title: ACTD DNA-DNA SPRITE 05

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

value: Female ES cells

value: DNA-DNA SPRITE

value: 4hr Actinomycin D or DMSO


title: ACTD DNA-DNA SPRITE 04

status: Public on Nov 04 2021

type: SRA

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

country: USA

institute: Princeton University

library_source: genomic

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

molecule: genomic DNA

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).

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

tag: cell line

tag: cell type

tag: protocol

tag: treatment


title: polyA plus RNA-seq from IgD-negative memory B cell (ENCLB186SOM)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR678LBL/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of IgD-negative memory B cell.
experiment encode accession: ENCSR678LBL
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB186SOM
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

value: IgD-negative memory B cell

value: primary cell

tag: description

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

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: healthy

tag: dev stage

value: unknown

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

value: ENCBS793OUV at ENCODE; https://www.encodeproject.org/ENCBS793OUV/

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


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB302DAG)

description:
https://www.encodeproject.org/experiments/ENCSR596AQY/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD4-positive, alpha-beta T cell.
experiment encode accession: ENCSR596AQY
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB302DAG
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

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

value: ENCBS370LJB at ENCODE; https://www.encodeproject.org/ENCBS370LJB/

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


title: DNase-seq from T-helper 17 cell (ENCLB402TRK)

description:
https://www.encodeproject.org/experiments/ENCSR731KDL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR731KDL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB402TRK

source_name: Homo sapiens male adult (48 years) T-helper 17 primary cell

value: T-helper 17 cell

value: male

value: adult

value: 48 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS470DYX at ENCODE; https://www.encodeproject.org/ENCBS470DYX/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/


title: BruUV-seq from MCF-7 (ENCLB709JEK)

description:
https://www.encodeproject.org/experiments/ENCSR997GMY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR997GMY
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR727IHV
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB709JEK
size range: 400-500

source_name: Homo sapiens MCF-7 cell line

tag: line

value: cell line

value: female

value: 69 year

value: Mats Ljungman, UMichigan

value: ATCC

value: breast cancer (adenocarcinoma)

value: ENCBS437OSQ at ENCODE; https://www.encodeproject.org/ENCBS437OSQ/

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


title: BruUV-seq from MCF-7 (ENCLB744DEO)

description:
https://www.encodeproject.org/experiments/ENCSR997GMY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR997GMY
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR727IHV
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB744DEO
size range: 400-500

value: ENCBS684RBW at ENCODE; https://www.encodeproject.org/ENCBS684RBW/


title: ACTD DNA-DNA SPRITE 02

value: Female ES cells

value: DNA-DNA SPRITE

value: 4hr Actinomycin D or DMSO


title: ACTD DNA-DNA SPRITE 03


title: ATAC-seq from HCT116 (ENCLB786NFH)

description:
https://www.encodeproject.org/experiments/ENCSR988ITF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR988ITF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB786NFH
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 SUPT16H treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

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

value: colorectal carcinoma

value: ENCBS035RPQ at ENCODE; https://www.encodeproject.org/ENCBS035RPQ/

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


title: polyA plus RNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB274KPS)

description:
https://www.encodeproject.org/experiments/ENCSR673DJS/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, alpha-beta memory T cell with multiple sclerosis.
experiment encode accession: ENCSR673DJS
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-10-12
lab: David Hafler, Yale
library encode accession: ENCLB274KPS
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS437FZY at ENCODE; https://www.encodeproject.org/ENCBS437FZY/

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


title: ATAC-seq from HCT116 (ENCLB657WYO)

description:
https://www.encodeproject.org/experiments/ENCSR998BBI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR998BBI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB657WYO
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: cell line

value: male

value: adult

value: 48 year

value: ENCBS518VQW at ENCODE; https://www.encodeproject.org/ENCBS518VQW/


title: ACTD DNA-DNA SPRITE 01

value: Female ES cells

value: DNA-DNA SPRITE

value: 4hr Actinomycin D or DMSO


title: polyA plus RNA-seq from IgD-negative memory B cell (ENCLB083OJW)

description:
https://www.encodeproject.org/experiments/ENCSR535YOP/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of IgD-negative memory B cell with multiple sclerosis.
experiment encode accession: ENCSR535YOP
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB083OJW
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: IgD-negative memory B cell

value: primary cell

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

value: ENCBS091EUT at ENCODE; https://www.encodeproject.org/ENCBS091EUT/

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


title: ACTD RNA-DNA SPRITE 16

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
ACTD.RDSPRITE.clusters
DMSO.RDSPRITE.clusters

value: RNA-DNA SPRITE


title: DNase-seq from naive B cell (ENCLB583NNR)

description:
https://www.encodeproject.org/experiments/ENCSR480SNC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR480SNC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB583NNR

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

value: naive B cell

value: 40 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS316WCD at ENCODE; https://www.encodeproject.org/ENCBS316WCD/

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


title: Bru-seq from Caco-2 (ENCLB293DZM)

description:
https://www.encodeproject.org/experiments/ENCSR892NYB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR892NYB
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB293DZM
size range: 400-500

source_name: Homo sapiens Caco-2 cell line

value: cell line

value: male

value: adult

value: 72 year

value: Mats Ljungman, UMichigan

value: ATCC

value: colorectal adenocarcinoma

value: ENCBS285LUN at ENCODE; https://www.encodeproject.org/ENCBS285LUN/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: ACTD RNA-DNA SPRITE 15

value: Female ES cells

value: 4hr Actinomycin D or DMSO


title: Bru-seq from Caco-2 (ENCLB285JRJ)

description:
https://www.encodeproject.org/experiments/ENCSR892NYB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR892NYB
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB285JRJ
size range: 400-500

value: ENCBS568IBG at ENCODE; https://www.encodeproject.org/ENCBS568IBG/


title: ACTD RNA-DNA SPRITE 13

value: RNA-DNA SPRITE


title: ATAC-seq from HCT116 (ENCLB108MBC)

description:
https://www.encodeproject.org/experiments/ENCSR477YZA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR477YZA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB108MBC
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS956YAX at ENCODE; https://www.encodeproject.org/ENCBS956YAX/

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


title: Patient22

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: None (chemoXRT for concurrent ACC)

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: NED


title: Patient341

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

value: No

value: DOC


title: Patient340

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


title: Patient339

value: Neoadj Xeloda/RT; adj FOLFOX-->CAPOX

value: AWD


title: ACTD RNA-DNA SPRITE 12

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

tag: treatment


title: polyA plus RNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB129PWR)

description:
https://www.encodeproject.org/experiments/ENCSR588TSF/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR588TSF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB129PWR
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: healthy

tag: dev stage

value: unknown

tag: age

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS668VBU at ENCODE; https://www.encodeproject.org/ENCBS668VBU/

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


title: Patient338

tag: subject status

value: colorectal cancer (CRC) patient


title: Patient174

tag: clinical stage


title: Patient400

tag: recurrence

value: NED


title: polyA plus RNA-seq from immature natural killer cell (ENCLB564TYC)

description:
https://www.encodeproject.org/experiments/ENCSR672OYP/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of immature natural killer cell.
experiment encode accession: ENCSR672OYP
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB564TYC
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

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

tag: lab

tag: source

tag: link

value: ENCBS497KWS at ENCODE; https://www.encodeproject.org/ENCBS497KWS/


title: ATAC-seq from HCT116 (ENCLB168JEO)

description:
https://www.encodeproject.org/experiments/ENCSR477YZA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR477YZA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB168JEO
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

tag: line

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS852MNL at ENCODE; https://www.encodeproject.org/ENCBS852MNL/

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


title: ATAC-seq from HCT116 (ENCLB526INF)

description:
https://www.encodeproject.org/experiments/ENCSR780PLN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR780PLN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB526INF
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14

value: ENCBS965UXX at ENCODE; https://www.encodeproject.org/ENCBS965UXX/


title: Patient398

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status


title: Patient399


title: Patient397

value: Adjuvant Xeloda/oxaliplatin


title: Patient101

value: No

value: DOC


title: ACTD RNA-DNA SPRITE 14

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 4hr Actinomycin D or DMSO


title: ATAC-seq from HCT116 (ENCLB600TMD)

description:
https://www.encodeproject.org/experiments/ENCSR780PLN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR780PLN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB600TMD
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: health state

value: ENCBS403RYX at ENCODE; https://www.encodeproject.org/ENCBS403RYX/


title: ACTD RNA-DNA SPRITE 11


title: ACTD RNA-DNA SPRITE 09


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB612XUA)

description:
https://www.encodeproject.org/experiments/ENCSR585DJN/
***************
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: ENCSR585DJN
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB612XUA
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, preserved by cryopreservation

value: primary cell

tag: description

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

value: not collected

value: multiple sclerosis

value: unknown

tag: age

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS512HTQ at ENCODE; https://www.encodeproject.org/ENCBS512HTQ/

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


title: DNase-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB833JLZ)

description:
https://www.encodeproject.org/experiments/ENCSR892LQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR892LQT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB833JLZ

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

value: male

value: adult

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: StemExpress

value: ENCBS507ZTM at ENCODE; https://www.encodeproject.org/ENCBS507ZTM/

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


title: ACTD RNA-DNA SPRITE 08

source_name: Mouse Embryonic Stem cells

value: Female ES cells

value: RNA-DNA SPRITE

value: 4hr Actinomycin D or DMSO


title: Patient180

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: Xeloda discont./completed 5-FU/LV 2005

tag: recurrence

value: NED


title: polyA plus RNA-seq from naive B cell (ENCLB039YUP)

description:
https://www.encodeproject.org/experiments/ENCSR416UGB/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive B cell with multiple sclerosis.
experiment encode accession: ENCSR416UGB
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB039YUP
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens naive B primary cell with multiple sclerosis

value: naive B cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

tag: link

value: ENCBS049BNE at ENCODE; https://www.encodeproject.org/ENCBS049BNE/

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


title: DNase-seq from posterior cingulate gyrus (ENCLB324VJJ)

description:
https://www.encodeproject.org/experiments/ENCSR579RVI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR579RVI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB324VJJ

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

value: posterior cingulate gyrus

value: tissue

value: female

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS589FFO at ENCODE; https://www.encodeproject.org/ENCBS589FFO/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: TF ChIP-seq from HepG2 (ENCLB061XAX)

description:
https://www.encodeproject.org/experiments/ENCSR891KPP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR891KPP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615JHA
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB061XAX
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF865

tag: antibody

tag: line

value: cell line

value: male

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS532HYC at ENCODE; https://www.encodeproject.org/ENCBS532HYC/

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


title: ACTD RNA-DNA SPRITE 07

tag: cell line

tag: cell type

value: Female ES cells

value: RNA-DNA SPRITE

value: 4hr Actinomycin D or DMSO


title: ACTD RNA-DNA SPRITE 10

tag: protocol

tag: treatment


title: ATAC-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB317HRT)

description:
https://www.encodeproject.org/experiments/ENCSR477YSU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR477YSU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB317HRT
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: primary cell

tag: biosample encode accession

tag: Sex

value: adult

value: 42 year

value: AllCells

tag: treatments

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

value: ENCBS092CLB at ENCODE; https://www.encodeproject.org/ENCBS092CLB/

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


title: ATAC-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB047JPA)

description:
https://www.encodeproject.org/experiments/ENCSR983HXF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR983HXF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB047JPA
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: male

tag: dev stage

value: 30 year

value: Yijun Ruan, JAX

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: ENCBS488HSX at ENCODE; https://www.encodeproject.org/ENCBS488HSX/

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


title: TF ChIP-seq from HepG2 (ENCLB706JVT)

description:
https://www.encodeproject.org/experiments/ENCSR891KPP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR891KPP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615JHA
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB706JVT
fragmentation methods: sonication (generic)

value: cell line

tag: health state

value: hepatocellular carcinoma

value: child

tag: age

value: 15 year

tag: lab

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS847UWZ at ENCODE; https://www.encodeproject.org/ENCBS847UWZ/

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


title: Patient395

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: NED


title: Histone ChIP-seq from motor neuron (ENCLB750BMP)

description:
https://www.encodeproject.org/experiments/ENCSR778FKK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR778FKK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR744SMV
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB750BMP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

tag: antibody

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

value: female

value: Healthy donor

value: adult

value: unknown

value: Michael Snyder, Stanford

tag: source

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

tag: link

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

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


title: ACTD RNA-DNA SPRITE 05

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
ACTD.RDSPRITE.clusters
DMSO.RDSPRITE.clusters

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 4hr Actinomycin D or DMSO


title: ACTD RNA-DNA SPRITE 06


title: Patient394

tag: recurrence


title: ACTD RNA-DNA SPRITE 04


title: Patient392_2

value: DOD


title: Patient396

value: colorectal cancer (CRC) patient


title: ATAC-seq from HCT116 (ENCLB936DIX)

description:
https://www.encodeproject.org/experiments/ENCSR988ITF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR988ITF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB936DIX
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 SUPT16H treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

tag: age

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

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

tag: health state

value: colorectal carcinoma

value: ENCBS010NUS at ENCODE; https://www.encodeproject.org/ENCBS010NUS/

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


title: Patient393

tag: subject status

tag: clinical stage

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: DOC


title: ATAC-seq from activated T-cell (ENCLB809LPI)

description:
https://www.encodeproject.org/experiments/ENCSR411NFB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR411NFB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB809LPI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (33 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours

value: activated T-cell

value: primary cell

value: female

value: adult

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

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

tag: link

value: ENCBS182ROP at ENCODE; https://www.encodeproject.org/ENCBS182ROP/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: Histone ChIP-seq from motor neuron (ENCLB459GHR)

description:
https://www.encodeproject.org/experiments/ENCSR778FKK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR778FKK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR744SMV
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB459GHR
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: not collected

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: Control ChIP-seq from SK-N-SH (ENCLB869BTB)

description:
https://www.encodeproject.org/experiments/ENCSR411BTN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR411BTN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB869BTB
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

tag: line

value: SK-N-SH

value: cell line

tag: biosample encode accession

value: female

value: child

value: 4 year

value: ATCC

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: ENCBS126SRE at ENCODE; https://www.encodeproject.org/ENCBS126SRE/

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


title: ACTD RNA-DNA SPRITE 02

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 4hr Actinomycin D or DMSO


title: Patient390

tag: subject status

value: colorectal cancer (CRC) patient

tag: recurrence

value: DOD


title: DNase-seq from head of caudate nucleus (ENCLB486ZKU)

description:
https://www.encodeproject.org/experiments/ENCSR410MFU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR410MFU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB486ZKU
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens female adult (88 years) with mild cognitive impairment; head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

tag: Sex

tag: dev stage

value: adult

tag: age

value: 88 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS509GKH at ENCODE; https://www.encodeproject.org/ENCBS509GKH/

value: Derived from ENCODE donor ENCDO151OJB; https://www.encodeproject.org/ENCDO151OJB/


title: ATAC-seq from T-cell (ENCLB421APP)

description:
https://www.encodeproject.org/experiments/ENCSR977LVI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR977LVI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB421APP
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: T-cell

value: primary cell

value: female

value: 21 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS279AXJ at ENCODE; https://www.encodeproject.org/ENCBS279AXJ/

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


title: ATAC-seq from T-cell (ENCLB553GPI)

description:
https://www.encodeproject.org/experiments/ENCSR977LVI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR977LVI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB553GPI
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: ENCBS918RAZ at ENCODE; https://www.encodeproject.org/ENCBS918RAZ/


title: ACTD RNA-DNA SPRITE 01

value: Female ES cells

value: RNA-DNA SPRITE

value: 4hr Actinomycin D or DMSO


title: PBS-treated sample

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Reads were processed using 10X’s Cell Ranger version 3.0.2 using the mm10 reference genome, resulting in a filtered HDF5 file
Further processing and analysis of scRNA-Seq data were performed in R version 3.6.3 using the Seurat package version 3.2.1
Cell Ranger output was imported using the Read10X_h5. Seurat objects were created using only genes appearing in at least 3 cells. Cells were further filtered to exclude those with fewer than 1000 genes detected, more than 5000 genes detected, or more than 10 percent mitochondrial reads.
Read counts were then normalized using the SCTransform function. Data from PBS- and TNF-treated samples were then integrated using the functions SelectIntegrationFeatures (with 3000 integration features), PrepSCTIntegration, FindIntegrationAnchors, and IntegrateData.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 (.h5) files generated by CellRanger 3.0.2
Supplementary_files_format_and_content: TSV file contains cell (barcode) metadata from final processed, integrated Seurat object. Includes cluster identities and UMAP embedding coordinates

source_name: Sorted ILCs

extract_protocol:
scRNA-Seq libraries were generated from sorted ILCs (CD45+CD3epsilon-CD5-CD8alpha-ΝΚ1.1-ΤCR-gamma-delta-CD11b-CD11c-B220-CD127+) using the 10X Genomics Chromium system with 3’ version 3 chemistry
Standard Illumina/10X protocols
single cell RNAseq

tag: treaatment

value: PBS

tag: strain


title: polyA plus RNA-seq from CD8-positive, alpha-beta memory T cell (ENCLB597HUQ)

description:
https://www.encodeproject.org/experiments/ENCSR491XNW/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD8-positive, alpha-beta memory T cell with multiple sclerosis.
experiment encode accession: ENCSR491XNW
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB597HUQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

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

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

value: not collected

tag: health state

value: multiple sclerosis

value: unknown

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

value: ENCBS757PLC at ENCODE; https://www.encodeproject.org/ENCBS757PLC/

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


title: DNase-seq from head of caudate nucleus (ENCLB415DRL)

description:
https://www.encodeproject.org/experiments/ENCSR311EEL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR311EEL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB415DRL
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens female adult (90 or above years) with mild cognitive impairment; head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

value: female

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

tag: link

value: ENCBS049WJJ at ENCODE; https://www.encodeproject.org/ENCBS049WJJ/

value: Derived from ENCODE donor ENCDO471EKG; https://www.encodeproject.org/ENCDO471EKG/


title: BruUV-seq from K562 (ENCLB158QBT)

description:
https://www.encodeproject.org/experiments/ENCSR974RZE/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR974RZE
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR729WFH
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB158QBT
size range: 400-500

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

value: 53 year

value: Mats Ljungman, UMichigan

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS312GCD at ENCODE; https://www.encodeproject.org/ENCBS312GCD/

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


title: Patient389

source_name: Human Colorectal cancer tissue

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: DOD


title: TNF-treated sample

value: TNF


title: Patient388

tag: subject status


title: WT2

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

data_processing:
FASTQ files were uploaded to the sevenbridges genomics platform and processed using BD's Rhapsody Targeted Pipeline
Genome_build: mm10
Supplementary_files_format_and_content: DBEC-adjusted read counts per cell

source_name: Right brain hemisphere without cerebellum or olfactory bulb

growth_protocol: Mice were housed under standard conditions with free access to food and water.

extract_protocol:
Nine-month-old male Abi3+/+ and Abi3-/- mice were anesthetised, transcardially perfused with sterile PBS and the brain was removed. The cerebellum was removed from the right hemisphere, which was immediately finely minced on ice and transferred to a polypropylene tube containing ice-cold Accutase (Gibco, A11105-01). Tissue was incubated with rocking at 4oC for 30 minutes and then pelleted through centrifugation at 300 g for 5 minutes at 4oC. Supernatant was aspirated and samples were resuspended in ice-cold wash buffer (1X HBSS (Gibco, 14175095), 0.04% BSA (Miltenyi, 130-091-376)) and gently dissociated through pipetting. After all samples were processed, the cloudy upper suspension was transferred to a fresh tube and the remaining clumps of tissue were further dissociated using additional ice-cold wash buffer. Cell suspensions were pelleted through centrifugation at 300 g for 10 min at 4oC. The supernatant was aspirated and cells were resuspended in degassed MACS Myelin Removal Buffer (1X DPS (Gibco 14190250), 0.5% BSA (Miltenyi, 130-091-376)). Myelin removal beads (Miltenyi, 130-096-733) were added to each sample and mixed thoroughly. Samples and beads were incubated for 15 min at 4oC with rotating, washed with myelin removal buffer, then pelleted through centrifugation at 300 g for 10 min at 4oC. Supernatant was aspirated and samples were resuspended in myelin removal buffer. LS columns (Miltenyi, 130-042-401) were loaded into a QuadroMACS separator on a MACS MultiStand with Tube Rack (Miltenyi, 130-090-976 & 130-042-303 & 130-091-052). Columns were equilibrated with myelin removal buffer. Cell suspensions were loaded onto columns and myelin-depleted cell suspensions were washed through using myelin removal buffer. Cells were pelleted through centrifugation at 300 g for 5 min at 4oC. Supernatant was aspirated and cells were gently resuspended using a pipette. Cell numbers and viability were quantified using Draq7 (BD Biosciences, 564904) and Calcein-AM (BD Biosciences, 564061) staining. BD Rhapsody™ Mouse Immune Response Panel (BD, 633701 & 633753) was used for the targeted scRNA-seq library preparation. Single Cell RNA libraries were checked for quality using QuBit (ThermoFisher) and Tapestation (Agilent), then submitted to the Centre for Medical Genomics and sequenced on an Illumina NovaSeq 6000 SP (200 cycle kit) with 20% PhiX spike-in.
BD Rhapsody™ Mouse Immune Response Panel (BD, 633701 & 633753)

tag: tissue

tag: genotype

value: 9 months

value: Male


title: ATAC-seq from motor neuron (ENCLB337TLO)

description:
https://www.encodeproject.org/experiments/ENCSR459PVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR459PVP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB337TLO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iNPC-derived motor neuron

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: 55 year

value: Michael Snyder, Stanford

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

value: Healthy donor

value: ENCBS584TFX at ENCODE; https://www.encodeproject.org/ENCBS584TFX/

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


title: ACTD RNA-DNA SPRITE 03

source_name: Mouse Embryonic Stem cells

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 4hr Actinomycin D or DMSO


title: ATAC-seq from motor neuron (ENCLB885KOI)

description:
https://www.encodeproject.org/experiments/ENCSR459PVP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR459PVP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB885KOI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

tag: age

tag: lab

tag: source

tag: health state

tag: link

value: ENCBS716FYZ at ENCODE; https://www.encodeproject.org/ENCBS716FYZ/


title: WT1

value: Right brain hemisphere without cerebellum or olfactory bulb

value: 9 months


title: polyA plus RNA-seq from CD14-positive monocyte (ENCLB100NQW)

description:
https://www.encodeproject.org/experiments/ENCSR384HOK/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD14-positive monocyte.
experiment encode accession: ENCSR384HOK
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB100NQW
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS747UFJ at ENCODE; https://www.encodeproject.org/ENCBS747UFJ/

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


title: DNase-seq from head of caudate nucleus (ENCLB320RGD)

description:
https://www.encodeproject.org/experiments/ENCSR400MOP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR400MOP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB320RGD

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

value: head of caudate nucleus

value: tissue

value: male

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS882RWT at ENCODE; https://www.encodeproject.org/ENCBS882RWT/

value: Derived from ENCODE donor ENCDO921RVK; https://www.encodeproject.org/ENCDO921RVK/


title: ATAC-seq from CD4-positive naive resting alpha-beta T cell (ENCLB841VFA)

description:
https://www.encodeproject.org/experiments/ENCSR452COS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR452COS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB841VFA
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (50 years) CD4-positive naive resting alpha-beta T primary cell

value: primary cell

value: 50 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS073UMS at ENCODE; https://www.encodeproject.org/ENCBS073UMS/

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


title: KO2

value: Right brain hemisphere without cerebellum or olfactory bulb

value: 9 months

value: Male


title: ATAC-seq from T-cell (ENCLB582XNM)

description:
https://www.encodeproject.org/experiments/ENCSR299LSN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR299LSN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB582XNM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: T-cell

value: 42 year

value: AllCells

value: ENCBS555FTZ at ENCODE; https://www.encodeproject.org/ENCBS555FTZ/

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


title: ATAC-seq from CD4-positive naive resting alpha-beta T cell (ENCLB543CVA)

description:
https://www.encodeproject.org/experiments/ENCSR452COS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR452COS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB543CVA
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: male

value: adult

value: ENCBS003XXD at ENCODE; https://www.encodeproject.org/ENCBS003XXD/


title: BruUV-seq from K562 (ENCLB927XPB)

description:
https://www.encodeproject.org/experiments/ENCSR974RZE/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR974RZE
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR729WFH
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB927XPB
size range: 400-500

tag: line

value: cell line

value: female

value: 53 year

value: Mats Ljungman, UMichigan

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS217AJA at ENCODE; https://www.encodeproject.org/ENCBS217AJA/

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


title: Patient387

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: XRT, 5FU/LV

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: NED


title: polyA plus RNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB121ZHF)

description:
https://www.encodeproject.org/experiments/ENCSR296LJV/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR296LJV
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB121ZHF
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

tag: biosample encode accession

tag: Sex

value: not collected

value: healthy

tag: dev stage

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS300QBR at ENCODE; https://www.encodeproject.org/ENCBS300QBR/

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


title: Patient384

value: DOC


title: Patient383

value: AWD


title: Patient385

value: DOD


title: Patient381


title: Patient382

value: FOLFOX


title: Patient391

value: colorectal cancer (CRC) patient


title: RNA-DNA SPRITE 143

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.

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 144


title: Patient386

value: Adjuvant 5FU/LV


title: ATAC-seq from HCT116 (ENCLB412JAI)

description:
https://www.encodeproject.org/experiments/ENCSR874GXS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR874GXS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB412JAI
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 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: male

value: adult

tag: age

value: 48 year

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Dr. Masato Kanemaki

tag: treatments

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

tag: health state

value: colorectal carcinoma

tag: link

value: ENCBS361VOK at ENCODE; https://www.encodeproject.org/ENCBS361VOK/

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


title: polyA plus RNA-seq from naive B cell (ENCLB664MVX)

description:
https://www.encodeproject.org/experiments/ENCSR307FAG/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive B cell.
experiment encode accession: ENCSR307FAG
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB664MVX
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: naive B cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS644KFM at ENCODE; https://www.encodeproject.org/ENCBS644KFM/

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


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB392SZX)

description:
https://www.encodeproject.org/experiments/ENCSR211CKX/
***************
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: ENCSR211CKX
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB392SZX
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, preserved by cryopreservation

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

value: multiple sclerosis

value: ENCBS671UYD at ENCODE; https://www.encodeproject.org/ENCBS671UYD/

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


title: ATAC-seq from HCT116 (ENCLB469RNN)

description:
https://www.encodeproject.org/experiments/ENCSR874GXS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR874GXS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB469RNN
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 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS885QKO at ENCODE; https://www.encodeproject.org/ENCBS885QKO/


title: Patient379

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)

value: NED


title: Control ChIP-seq from K562 (ENCLB749AYP)

description:
https://www.encodeproject.org/experiments/ENCSR210QQQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR210QQQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB749AYP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens THAP7

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS315XIC at ENCODE; https://www.encodeproject.org/ENCBS315XIC/

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


title: Patient380

tag: disease status

value: DOD


title: TF ChIP-seq from WTC11 (ENCLB632NKU)

description:
https://www.encodeproject.org/experiments/ENCSR963EQY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR963EQY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR922EQL
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB632NKU
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NR1H2

tag: antibody

value: cell line

value: male

value: adult

tag: age

value: 30 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS638AJL at ENCODE; https://www.encodeproject.org/ENCBS638AJL/

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


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB292QNO)

description:
https://www.encodeproject.org/experiments/ENCSR108XUM/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive thymus-derived CD4-positive, alpha-beta T cell.
experiment encode accession: ENCSR108XUM
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB292QNO
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: primary cell

tag: description

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

value: not collected

value: healthy

value: unknown

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

value: ENCBS892TKW at ENCODE; https://www.encodeproject.org/ENCBS892TKW/

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


title: RNA-DNA SPRITE 141

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: TF ChIP-seq from WTC11 (ENCLB780QBJ)

description:
https://www.encodeproject.org/experiments/ENCSR963EQY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR963EQY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR922EQL
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB780QBJ
fragmentation methods: sonication (generic)

tag: line

value: cell line

value: male

value: adult

value: 30 year

tag: link

value: ENCBS951DZD at ENCODE; https://www.encodeproject.org/ENCBS951DZD/


title: RNA-DNA SPRITE 140


title: RNA-DNA SPRITE 139


title: RNA-DNA SPRITE 142


title: BruUV-seq from GM12878 (ENCLB736NYE)

description:
https://www.encodeproject.org/experiments/ENCSR872EBO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR872EBO
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR267RPG
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB736NYE
size range: 400-500

source_name: Homo sapiens GM12878 cell line

value: female

value: Mats Ljungman, UMichigan

value: Coriell

tag: health state

value: ENCBS244NXA at ENCODE; https://www.encodeproject.org/ENCBS244NXA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: Patient378

source_name: Human Colorectal cancer tissue

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)

value: NED


title: RNA-DNA SPRITE 138


title: polyA plus RNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB943KYU)

description:
https://www.encodeproject.org/experiments/ENCSR377HQQ/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, alpha-beta memory T cell with multiple sclerosis.
experiment encode accession: ENCSR377HQQ
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB943KYU
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

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

value: primary cell

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

tag: biosample encode accession

tag: Sex

value: not collected

value: multiple sclerosis

tag: dev stage

value: unknown

tag: age

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS702KJW at ENCODE; https://www.encodeproject.org/ENCBS702KJW/

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


title: BruUV-seq from GM12878 (ENCLB858GCM)

description:
https://www.encodeproject.org/experiments/ENCSR872EBO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR872EBO
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR267RPG
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB858GCM
size range: 400-500

value: cell line

value: female

value: adult

tag: lab

value: Mats Ljungman, UMichigan

tag: source

value: ENCBS153PQV at ENCODE; https://www.encodeproject.org/ENCBS153PQV/


title: DNase-seq from head of caudate nucleus (ENCLB375TZY)

description:
https://www.encodeproject.org/experiments/ENCSR373TLU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373TLU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB375TZY
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens female adult (86 years) with Alzheimer's disease; head of caudate nucleus tissue

value: head of caudate nucleus

value: tissue

value: 86 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS837FRZ at ENCODE; https://www.encodeproject.org/ENCBS837FRZ/

value: Derived from ENCODE donor ENCDO997SGX; https://www.encodeproject.org/ENCDO997SGX/


title: Patient98

value: colorectal cancer (CRC) patient

tag: disease status

value: DOC


title: BruUV-seq from Calu3 (ENCLB922QGP)

description:
https://www.encodeproject.org/experiments/ENCSR870SVX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR870SVX
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR692DCF
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB922QGP
size range: 400-500

source_name: Homo sapiens Calu3 cell line

value: male

value: 25 year

value: ATCC

value: Lung adenocarcinoma

value: ENCBS212GXM at ENCODE; https://www.encodeproject.org/ENCBS212GXM/

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


title: ATAC-seq from T-cell (ENCLB682DRL)

description:
https://www.encodeproject.org/experiments/ENCSR102RXG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR102RXG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB682DRL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: T-cell

value: primary cell

value: female

value: adult

value: 33 year

value: AllCells

value: ENCBS601TRT at ENCODE; https://www.encodeproject.org/ENCBS601TRT/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: Patient377

value: NED


title: Patient562

value: colorectal cancer (CRC) patient

value: No


title: RNA-DNA SPRITE 136

source_name: Mouse Embryonic Stem cells

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 CD14-negative NK cell (ENCLB128MCF)

description:
https://www.encodeproject.org/experiments/ENCSR373GMM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373GMM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB128MCF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (33 years) CD14-negative NK primary cell

value: CD14-negative NK cell

value: male

value: Yijun Ruan, JAX

tag: link

value: ENCBS423RCQ at ENCODE; https://www.encodeproject.org/ENCBS423RCQ/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: RNA-DNA SPRITE 134


title: Histone ChIP-seq from motor neuron (ENCLB400NXM)

description:
https://www.encodeproject.org/experiments/ENCSR962OTG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR962OTG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR175HRD
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB400NXM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

tag: antibody

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

value: child

value: 6 year

value: Michael Snyder, Stanford

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

tag: health state

value: Healthy donor

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

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


title: Histone ChIP-seq from motor neuron (ENCLB719QCK)

description:
https://www.encodeproject.org/experiments/ENCSR962OTG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR962OTG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR175HRD
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB719QCK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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


title: RNA-DNA SPRITE 133

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: TF ChIP-seq from K562 (ENCLB169HBY)

description:
https://www.encodeproject.org/experiments/ENCSR193ZLW/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-THAP7 ChIP-seq on human K562
experiment encode accession: ENCSR193ZLW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR012KTG, ENCSR210QQQ
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB169HBY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS768FFV at ENCODE; https://www.encodeproject.org/ENCBS768FFV/

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


title: Control ChIP-seq from HepG2 (ENCLB520BHH)

description:
https://www.encodeproject.org/experiments/ENCSR661ZUK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR661ZUK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-22
lab: Richard Myers, HAIB
library encode accession: ENCLB520BHH
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS744ZYE at ENCODE; https://www.encodeproject.org/ENCBS744ZYE/

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


title: BruUV-seq from Calu3 (ENCLB305VZT)

description:
https://www.encodeproject.org/experiments/ENCSR870SVX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR870SVX
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR692DCF
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB305VZT
size range: 400-500

value: 25 year

value: Mats Ljungman, UMichigan

value: Lung adenocarcinoma

value: ENCBS645HKA at ENCODE; https://www.encodeproject.org/ENCBS645HKA/

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


title: RNA-DNA SPRITE 137

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: TF ChIP-seq from HepG2 (ENCLB918EQM)

description:
https://www.encodeproject.org/experiments/ENCSR658UQD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR658UQD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB918EQM
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZUP1

value: ZUFSP

value: cell line

value: ENCBS742OHL at ENCODE; https://www.encodeproject.org/ENCBS742OHL/


title: RNA-DNA SPRITE 135


title: RNA-DNA SPRITE 132


title: TF ChIP-seq from HepG2 (ENCLB238VMR)

description:
https://www.encodeproject.org/experiments/ENCSR658UQD/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR658UQD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB238VMR
fragmentation methods: sonication (generic)

value: male

value: child

value: hepatocellular carcinoma

value: ENCBS224GOW at ENCODE; https://www.encodeproject.org/ENCBS224GOW/


title: Patient553

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)

value: NED


title: RNA-DNA SPRITE 131


title: Patient554

value: DOC


title: KO1

source_name: Right brain hemisphere without cerebellum or olfactory bulb

tag: tissue

tag: genotype

tag: age

value: 9 months

tag: Sex

value: Male


title: polyA plus RNA-seq from CD8-positive, alpha-beta memory T cell (ENCLB492JVB)

description:
https://www.encodeproject.org/experiments/ENCSR279VNR/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD8-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR279VNR
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB492JVB
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

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

value: primary cell

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

tag: biosample encode accession

value: not collected

value: healthy

tag: dev stage

value: unknown

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

value: ENCBS020LPJ at ENCODE; https://www.encodeproject.org/ENCBS020LPJ/

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


title: BruUV-seq from MCF 10A (ENCLB637WBP)

description:
https://www.encodeproject.org/experiments/ENCSR870JRO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR870JRO
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR444JTC
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB637WBP
size range: 400-500

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: cell line

value: female

value: adult

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

value: fibrocystic disease

tag: link

value: ENCBS005BDC at ENCODE; https://www.encodeproject.org/ENCBS005BDC/

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


title: Patient335

value: colorectal cancer (CRC) patient

value: RT/Xeloda, FOLFOX

tag: disease status

value: DOD


title: Patient273

value: FOLFOX

value: NED


title: RNA-DNA SPRITE 129

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 activated T-cell (ENCLB164LFD)

description:
https://www.encodeproject.org/experiments/ENCSR092SRS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR092SRS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB164LFD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (42 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours

value: activated T-cell

value: primary cell

value: male

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

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

value: ENCBS881ZXA at ENCODE; https://www.encodeproject.org/ENCBS881ZXA/

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


title: RNA-DNA SPRITE 130


title: BruUV-seq from MCF 10A (ENCLB393WNF)

description:
https://www.encodeproject.org/experiments/ENCSR870JRO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR870JRO
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR444JTC
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB393WNF
size range: 400-500

tag: line

value: MCF 10A

value: cell line

value: female

value: adult

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

tag: health state

value: fibrocystic disease

value: ENCBS614ZIR at ENCODE; https://www.encodeproject.org/ENCBS614ZIR/

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


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB304AQT)

description:
https://www.encodeproject.org/experiments/ENCSR092KKW/
***************
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: ENCSR092KKW
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB304AQT
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

tag: description

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: ENCBS067WEN at ENCODE; https://www.encodeproject.org/ENCBS067WEN/

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


title: polyA plus RNA-seq from IgD-negative memory B cell (ENCLB762WJK)

description:
https://www.encodeproject.org/experiments/ENCSR092CNB/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of IgD-negative memory B cell.
experiment encode accession: ENCSR092CNB
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB762WJK
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: IgD-negative memory B cell

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

value: healthy

value: ENCBS318ZNB at ENCODE; https://www.encodeproject.org/ENCBS318ZNB/

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


title: TF ChIP-seq from K562 (ENCLB989TRK)

description:
https://www.encodeproject.org/experiments/ENCSR193ZLW/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-THAP7 ChIP-seq on human K562
experiment encode accession: ENCSR193ZLW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR012KTG, ENCSR210QQQ
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB989TRK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens THAP7

tag: antibody

value: cell line

value: female

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS682XCQ at ENCODE; https://www.encodeproject.org/ENCBS682XCQ/

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


title: RNA-DNA SPRITE 128

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: BruUV-seq from Caco-2 (ENCLB887HUC)

description:
https://www.encodeproject.org/experiments/ENCSR712JHP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR712JHP
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR892NYB
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB887HUC
size range: 400-500

source_name: Homo sapiens Caco-2 cell line

value: male

value: colorectal adenocarcinoma

tag: age

value: 72 year

value: Mats Ljungman, UMichigan

value: ENCBS963LYN at ENCODE; https://www.encodeproject.org/ENCBS963LYN/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: Patient265

source_name: Human Colorectal cancer tissue

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

value: NED


title: BruUV-seq from Caco-2 (ENCLB499ITA)

description:
https://www.encodeproject.org/experiments/ENCSR712JHP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR712JHP
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR892NYB
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB499ITA
size range: 400-500

value: cell line

tag: biosample encode accession

tag: Sex

tag: dev stage

value: adult

tag: lab

tag: source

tag: link

value: ENCBS058JYC at ENCODE; https://www.encodeproject.org/ENCBS058JYC/


title: polyA plus RNA-seq from naive B cell (ENCLB472ZKP)

description:
https://www.encodeproject.org/experiments/ENCSR363BVN/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive B cell.
experiment encode accession: ENCSR363BVN
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB472ZKP
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

source_name: Homo sapiens naive B primary cell

value: naive B cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS973SPF at ENCODE; https://www.encodeproject.org/ENCBS973SPF/

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


title: Patient225

value: FOLFOX

tag: disease status


title: DNase-seq from mesothelial cell of epicardium (ENCLB261VER)

description:
https://www.encodeproject.org/experiments/ENCSR658EHM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR658EHM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB261VER

source_name: Homo sapiens female embryo (5 days) mesothelial of epicardium in vitro differentiated cells

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: female

tag: health state

value: embryonic

value: 5 day

value: SESCC

value: ENCBS918RHD at ENCODE; https://www.encodeproject.org/ENCBS918RHD/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: RNA-DNA SPRITE 125

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: RNA-DNA SPRITE 126


title: Patient139

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: DOC


title: TF ChIP-seq from HepG2 (ENCLB770IDA)

description:
https://www.encodeproject.org/experiments/ENCSR756CJS/
***************
biological replicate number: 2
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: ENCLB770IDA
fragmentation methods: sonication (generic)

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

tag: antibody

tag: line

value: cell line

value: male

value: child

tag: age

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS682YHF at ENCODE; https://www.encodeproject.org/ENCBS682YHF/

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


title: DNase-seq from head of caudate nucleus (ENCLB303XMT)

description:
https://www.encodeproject.org/experiments/ENCSR355PNF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR355PNF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB303XMT

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

value: female

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS689UXR at ENCODE; https://www.encodeproject.org/ENCBS689UXR/

value: Derived from ENCODE donor ENCDO150EBZ; https://www.encodeproject.org/ENCDO150EBZ/


title: Patient28_176

value: colorectal cancer (CRC) patient

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

value: DOD


title: Patient130

value: No

value: DOC


title: RNA-DNA SPRITE 127

source_name: Mouse Embryonic Stem cells

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 124


title: Patient27_334


title: Patient128

value: NED


title: Patient26_287

value: FOLFOX, RT


title: RNA-DNA SPRITE 123


title: DNase-seq from head of caudate nucleus (ENCLB767GXK)

description:
https://www.encodeproject.org/experiments/ENCSR274FZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR274FZD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB767GXK
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

tag: dev stage

tag: lab

tag: source

tag: link

value: ENCBS066OMC at ENCODE; https://www.encodeproject.org/ENCBS066OMC/

value: Derived from ENCODE donor ENCDO206ZSI; https://www.encodeproject.org/ENCDO206ZSI/


title: Patient132

value: FOLFOX

tag: disease status


title: DNase-seq from middle frontal area 46 (ENCLB653XLD)

description:
https://www.encodeproject.org/experiments/ENCSR865CYW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR865CYW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB653XLD

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

value: middle frontal area 46

value: female

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS192OHK at ENCODE; https://www.encodeproject.org/ENCBS192OHK/

value: Derived from ENCODE donor ENCDO081AHA; https://www.encodeproject.org/ENCDO081AHA/


title: polyA plus RNA-seq from IgD-negative memory B cell (ENCLB165PSP)

description:
https://www.encodeproject.org/experiments/ENCSR348YVF/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of IgD-negative memory B cell.
experiment encode accession: ENCSR348YVF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB165PSP
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

value: IgD-negative memory B cell

value: primary 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/