homo sapiens HepG2 cell line

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

tag: link

value: ENCBS989VRY at ENCODE; https://www.encodeproject.org/ENCBS989VRY/

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


title: ATAC-seq from activated T-cell (ENCLB543VOL)

description:
https://www.encodeproject.org/experiments/ENCSR558ZSN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR558ZSN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB543VOL
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: activated T-cell

value: primary cell

value: adult

value: 21 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS935VDH at ENCODE; https://www.encodeproject.org/ENCBS935VDH/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: radiosensitive, 11

tag: tissue

value: CRC

tag: phenotype

value: radiosensitive


title: BruUV-seq from HepG2 (ENCLB906SWG)

description:
https://www.encodeproject.org/experiments/ENCSR555WGR/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR555WGR
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR974AQD
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB906SWG
size range: 400-500

value: cell line

tag: biosample encode accession

value: male

value: hepatocellular carcinoma

value: ENCBS768FMB at ENCODE; https://www.encodeproject.org/ENCBS768FMB/


title: radiosensitive, 10


title: RNA-DNA SPRITE 084

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 088


title: BruUV-seq from mammary epithelial cell (ENCLB709CJD)

description:
https://www.encodeproject.org/experiments/ENCSR552JIG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR552JIG
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR419IWZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB709CJD
size range: 400-500

source_name: Homo sapiens female mammary epithelial primary cell

value: mammary epithelial cell

tag: Sex

value: female

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS489GRO at ENCODE; https://www.encodeproject.org/ENCBS489GRO/

value: Derived from ENCODE donor ENCDO343AAA; https://www.encodeproject.org/ENCDO343AAA/


title: BruUV-seq from mammary epithelial cell (ENCLB952ZLW)

description:
https://www.encodeproject.org/experiments/ENCSR552JIG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR552JIG
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR419IWZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB952ZLW
size range: 400-500

value: primary cell

tag: dev stage

value: ENCBS161KQZ at ENCODE; https://www.encodeproject.org/ENCBS161KQZ/


title: radiosensitive, 9

value: CRC

value: radiosensitive


title: RNA-DNA SPRITE 083


title: radiosensitive, 8


title: radiosensitive, 7


title: RNA-DNA SPRITE 082


title: RNA-DNA SPRITE 081


title: radioresistant, 13

value: radioresistant


title: radioresistant, 6


title: Patient217

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

value: DOD


title: RNA-DNA SPRITE 080

value: Female ES cells

value: RNA-DNA SPRITE


title: TF ChIP-seq from HepG2 (ENCLB275XQL)

description:
https://www.encodeproject.org/experiments/ENCSR618END/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR618END
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB275XQL
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF430

tag: antibody

tag: line

value: cell line

value: male

value: child

tag: age

value: 15 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS196LHJ at ENCODE; https://www.encodeproject.org/ENCBS196LHJ/

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


title: RNA-DNA SPRITE 079

tag: cell line

tag: cell type

tag: protocol

tag: treatment

value: 24hr doxycycline for Xist induction


title: TF ChIP-seq from HepG2 (ENCLB439MAV)

description:
https://www.encodeproject.org/experiments/ENCSR618END/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR618END
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB439MAV
fragmentation methods: sonication (generic)

tag: biosample encode accession

tag: health state

tag: link

value: ENCBS129IHS at ENCODE; https://www.encodeproject.org/ENCBS129IHS/


title: radioresistant, 5

tag: tissue

value: CRC

tag: phenotype


title: Patient202

tag: subject status

tag: clinical stage

value: FOLFOX

tag: recurrence

tag: overall survival (days)

tag: disease status


title: radiosensitive, 4

value: radiosensitive


title: radioresistant, 3

value: radioresistant


title: Patient196

value: colorectal cancer (CRC) patient

tag: disease free survival (days)

tag: death

value: DOD


title: Patient141


title: RNA-DNA SPRITE 078

value: Female ES cells

value: RNA-DNA SPRITE


title: Patient165

value: No


title: ATAC-seq from HCT116 (ENCLB209CMY)

description:
https://www.encodeproject.org/experiments/ENCSR441BDP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR441BDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB209CMY
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 CDK7

tag: line

value: cell line

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 48 year

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Dr. Masato Kanemaki

value: colorectal carcinoma

value: ENCBS200JDW at ENCODE; https://www.encodeproject.org/ENCBS200JDW/

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


title: Patient156

value: Unknown


title: Patient211

value: DOC


title: Patient136


title: Patient125

value: Unknown:5-FU and Leucovorin (5/1996-6/1996)


title: ATAC-seq from HCT116 (ENCLB358OTX)

description:
https://www.encodeproject.org/experiments/ENCSR441BDP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR441BDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB358OTX
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

tag: biosample encode accession

tag: health state

value: ENCBS149SOW at ENCODE; https://www.encodeproject.org/ENCBS149SOW/


title: RNA-DNA SPRITE 077

tag: cell line

tag: cell type

tag: protocol

tag: treatment

value: 24hr doxycycline for Xist induction


title: Patient114

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

value: DOD


title: RNA-DNA SPRITE 076

value: Female ES cells

value: RNA-DNA SPRITE


title: radioresistant, 1

tag: tissue

value: CRC

tag: phenotype

value: radioresistant


title: RNA-DNA SPRITE 075


title: Patient113

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status


title: TF ChIP-seq from HepG2 (ENCLB099KAU)

description:
https://www.encodeproject.org/experiments/ENCSR617CDJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR617CDJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB099KAU
fragmentation methods: sonication (generic)

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

tag: antibody

value: CENPX

tag: line

value: cell line

tag: Sex

value: male

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

tag: link

value: ENCBS310ULM at ENCODE; https://www.encodeproject.org/ENCBS310ULM/

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


title: RNA-DNA SPRITE 074

description:
RNA and 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
HL522DSXX.all.20190924.clusters.gz

tag: cell line

tag: cell type

tag: protocol

tag: treatment

value: 24hr doxycycline for Xist induction


title: TF ChIP-seq from HepG2 (ENCLB221YVB)

description:
https://www.encodeproject.org/experiments/ENCSR617CDJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR617CDJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB221YVB
fragmentation methods: sonication (generic)

tag: biosample encode accession

tag: source

tag: health state

value: ENCBS588DLI at ENCODE; https://www.encodeproject.org/ENCBS588DLI/


title: ATAC-seq from CD8-positive naive resting alpha-beta T cell (ENCLB494JEI)

description:
https://www.encodeproject.org/experiments/ENCSR614JAG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR614JAG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB494JEI
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (36 years) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: adult

value: 36 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS335DEQ at ENCODE; https://www.encodeproject.org/ENCBS335DEQ/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: total RNA-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB220GHR)

description:
https://www.encodeproject.org/experiments/ENCSR694AWV/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD4+ T cell, activated Day 2
experiment encode accession: ENCSR694AWV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB220GHR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell

tag: description

value: Memory CD4+ T cell, activated Day 2

value: male

value: 43 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS714OYB at ENCODE; https://www.encodeproject.org/ENCBS714OYB/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: RNA-DNA SPRITE 073

source_name: Mouse Embryonic Stem cells

value: Female ES cells

value: RNA-DNA SPRITE


title: Patient112

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: ChemoRT (5FU/LV)

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

value: NED


title: total RNA-seq from CD4-positive naive resting alpha-beta T cell (ENCLB664TDN)

description:
https://www.encodeproject.org/experiments/ENCSR956ZVR/
***************
biological replicate number: 1
technical replicate number: 1
description: naïve CD4+ T cell(CD45RO- RA+CCR7+)
experiment encode accession: ENCSR956ZVR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB664TDN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (43 years) CD4-positive naive resting alpha-beta T primary cell

value: primary cell

value: naïve CD4+ T cell(CD45RO- RA+CCR7+)

tag: Sex

tag: dev stage

value: adult

tag: age

value: ENCBS054ELI at ENCODE; https://www.encodeproject.org/ENCBS054ELI/


title: Patient111

source_name: Human Colorectal cancer tissue

tag: disease status


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB870PKK)

description:
https://www.encodeproject.org/experiments/ENCSR929AUK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human IgD-negative memory B cell.
experiment encode accession: ENCSR929AUK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR469VTN
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB870PKK
fragmentation methods: none

source_name: Homo sapiens IgD-negative memory B primary cell, preserved by cryopreservation

tag: antibody

value: IgD-negative memory B cell

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

value: not collected

value: healthy

value: unknown

tag: lab

value: Bradley Bernstein, Broad

value: David Hafler

tag: link

value: ENCBS677QPD at ENCODE; https://www.encodeproject.org/ENCBS677QPD/

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


title: ATAC-seq from T-helper 17 cell (ENCLB496HHR)

description:
https://www.encodeproject.org/experiments/ENCSR611BQR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR611BQR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB496HHR
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (50 years) T-helper 17 primary cell

value: T-helper 17 cell

tag: biosample encode accession

value: male

value: 50 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS550GOJ at ENCODE; https://www.encodeproject.org/ENCBS550GOJ/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: Patient93

value: colorectal cancer (CRC) patient

value: No

value: DOD


title: RNA-DNA SPRITE 072

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: ATAC-seq from T-helper 17 cell (ENCLB289ODX)

description:
https://www.encodeproject.org/experiments/ENCSR611BQR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR611BQR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB289ODX
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: primary cell

value: adult

tag: source

value: ENCBS339YKS at ENCODE; https://www.encodeproject.org/ENCBS339YKS/


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB076NHQ)

description:
https://www.encodeproject.org/experiments/ENCSR929AUK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human IgD-negative memory B cell.
experiment encode accession: ENCSR929AUK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR469VTN
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB076NHQ
fragmentation methods: none

value: IgD-negative memory B cell

tag: description

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

value: not collected

tag: health state

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS677QPD at ENCODE; https://www.encodeproject.org/ENCBS677QPD/

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


title: Patient287

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: No

tag: recurrence

tag: disease free survival (days)

tag: death

value: DOC


title: total RNA-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB356VAN)

description:
https://www.encodeproject.org/experiments/ENCSR944OIX/
***************
biological replicate number: 1
technical replicate number: 1
description: Naïve CD4+ T cell, activated Day 2
experiment encode accession: ENCSR944OIX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB356VAN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (43 years) activated CD4 positive, naive alpha-beta T primary cell

value: Naïve CD4+ T cell, activated Day 2

tag: Sex

value: male

tag: dev stage

tag: age

value: 43 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS545EHI at ENCODE; https://www.encodeproject.org/ENCBS545EHI/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: RNA-DNA SPRITE 071

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 069


title: total RNA-seq from CD8-positive naive resting alpha-beta T cell (ENCLB112KJI)

description:
https://www.encodeproject.org/experiments/ENCSR692DIM/
***************
biological replicate number: 1
technical replicate number: 1
description: naïve CD8+ T cell(CD45RO-CCR7+)
experiment encode accession: ENCSR692DIM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB112KJI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (30 years) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: naïve CD8+ T cell(CD45RO-CCR7+)

value: adult

value: 30 year

tag: lab

tag: link

value: ENCBS585VPF at ENCODE; https://www.encodeproject.org/ENCBS585VPF/

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


title: DNase-seq from activated naive B cell (ENCLB050SPS)

description:
https://www.encodeproject.org/experiments/ENCSR438LZG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR438LZG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB050SPS

source_name: Homo sapiens female adult (39 years) activated naive B primary cell treated with 10 μg/mL anti-IgM for 72 hours, 1 μg/mL anti-CD40 for 72 hours, 100 ng/mL Interleukin-4 for 72 hours

value: activated naive B cell

tag: biosample encode accession

value: female

value: 39 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS727KFR at ENCODE; https://www.encodeproject.org/ENCBS727KFR/

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


title: ATAC-seq from CD8-positive naive resting alpha-beta T cell (ENCLB064MZN)

description:
https://www.encodeproject.org/experiments/ENCSR614JAG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR614JAG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB064MZN
fragmentation methods: sonication (Bioruptor Pico)
size range: 150-1000

value: male

value: 36 year

value: Michael Snyder, Stanford

value: ENCBS051GSS at ENCODE; https://www.encodeproject.org/ENCBS051GSS/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: RNA-DNA SPRITE 068

tag: cell line

tag: cell type

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB861DRR)

description:
https://www.encodeproject.org/experiments/ENCSR925GFP/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4+ T cells, activated day 2
experiment encode accession: ENCSR925GFP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB861DRR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

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

value: ENCBS555KPW at ENCODE; https://www.encodeproject.org/ENCBS555KPW/

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


title: ATAC-seq from activated CD8-positive, alpha-beta T cell (ENCLB367YLI)

description:
https://www.encodeproject.org/experiments/ENCSR545UJP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR545UJP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB367YLI
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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 , 10 ng/mL Interleukin-2 nuclear fraction

value: 21 year

tag: source

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: ENCBS501DVY at ENCODE; https://www.encodeproject.org/ENCBS501DVY/

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


title: RNA-DNA SPRITE 067

tag: protocol

tag: treatment


title: total RNA-seq from HFFc6 (ENCLB656HIH)

description:
https://www.encodeproject.org/experiments/ENCSR841QAC/
***************
biological replicate number: 3
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 900 ng
experiment encode accession: ENCSR841QAC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB656HIH
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 900
nucleic acid starting quantity units: ng

source_name: Homo sapiens HFFc6 cell line, preserved by flash-freezing

extract_protocol:
extraction method: Animal tissue kit (Norgen Biotek cat#: 25700)
extraction protocol: https://www.encodeproject.org/documents/33482357-bcb8-43d0-ac76-d58ff785b710/@@download/attachment/Norgen_Animal-Tissue-RNA-Purification-Kit-Insert-PI25700-8-M14.pdf, general protocol: https://www.encodeproject.org/documents/01a7807d-0d18-4a4a-ac90-f4056a25a681/@@download/attachment/manualE7760_Directional_RNA_library_kit_October30_2018.pdf

tag: line

value: cell line

tag: description

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

tag: health state

value: normal

tag: passage number

value: ENCBS249LEB at ENCODE; https://www.encodeproject.org/ENCBS249LEB/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: total RNA-seq from HFFc6 (ENCLB660USF)

description:
https://www.encodeproject.org/experiments/ENCSR841QAC/
***************
biological replicate number: 2
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 900 ng
experiment encode accession: ENCSR841QAC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB660USF
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 900
nucleic acid starting quantity units: ng

tag: Sex

value: ENCBS508JLR at ENCODE; https://www.encodeproject.org/ENCBS508JLR/


title: RNA-DNA SPRITE 070

description:
RNA and 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
HL522DSXX.all.20190924.clusters.gz

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: Patient283_RDB285

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: Patient282

value: No

value: DOC


title: Patient272_RDB288

value: NED


title: Patient259


title: Patient302


title: Patient258

value: Yes (unknown type):5-FU and Leucovorin was treatment plan completed 4/2000


title: Patient266

value: FOLFOX


title: RNA-DNA SPRITE 066

tag: cell line

tag: cell type


title: RNA-DNA SPRITE 064


title: ATAC-seq from memory B cell (ENCLB617LDB)

description:
https://www.encodeproject.org/experiments/ENCSR610AQP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR610AQP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB617LDB
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: memory B cell

value: primary cell

tag: biosample encode accession

value: male

tag: dev stage

value: adult

tag: age

value: 40 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: StemExpress

tag: link

value: ENCBS053JES at ENCODE; https://www.encodeproject.org/ENCBS053JES/

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


title: TF ChIP-seq from HepG2 (ENCLB494FOF)

description:
https://www.encodeproject.org/experiments/ENCSR605KVV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR605KVV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042HRU
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB494FOF
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF251

tag: antibody

tag: line

value: cell line

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

tag: health state

value: hepatocellular carcinoma

value: ENCBS232JFB at ENCODE; https://www.encodeproject.org/ENCBS232JFB/

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


title: RNA-DNA SPRITE 065

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction