title: CRISPRi RNA-seq from K562 (ENCLB815FCS)

description:
https://www.encodeproject.org/experiments/ENCSR160YSN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGN3.
experiment encode accession: ENCSR160YSN
assay title: CRISPRi RNA-seq
assembly: GRCh38
possible controls: ENCSR095PIC
encode release date: 2018-01-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB815FCS
size range: >200

value: female

value: ENCBS486LUF at ENCODE; https://www.encodeproject.org/ENCBS486LUF/


title: WGBS from OCI-LY7 (ENCLB172JDR)

status: Public on Mar 02 2019

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR999CXD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR999CXD
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB172JDR

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens OCI-LY7 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: B cell lymphoma

tag: dev stage

value: adult

tag: age

value: 48 year

tag: lab

value: Richard Myers, HAIB

tag: link

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCBS182NFY at ENCODE; https://www.encodeproject.org/ENCBS182NFY/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; https://web.expasy.org/cellosaurus/CVCL_1881


title: WGBS from smooth muscle cell (ENCLB767YYU)

description:
https://www.encodeproject.org/experiments/ENCSR959RNH/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing, frozen or fixed in vitro differentiated smooth muscle cells from ES WA09 (H9)
experiment encode accession: ENCSR959RNH
assay title: WGBS
assembly: GRCh38
encode release date: 2016-03-22
lab: Richard Myers, HAIB
library encode accession: ENCLB767YYU

source_name: Homo sapiens smooth muscle in vitro differentiated cells female embryo (5 days) derived from H9

value: smooth muscle cell

value: in vitro differentiated cells

tag: description

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: healthy

value: ENCBS899TTJ at ENCODE; https://www.encodeproject.org/ENCBS899TTJ/

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


title: WGBS from lower leg skin (ENCLB460MSR)

description:
https://www.encodeproject.org/experiments/ENCSR930WUY/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on skin tissue
experiment encode accession: ENCSR930WUY
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-22
lab: Richard Myers, HAIB
library encode accession: ENCLB460MSR

source_name: Homo sapiens female adult (51 year) lower leg skin tissue

value: lower leg skin

value: tissue

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS577EBP at ENCODE; https://www.encodeproject.org/ENCBS577EBP/


title: CRISPRi RNA-seq from K562 (ENCLB642TWR)

description:
https://www.encodeproject.org/experiments/ENCSR171KMM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFYB.
experiment encode accession: ENCSR171KMM
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2018-01-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB642TWR
size range: >200

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting NFYB

tag: antibody

value: NFYB

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS989PIL at ENCODE; https://www.encodeproject.org/ENCBS989PIL/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from esophagus squamous epithelium (ENCLB776RBC)

description:
https://www.encodeproject.org/experiments/ENCSR853BXB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR853BXB
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB776RBC

source_name: Homo sapiens male adult (54 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: male

value: 54 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS421TQI at ENCODE; https://www.encodeproject.org/ENCBS421TQI/


title: WGBS from smooth muscle cell (ENCLB125PJJ)

description:
https://www.encodeproject.org/experiments/ENCSR959RNH/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing, frozen or fixed in vitro differentiated smooth muscle cells from ES WA09 (H9)
experiment encode accession: ENCSR959RNH
assay title: WGBS
assembly: GRCh38
encode release date: 2016-03-22
lab: Richard Myers, HAIB
library encode accession: ENCLB125PJJ

value: smooth muscle cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: female

value: healthy

value: ENCBS780PCJ at ENCODE; https://www.encodeproject.org/ENCBS780PCJ/

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


title: WGBS from esophagus muscularis mucosa (ENCLB195SCD)

description:
https://www.encodeproject.org/experiments/ENCSR882FJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR882FJT
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB195SCD

source_name: Homo sapiens female adult (51 year) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: tissue

value: adult

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS662XOH at ENCODE; https://www.encodeproject.org/ENCBS662XOH/


title: WGBS from body of pancreas (ENCLB417QPU)

description:
https://www.encodeproject.org/experiments/ENCSR996BJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR996BJT
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB417QPU

source_name: Homo sapiens male adult (37 years) body of pancreas tissue

value: body of pancreas

value: male

value: 37 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS859PLO at ENCODE; https://www.encodeproject.org/ENCBS859PLO/


title: siRNA RNA-seq from C4-2B (ENCLB865VHD)

description:
https://www.encodeproject.org/experiments/ENCSR142YZV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on CB-24 cells treated with siRNA targeting a non-specific control siRNA.
experiment encode accession: ENCSR142YZV
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB865VHD
size range: >200

source_name: Homo sapiens C4-2B cell line expressing RNAi targeting Non-specific target control

value: Control

value: cell line

value: C4-2B cells treated with a siRNA knockdown against a non-specific target control, used in RNA-seq experiments.

value: prostate adenocarcinoma

value: 50 year

value: Peggy Farnham, USC

value: Derived from ENCODE donor ENCDO000ACX; https://www.encodeproject.org/ENCDO000ACX/

value: ENCBS440KYC at ENCODE; https://www.encodeproject.org/ENCBS440KYC/

value: ENCODE dbxrefs Cellosaurus CVCL_4784; https://web.expasy.org/cellosaurus/CVCL_4784


title: siRNA RNA-seq from C4-2B (ENCLB688SFZ)

description:
https://www.encodeproject.org/experiments/ENCSR142YZV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on CB-24 cells treated with siRNA targeting a non-specific control siRNA.
experiment encode accession: ENCSR142YZV
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB688SFZ
size range: >200

value: adult

value: ENCBS002MOV at ENCODE; https://www.encodeproject.org/ENCBS002MOV/


title: WGBS from gastroesophageal sphincter (ENCLB515SVA)

description:
https://www.encodeproject.org/experiments/ENCSR839GNN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR839GNN
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB515SVA

source_name: Homo sapiens female adult (53 years) gastroesophageal sphincter tissue

value: gastroesophageal sphincter

value: tissue

value: female

value: 53 year

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS792QPO at ENCODE; https://www.encodeproject.org/ENCBS792QPO/


title: siRNA RNA-seq from C4-2B (ENCLB240YXC)

description:
https://www.encodeproject.org/experiments/ENCSR142YZV/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on CB-24 cells treated with siRNA targeting a non-specific control siRNA.
experiment encode accession: ENCSR142YZV
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB240YXC
size range: >200

value: Control

value: male

value: ENCBS582KTC at ENCODE; https://www.encodeproject.org/ENCBS582KTC/


title: WGBS from testis (ENCLB095PBB)

description:
https://www.encodeproject.org/experiments/ENCSR806NNG/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on testis
experiment encode accession: ENCSR806NNG
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-18
lab: Richard Myers, HAIB
library encode accession: ENCLB095PBB

source_name: Homo sapiens male adult (37 years) testis tissue

value: testis

value: 37 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS726XJU at ENCODE; https://www.encodeproject.org/ENCBS726XJU/


title: CRISPRi RNA-seq from K562 (ENCLB808QWX)

description:
https://www.encodeproject.org/experiments/ENCSR126GEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SMARCA4.
experiment encode accession: ENCSR126GEQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB808QWX
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting SMARCA4

value: cell line

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

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

value: ENCBS004VDW at ENCODE; https://www.encodeproject.org/ENCBS004VDW/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from HepG2 (ENCLB443JJF)

description:
https://www.encodeproject.org/experiments/ENCSR786DCL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR786DCL
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-01
lab: Richard Myers, HAIB
library encode accession: ENCLB443JJF

source_name: Homo sapiens HepG2 cell line

value: hepatocellular carcinoma

value: child

value: 15 year

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

value: ENCBS773GMP at ENCODE; https://www.encodeproject.org/ENCBS773GMP/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; https://web.expasy.org/cellosaurus/CVCL_0027


title: WGBS from OCI-LY7 (ENCLB588PCW)

description:
https://www.encodeproject.org/experiments/ENCSR999CXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR999CXD
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB588PCW

value: male

value: B cell lymphoma

value: adult

value: 48 year

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCBS062JSC at ENCODE; https://www.encodeproject.org/ENCBS062JSC/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; https://web.expasy.org/cellosaurus/CVCL_1881


title: WGBS from HepG2 (ENCLB890RFU)

description:
https://www.encodeproject.org/experiments/ENCSR786DCL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR786DCL
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-01
lab: Richard Myers, HAIB
library encode accession: ENCLB890RFU

value: cell line

value: Richard Myers, HAIB

value: ENCBS333JNJ at ENCODE; https://www.encodeproject.org/ENCBS333JNJ/


title: WGBS from prostate gland (ENCLB428IRX)

description:
https://www.encodeproject.org/experiments/ENCSR779PPR/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on prostate
experiment encode accession: ENCSR779PPR
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-18
lab: Richard Myers, HAIB
library encode accession: ENCLB428IRX

source_name: Homo sapiens male adult (54 years) prostate gland tissue

value: prostate gland

value: tissue

value: 54 year

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS739QPP at ENCODE; https://www.encodeproject.org/ENCBS739QPP/


title: CRISPRi RNA-seq from K562 (ENCLB684NMF)

description:
https://www.encodeproject.org/experiments/ENCSR171KMM/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFYB.
experiment encode accession: ENCSR171KMM
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2018-01-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB684NMF
size range: >200

value: NFYB

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

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

value: ENCBS866QHV at ENCODE; https://www.encodeproject.org/ENCBS866QHV/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: CRISPRi RNA-seq from K562 (ENCLB290KCL)

description:
https://www.encodeproject.org/experiments/ENCSR126GEQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SMARCA4.
experiment encode accession: ENCSR126GEQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB290KCL
size range: >200

value: adult

value: Sherman Weissman, Yale

value: ENCBS916GJM at ENCODE; https://www.encodeproject.org/ENCBS916GJM/


title: CRISPRi RNA-seq from K562 (ENCLB325TDX)

description:
https://www.encodeproject.org/experiments/ENCSR123IMQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ATF3.
experiment encode accession: ENCSR123IMQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB325TDX
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting ATF3

value: cell line

value: ENCBS502YUG at ENCODE; https://www.encodeproject.org/ENCBS502YUG/


title: WGBS from heart left ventricle (ENCLB560LZP)

description:
https://www.encodeproject.org/experiments/ENCSR766GKN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR766GKN
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB560LZP

source_name: Homo sapiens female adult (53 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS024WND at ENCODE; https://www.encodeproject.org/ENCBS024WND/


title: CRISPRi RNA-seq from K562 (ENCLB307ZOH)

description:
https://www.encodeproject.org/experiments/ENCSR104QKG/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SIX5.
experiment encode accession: ENCSR104QKG
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB307ZOH
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting SIX5

value: female

value: ENCBS973QZJ at ENCODE; https://www.encodeproject.org/ENCBS973QZJ/


title: CRISPRi RNA-seq from K562 (ENCLB033TRG)

description:
https://www.encodeproject.org/experiments/ENCSR104QKG/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SIX5.
experiment encode accession: ENCSR104QKG
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB033TRG
size range: >200

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS165FFQ at ENCODE; https://www.encodeproject.org/ENCBS165FFQ/


title: WGBS from spleen (ENCLB353RJB)

description:
https://www.encodeproject.org/experiments/ENCSR757JTX/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on spleen tissue
experiment encode accession: ENCSR757JTX
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-18
lab: Richard Myers, HAIB
library encode accession: ENCLB353RJB

source_name: Homo sapiens male adult (37 years) spleen tissue

value: spleen

value: male

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS880LFZ at ENCODE; https://www.encodeproject.org/ENCBS880LFZ/


title: CRISPRi RNA-seq from K562 (ENCLB736LMS)

description:
https://www.encodeproject.org/experiments/ENCSR104JMN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting MXD3.
experiment encode accession: ENCSR104JMN
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB736LMS
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting MXD3

value: cell line

value: adult

value: Sherman Weissman, Yale

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

value: ENCBS632URD at ENCODE; https://www.encodeproject.org/ENCBS632URD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from tibial nerve (ENCLB901CGI)

description:
https://www.encodeproject.org/experiments/ENCSR752OCM/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on tibial nerve tissue
experiment encode accession: ENCSR752OCM
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-18
lab: Richard Myers, HAIB
library encode accession: ENCLB901CGI

source_name: Homo sapiens female adult (53 years) tibial nerve tissue

value: tibial nerve

value: tissue

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS431KBQ at ENCODE; https://www.encodeproject.org/ENCBS431KBQ/


title: WGBS from upper lobe of left lung (ENCLB271HNF)

description:
https://www.encodeproject.org/experiments/ENCSR674VXR/
***************
biological replicate number: 1
technical replicate number: 1
description: whole genome bisulfite sequencing from human lung tissue
experiment encode accession: ENCSR674VXR
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-09
lab: Richard Myers, HAIB
library encode accession: ENCLB271HNF

source_name: Homo sapiens female adult (51 year) upper lobe of left lung tissue

value: upper lobe of left lung

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS621MSH at ENCODE; https://www.encodeproject.org/ENCBS621MSH/


title: WGBS from spleen (ENCLB845KXJ)

description:
https://www.encodeproject.org/experiments/ENCSR750CPN/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on spleen tissue
experiment encode accession: ENCSR750CPN
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-22
lab: Richard Myers, HAIB
library encode accession: ENCLB845KXJ

source_name: Homo sapiens female adult (51 year) spleen tissue

value: spleen

value: ENCBS142WXB at ENCODE; https://www.encodeproject.org/ENCBS142WXB/


title: WGBS from transverse colon (ENCLB373KCT)

description:
https://www.encodeproject.org/experiments/ENCSR668FTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this Experiment comes from whole genome bisulfite sequencing of human transverse colon tissue
experiment encode accession: ENCSR668FTZ
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB373KCT

source_name: Homo sapiens female adult (53 years) transverse colon tissue

value: transverse colon

value: adult

value: 53 year

value: ENCBS293ZWZ at ENCODE; https://www.encodeproject.org/ENCBS293ZWZ/


title: CRISPRi RNA-seq from K562 (ENCLB234ORW)

description:
https://www.encodeproject.org/experiments/ENCSR103URL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ZNF384.
experiment encode accession: ENCSR103URL
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB234ORW
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting ZNF384

value: cell line

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

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

value: ENCBS603QVT at ENCODE; https://www.encodeproject.org/ENCBS603QVT/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: CRISPRi RNA-seq from K562 (ENCLB177UKQ)

description:
https://www.encodeproject.org/experiments/ENCSR103URL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ZNF384.
experiment encode accession: ENCSR103URL
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB177UKQ
size range: >200

value: ENCBS797AKK at ENCODE; https://www.encodeproject.org/ENCBS797AKK/


title: CRISPRi RNA-seq from K562 (ENCLB236XLU)

description:
https://www.encodeproject.org/experiments/ENCSR096VPS/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFYA.
experiment encode accession: ENCSR096VPS
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB236XLU
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting NFYA

value: NFYA

value: female

value: Michael Snyder, Stanford

value: ENCBS987XDS at ENCODE; https://www.encodeproject.org/ENCBS987XDS/


title: CRISPRi RNA-seq from K562 (ENCLB553MYD)

description:
https://www.encodeproject.org/experiments/ENCSR096VPS/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFYA.
experiment encode accession: ENCSR096VPS
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB553MYD
size range: >200

value: ENCBS847LZX at ENCODE; https://www.encodeproject.org/ENCBS847LZX/


title: WGBS from ovary (ENCLB056RXQ)

description:
https://www.encodeproject.org/experiments/ENCSR803SIO/
***************
biological replicate number: 1
technical replicate number: 1
description: whole genome bisulfite sequencing from human ovary tissue
experiment encode accession: ENCSR803SIO
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB056RXQ

source_name: Homo sapiens female adult (51 year) ovary tissue

value: ovary

value: tissue

value: 51 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS955MMY at ENCODE; https://www.encodeproject.org/ENCBS955MMY/


title: CRISPRi RNA-seq from K562 (ENCLB177QFO)

description:
https://www.encodeproject.org/experiments/ENCSR084NTT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SRF.
experiment encode accession: ENCSR084NTT
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB177QFO
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting SRF

value: SRF

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS814DBT at ENCODE; https://www.encodeproject.org/ENCBS814DBT/


title: CRISPRi RNA-seq from K562 (ENCLB288NKH)

description:
https://www.encodeproject.org/experiments/ENCSR095PIC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference for a non-specific target (batch E control).
experiment encode accession: ENCSR095PIC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB288NKH
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting Non-specific target control

value: Control

value: Sherman Weissman, Yale

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

value: ENCBS935HPR at ENCODE; https://www.encodeproject.org/ENCBS935HPR/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: CRISPRi RNA-seq from K562 (ENCLB462TRJ)

description:
https://www.encodeproject.org/experiments/ENCSR123IMQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ATF3.
experiment encode accession: ENCSR123IMQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB462TRJ
size range: >200

value: female

value: ENCBS919KGG at ENCODE; https://www.encodeproject.org/ENCBS919KGG/


title: WGBS from thyroid gland (ENCLB295YNJ)

description:
https://www.encodeproject.org/experiments/ENCSR601MHU/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS sequencing from thyroid gland tissue
experiment encode accession: ENCSR601MHU
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-13
lab: Richard Myers, HAIB
library encode accession: ENCLB295YNJ

source_name: Homo sapiens female adult (51 year) thyroid gland tissue

value: thyroid gland

value: tissue

value: 51 year

value: ENCBS043EZB at ENCODE; https://www.encodeproject.org/ENCBS043EZB/


title: WGBS from stomach (ENCLB479ACS)

description:
https://www.encodeproject.org/experiments/ENCSR598OBF/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on stomach tissue
experiment encode accession: ENCSR598OBF
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-22
lab: Richard Myers, HAIB
library encode accession: ENCLB479ACS

source_name: Homo sapiens female adult (51 year) stomach tissue

value: stomach

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS901YQB at ENCODE; https://www.encodeproject.org/ENCBS901YQB/


title: CRISPRi RNA-seq from K562 (ENCLB200TKB)

description:
https://www.encodeproject.org/experiments/ENCSR074FBG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TEAD2.
experiment encode accession: ENCSR074FBG
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB200TKB
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting TEAD2

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS430GZL at ENCODE; https://www.encodeproject.org/ENCBS430GZL/


title: WGBS from HeLa-S3 (ENCLB756LAB)

description:
https://www.encodeproject.org/experiments/ENCSR550RTN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR550RTN
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-09
lab: Richard Myers, HAIB
library encode accession: ENCLB756LAB

source_name: Homo sapiens HeLa-S3 cell line

value: cervical adenocarcinoma

value: 31 year

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCBS979JZP at ENCODE; https://www.encodeproject.org/ENCBS979JZP/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; https://web.expasy.org/cellosaurus/CVCL_0058


title: CRISPRi RNA-seq from K562 (ENCLB722VEH)

description:
https://www.encodeproject.org/experiments/ENCSR084NTT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SRF.
experiment encode accession: ENCSR084NTT
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB722VEH
size range: >200

value: SRF

value: female

value: Sherman Weissman, Yale

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

value: ENCBS301VUL at ENCODE; https://www.encodeproject.org/ENCBS301VUL/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from HeLa-S3 (ENCLB145KPM)

description:
https://www.encodeproject.org/experiments/ENCSR550RTN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR550RTN
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-09
lab: Richard Myers, HAIB
library encode accession: ENCLB145KPM

value: Richard Myers, HAIB

value: ENCBS585KIN at ENCODE; https://www.encodeproject.org/ENCBS585KIN/


title: WGBS from gastroesophageal sphincter (ENCLB201VYW)

description:
https://www.encodeproject.org/experiments/ENCSR517MZU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR517MZU
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB201VYW

source_name: Homo sapiens male adult (54 years) gastroesophageal sphincter tissue

value: gastroesophageal sphincter

value: tissue

value: male

value: 54 year

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS180XYE at ENCODE; https://www.encodeproject.org/ENCBS180XYE/


title: CRISPRi RNA-seq from K562 (ENCLB520OUW)

description:
https://www.encodeproject.org/experiments/ENCSR104JMN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting MXD3.
experiment encode accession: ENCSR104JMN
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB520OUW
size range: >200

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS395YSI at ENCODE; https://www.encodeproject.org/ENCBS395YSI/


title: CRISPRi RNA-seq from K562 (ENCLB672LPH)

description:
https://www.encodeproject.org/experiments/ENCSR074FBG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TEAD2.
experiment encode accession: ENCSR074FBG
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB672LPH
size range: >200

value: female

value: Sherman Weissman, Yale

value: ENCBS196RVD at ENCODE; https://www.encodeproject.org/ENCBS196RVD/


title: WGBS from adrenal gland (ENCLB543VBP)

description:
https://www.encodeproject.org/experiments/ENCSR741FVM/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS sequencing from adrenal gland tissue
experiment encode accession: ENCSR741FVM
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB543VBP

source_name: Homo sapiens female adult (53 years) adrenal gland tissue

value: adrenal gland

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS184CGJ at ENCODE; https://www.encodeproject.org/ENCBS184CGJ/


title: WGBS from esophagus squamous epithelium (ENCLB186SWN)

description:
https://www.encodeproject.org/experiments/ENCSR515MHO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR515MHO
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB186SWN

source_name: Homo sapiens female adult (53 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: Richard Myers, HAIB

value: ENCBS126ZAB at ENCODE; https://www.encodeproject.org/ENCBS126ZAB/


title: CRISPRi RNA-seq from K562 (ENCLB855KMX)

description:
https://www.encodeproject.org/experiments/ENCSR069OUL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGA1.
experiment encode accession: ENCSR069OUL
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB855KMX
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting HMGA1

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

value: ENCBS016LVE at ENCODE; https://www.encodeproject.org/ENCBS016LVE/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: CRISPRi RNA-seq from K562 (ENCLB645QCZ)

description:
https://www.encodeproject.org/experiments/ENCSR073QLQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ILF2.
experiment encode accession: ENCSR073QLQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB645QCZ
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting ILF2

value: cell line

value: ENCBS716MXK at ENCODE; https://www.encodeproject.org/ENCBS716MXK/


title: WGBS from tibial nerve (ENCLB655QZP)

description:
https://www.encodeproject.org/experiments/ENCSR658MZU/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on tibial nerve tissue
experiment encode accession: ENCSR658MZU
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-22
lab: Richard Myers, HAIB
library encode accession: ENCLB655QZP

source_name: Homo sapiens male adult (54 years) tibial nerve tissue

value: tibial nerve

value: tissue

value: male

value: adult

value: 54 year

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS705RPQ at ENCODE; https://www.encodeproject.org/ENCBS705RPQ/


title: WGBS from thyroid gland (ENCLB955VCW)

description:
https://www.encodeproject.org/experiments/ENCSR403DTW/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS sequencing from thyroid gland tissue
experiment encode accession: ENCSR403DTW
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB955VCW

source_name: Homo sapiens male adult (37 years) thyroid gland tissue

value: thyroid gland

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS018LQY at ENCODE; https://www.encodeproject.org/ENCBS018LQY/


title: CRISPRi RNA-seq from K562 (ENCLB574XMH)

description:
https://www.encodeproject.org/experiments/ENCSR095PIC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference for a non-specific target (batch E control).
experiment encode accession: ENCSR095PIC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB574XMH
size range: >200

value: Control

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Sherman Weissman, Yale

value: ENCBS762WHJ at ENCODE; https://www.encodeproject.org/ENCBS762WHJ/


title: WGBS from A549 (ENCLB456FMY)

description:
https://www.encodeproject.org/experiments/ENCSR481JIW/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS sequencing from the A549 cell line
experiment encode accession: ENCSR481JIW
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB456FMY

source_name: Homo sapiens A549 cell line

value: cell line

value: 58 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCBS974OAE at ENCODE; https://www.encodeproject.org/ENCBS974OAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; https://web.expasy.org/cellosaurus/CVCL_0023


title: WGBS from A549 (ENCLB094KJP)

description:
https://www.encodeproject.org/experiments/ENCSR481JIW/
***************
biological replicate number: 2
technical replicate number: 1
description: WGBS sequencing from the A549 cell line
experiment encode accession: ENCSR481JIW
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB094KJP

value: male

value: adult

value: ENCBS766MZP at ENCODE; https://www.encodeproject.org/ENCBS766MZP/


title: CRISPRi RNA-seq from K562 (ENCLB016VXF)

description:
https://www.encodeproject.org/experiments/ENCSR052ZPX/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RELA.
experiment encode accession: ENCSR052ZPX
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB016VXF
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting RELA

value: RELA

value: Michael Snyder, Stanford

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

value: ENCBS278BMZ at ENCODE; https://www.encodeproject.org/ENCBS278BMZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: CRISPRi RNA-seq from K562 (ENCLB349URD)

description:
https://www.encodeproject.org/experiments/ENCSR052BWT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting USF2.
experiment encode accession: ENCSR052BWT
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB349URD
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting USF2

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS127EMJ at ENCODE; https://www.encodeproject.org/ENCBS127EMJ/


title: WGBS from hepatocyte (ENCLB409PWJ)

description:
https://www.encodeproject.org/experiments/ENCSR351IPU/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing, frozen or fixed in vitro differentiated hepatocyte-like cells from ES WA09 (H9)
experiment encode accession: ENCSR351IPU
assay title: WGBS
assembly: GRCh38
encode release date: 2016-03-22
lab: Richard Myers, HAIB
library encode accession: ENCLB409PWJ

source_name: Homo sapiens hepatocyte in vitro differentiated cells female embryo (5 days) derived from H9

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: healthy

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

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


title: CRISPRi RNA-seq from K562 (ENCLB221ABB)

description:
https://www.encodeproject.org/experiments/ENCSR052BWT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting USF2.
experiment encode accession: ENCSR052BWT
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB221ABB
size range: >200

value: cell line

value: adult

value: Sherman Weissman, Yale

value: ENCBS688IIQ at ENCODE; https://www.encodeproject.org/ENCBS688IIQ/


title: CRISPRi RNA-seq from K562 (ENCLB452SDX)

description:
https://www.encodeproject.org/experiments/ENCSR052ZPX/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RELA.
experiment encode accession: ENCSR052ZPX
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB452SDX
size range: >200

value: RELA

value: Michael Snyder, Stanford

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

value: ENCBS759GEB at ENCODE; https://www.encodeproject.org/ENCBS759GEB/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from body of pancreas (ENCLB777VZI)

description:
https://www.encodeproject.org/experiments/ENCSR344YUA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR344YUA
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB777VZI

source_name: Homo sapiens male adult (54 years) body of pancreas tissue

value: body of pancreas

value: tissue

value: male

value: 54 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS624VUQ at ENCODE; https://www.encodeproject.org/ENCBS624VUQ/


title: WGBS from hepatocyte (ENCLB757MBA)

description:
https://www.encodeproject.org/experiments/ENCSR351IPU/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing, frozen or fixed in vitro differentiated hepatocyte-like cells from ES WA09 (H9)
experiment encode accession: ENCSR351IPU
assay title: WGBS
assembly: GRCh38
encode release date: 2016-03-22
lab: Richard Myers, HAIB
library encode accession: ENCLB757MBA

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: female

value: healthy

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/

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


title: CRISPRi RNA-seq from K562 (ENCLB048PXY)

description:
https://www.encodeproject.org/experiments/ENCSR073QLQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ILF2.
experiment encode accession: ENCSR073QLQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB048PXY
size range: >200

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS360OMS at ENCODE; https://www.encodeproject.org/ENCBS360OMS/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from ovary (ENCLB858YYV)

description:
https://www.encodeproject.org/experiments/ENCSR305VIT/
***************
biological replicate number: 1
technical replicate number: 1
description: whole genome bisulfite sequencing from human ovary tissue
experiment encode accession: ENCSR305VIT
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB858YYV

source_name: Homo sapiens female adult (53 years) ovary tissue

value: ovary

value: tissue

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS886KXL at ENCODE; https://www.encodeproject.org/ENCBS886KXL/


title: ChIP-seq from K562 (ENCLB879JZQ)

description:
https://www.encodeproject.org/experiments/ENCSR986CDX/
***************
biological replicate number: 1
technical replicate number: 1
description: NEUROD1 ChIP-seq on human K562
experiment encode accession: ENCSR986CDX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB879JZQ
size range: 150-350

source_name: Homo sapiens K562 immortalized cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: female

value: Michael Snyder, Stanford

value: ENCBS489ZOH at ENCODE; https://www.encodeproject.org/ENCBS489ZOH/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: CRISPRi RNA-seq from K562 (ENCLB463VEK)

description:
https://www.encodeproject.org/experiments/ENCSR069OUL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGA1.
experiment encode accession: ENCSR069OUL
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB463VEK
size range: >200

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS499YBA at ENCODE; https://www.encodeproject.org/ENCBS499YBA/


title: CRISPRi RNA-seq from K562 (ENCLB973URW)

description:
https://www.encodeproject.org/experiments/ENCSR043UMW/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RNF2.
experiment encode accession: ENCSR043UMW
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB973URW
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting RNF2

value: 53 year

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

value: ENCBS385MHR at ENCODE; https://www.encodeproject.org/ENCBS385MHR/


title: WGBS from heart left ventricle (ENCLB439FZB)

description:
https://www.encodeproject.org/experiments/ENCSR307KDA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307KDA
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB439FZB

source_name: Homo sapiens female adult (51 year) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS053PTB at ENCODE; https://www.encodeproject.org/ENCBS053PTB/


title: CRISPRi RNA-seq from K562 (ENCLB365XGT)

description:
https://www.encodeproject.org/experiments/ENCSR046FQX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting LDB1.
experiment encode accession: ENCSR046FQX
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB365XGT
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting LDB1

value: female

value: Sherman Weissman, Yale

value: ENCBS051SQN at ENCODE; https://www.encodeproject.org/ENCBS051SQN/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from stomach (ENCLB658ATV)

description:
https://www.encodeproject.org/experiments/ENCSR267SNS/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on stomach tissue
experiment encode accession: ENCSR267SNS
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-18
lab: Richard Myers, HAIB
library encode accession: ENCLB658ATV

source_name: Homo sapiens male adult (54 years) stomach tissue

value: stomach

value: male

value: 54 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS009ZPZ at ENCODE; https://www.encodeproject.org/ENCBS009ZPZ/


title: ChIP-seq from HepG2 (ENCLB866IRQ)

description:
https://www.encodeproject.org/experiments/ENCSR382XLA/
***************
biological replicate number: 2
technical replicate number: 1
description: ZFP36 ChIP-seq on human HepG2
experiment encode accession: ENCSR382XLA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB866IRQ
size range: 150-350

source_name: Homo sapiens HepG2 cell line

value: cell line

value: Hepatocellular carcinoma

value: hepatocellular carcinoma

value: child

value: 15 year

value: Michael Snyder, Stanford

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

value: ENCBS504VHS at ENCODE; https://www.encodeproject.org/ENCBS504VHS/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; https://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from HepG2 (ENCLB318DYW)

description:
https://www.encodeproject.org/experiments/ENCSR382XLA/
***************
biological replicate number: 3
technical replicate number: 1
description: ZFP36 ChIP-seq on human HepG2
experiment encode accession: ENCSR382XLA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB318DYW
size range: 150-350

source_name: Homo sapiens HepG2 immortalized cell line

value: ENCBS523AAA at ENCODE; https://www.encodeproject.org/ENCBS523AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: CRISPRi RNA-seq from K562 (ENCLB613JSX)

description:
https://www.encodeproject.org/experiments/ENCSR043UMW/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RNF2.
experiment encode accession: ENCSR043UMW
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB613JSX
size range: >200

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

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

value: ENCBS322FON at ENCODE; https://www.encodeproject.org/ENCBS322FON/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from K562 (ENCLB521VLD)

description:
https://www.encodeproject.org/experiments/ENCSR364SNE/
***************
biological replicate number: 2
technical replicate number: 1
description: POU5F1 ChIP-seq on human K562
experiment encode accession: ENCSR364SNE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB521VLD
size range: 150-350

value: cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: CRISPRi RNA-seq from K562 (ENCLB344GZP)

description:
https://www.encodeproject.org/experiments/ENCSR046FQX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting LDB1.
experiment encode accession: ENCSR046FQX
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB344GZP
size range: >200

value: Sherman Weissman, Yale

value: ENCBS823CTS at ENCODE; https://www.encodeproject.org/ENCBS823CTS/


title: WGBS from upper lobe of left lung (ENCLB937HGI)

description:
https://www.encodeproject.org/experiments/ENCSR224CTR/
***************
biological replicate number: 1
technical replicate number: 1
description: whole genome bisulfite sequencing from human lung tissue
experiment encode accession: ENCSR224CTR
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB937HGI

source_name: Homo sapiens male adult (37 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: tissue

value: male

value: 37 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS482XWK at ENCODE; https://www.encodeproject.org/ENCBS482XWK/


title: WGBS from suprapubic skin (ENCLB852KRZ)

description:
https://www.encodeproject.org/experiments/ENCSR166VVF/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on skin tissue
experiment encode accession: ENCSR166VVF
assay title: WGBS
encode release date: 2018-04-19
lab: Richard Myers, HAIB
library encode accession: ENCLB852KRZ

source_name: Homo sapiens female adult (51 year) suprapubic skin tissue

value: suprapubic skin

value: female

value: adult

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS767XTZ at ENCODE; https://www.encodeproject.org/ENCBS767XTZ/


title: ChIP-seq from K562 (ENCLB950WMS)

description:
https://www.encodeproject.org/experiments/ENCSR364SNE/
***************
biological replicate number: 1
technical replicate number: 1
description: POU5F1 ChIP-seq on human K562
experiment encode accession: ENCSR364SNE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB950WMS
size range: 150-350

value: cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: 53 year

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS489ZOH at ENCODE; https://www.encodeproject.org/ENCBS489ZOH/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: CRISPRi RNA-seq from K562 (ENCLB128ZRG)

description:
https://www.encodeproject.org/experiments/ENCSR039VEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NONO.
experiment encode accession: ENCSR039VEQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB128ZRG
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting NONO

value: NONO

value: Sherman Weissman, Yale

value: ENCBS503KIX at ENCODE; https://www.encodeproject.org/ENCBS503KIX/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from SK-N-SH (ENCLB203HEW)

description:
https://www.encodeproject.org/experiments/ENCSR274SLQ/
***************
biological replicate number: 1
technical replicate number: 1
description: CHD2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR274SLQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FDA
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB203HEW
size range: 150-350

source_name: Homo sapiens SK-N-SH immortalized cell line

value: SK-N-SH

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 year

value: child

value: ENCBS007RAH at ENCODE; https://www.encodeproject.org/ENCBS007RAH/

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


title: ChIP-seq from SK-N-SH (ENCLB857MKV)

description:
https://www.encodeproject.org/experiments/ENCSR274SLQ/
***************
biological replicate number: 2
technical replicate number: 1
description: CHD2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR274SLQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FDA
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB857MKV
size range: 150-350

value: cell line

value: Neuroblastoma, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: ENCBS061YYT at ENCODE; https://www.encodeproject.org/ENCBS061YYT/

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


title: WGBS from transverse colon (ENCLB704GVM)

description:
https://www.encodeproject.org/experiments/ENCSR156JXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this Experiment comes from whole genome bisulfite sequencing of human transverse colon tissue
experiment encode accession: ENCSR156JXJ
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB704GVM

source_name: Homo sapiens male adult (54 years) transverse colon tissue

value: transverse colon

value: tissue

value: male

value: adult

value: 54 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS690YNV at ENCODE; https://www.encodeproject.org/ENCBS690YNV/


title: CRISPRi RNA-seq from K562 (ENCLB534JUG)

description:
https://www.encodeproject.org/experiments/ENCSR039VEQ/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NONO.
experiment encode accession: ENCSR039VEQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB534JUG
size range: >200

value: NONO

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

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

value: ENCBS934LFJ at ENCODE; https://www.encodeproject.org/ENCBS934LFJ/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from liver (ENCLB468YEW)

description:
https://www.encodeproject.org/experiments/ENCSR221IDN/
***************
biological replicate number: 2
technical replicate number: 1
description: Rabbit IgG control ChIP-seq on human liver
experiment encode accession: ENCSR221IDN
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-02-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB468YEW
size range: 150-350

source_name: Homo sapiens liver tissue male adult (32 years)

value: Control

value: liver

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: healthy with non-obstructive CAD (coronary artery disease)

value: Thomas Gingeras, CSHL

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: ChIP-seq from liver (ENCLB531NQK)

description:
https://www.encodeproject.org/experiments/ENCSR254YRM/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human liver
experiment encode accession: ENCSR254YRM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR221IDN
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB531NQK
size range: 150-350

source_name: Homo sapiens liver tissue female child (6 years)

value: CTCF

value: tissue

value: Human liver Tissue obtained from a healthy 6 year old Caucasian female donor

value: 6 year

value: child

value: healthy

value: ENCBS045RNA at ENCODE; https://www.encodeproject.org/ENCBS045RNA/

value: Derived from ENCODE donor ENCDO059AAA; https://www.encodeproject.org/ENCDO059AAA/

value: ENCODE dbxrefs Liver_STL004; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL004


title: ChIP-seq from K562 (ENCLB413MGV)

description:
https://www.encodeproject.org/experiments/ENCSR986CDX/
***************
biological replicate number: 2
technical replicate number: 1
description: NEUROD1 ChIP-seq on human K562
experiment encode accession: ENCSR986CDX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB413MGV
size range: 150-350

value: cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ENCBS118YJZ at ENCODE; https://www.encodeproject.org/ENCBS118YJZ/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from liver (ENCLB761UMI)

description:
https://www.encodeproject.org/experiments/ENCSR254YRM/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on human liver
experiment encode accession: ENCSR254YRM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR221IDN
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB761UMI
size range: 150-350

value: CTCF

value: liver

value: tissue

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: male

value: healthy with non-obstructive CAD (coronary artery disease)

value: Thomas Gingeras, CSHL

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: CRISPRi RNA-seq from K562 (ENCLB128OSK)

description:
https://www.encodeproject.org/experiments/ENCSR028FBD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting DPF2.
experiment encode accession: ENCSR028FBD
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB128OSK
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting DPF2

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Sherman Weissman, Yale

value: ENCBS600IGI at ENCODE; https://www.encodeproject.org/ENCBS600IGI/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from liver (ENCLB731IGZ)

description:
https://www.encodeproject.org/experiments/ENCSR221IDN/
***************
biological replicate number: 1
technical replicate number: 1
description: Rabbit IgG control ChIP-seq on human liver
experiment encode accession: ENCSR221IDN
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-02-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB731IGZ
size range: 150-350

value: Control

value: liver

value: tissue

value: Human liver Tissue obtained from a healthy 6 year old Caucasian female donor

value: 6 year

value: child

value: healthy

value: ENCBS045RNA at ENCODE; https://www.encodeproject.org/ENCBS045RNA/

value: Derived from ENCODE donor ENCDO059AAA; https://www.encodeproject.org/ENCDO059AAA/

value: ENCODE dbxrefs Liver_STL004; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL004


title: CRISPRi RNA-seq from K562 (ENCLB367MTJ)

description:
https://www.encodeproject.org/experiments/ENCSR028FBD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting DPF2.
experiment encode accession: ENCSR028FBD
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB367MTJ
size range: >200

value: cell line

value: female

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

value: ENCBS730PIW at ENCODE; https://www.encodeproject.org/ENCBS730PIW/


title: CRISPRi RNA-seq from K562 (ENCLB630RSE)

description:
https://www.encodeproject.org/experiments/ENCSR039VEQ/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NONO.
experiment encode accession: ENCSR039VEQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB630RSE
size range: >200

value: NONO

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS998IDD at ENCODE; https://www.encodeproject.org/ENCBS998IDD/


title: WGBS from SK-N-SH (ENCLB721ONH)

description:
https://www.encodeproject.org/experiments/ENCSR145HNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR145HNT
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-13
lab: Richard Myers, HAIB
library encode accession: ENCLB721ONH

source_name: Homo sapiens SK-N-SH cell line

value: SK-N-SH

value: Metastatic neuroblastoma from bone marrow

value: 4 year

value: Richard Myers, HAIB

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

value: ENCBS387WHS at ENCODE; https://www.encodeproject.org/ENCBS387WHS/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; https://web.expasy.org/cellosaurus/CVCL_0531


title: ChIP-seq from HeLa-S3 (ENCLB286KLD)

description:
https://www.encodeproject.org/experiments/ENCSR184MFH/
***************
biological replicate number: 3
technical replicate number: 1
description: ZFP36 ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR184MFH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB286KLD
size range: 150-350

source_name: Homo sapiens HeLa-S3 immortalized cell line

value: cell line

value: 31 year

value: cervical adenocarcinoma

value: ENCBS833ISA at ENCODE; https://www.encodeproject.org/ENCBS833ISA/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058


title: ChIP-seq from K562 (ENCLB335PLH)

description:
https://www.encodeproject.org/experiments/ENCSR776CYN/
***************
biological replicate number: 2
technical replicate number: 1
description: ZFP36 ChIP-seq on human K562
experiment encode accession: ENCSR776CYN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB335PLH
size range: 150-350

source_name: Homo sapiens K562 immortalized cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS351GWD at ENCODE; https://www.encodeproject.org/ENCBS351GWD/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from K562 (ENCLB824DZN)

description:
https://www.encodeproject.org/experiments/ENCSR776CYN/
***************
biological replicate number: 1
technical replicate number: 1
description: ZFP36 ChIP-seq on human K562
experiment encode accession: ENCSR776CYN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB824DZN
size range: 150-350

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS626KTH at ENCODE; https://www.encodeproject.org/ENCBS626KTH/


title: WGBS from right lobe of liver (ENCLB061REQ)

description:
https://www.encodeproject.org/experiments/ENCSR108ESU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR108ESU
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB061REQ

source_name: Homo sapiens female adult (53 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS034NFF at ENCODE; https://www.encodeproject.org/ENCBS034NFF/


title: ChIP-seq from HeLa-S3 (ENCLB397WWM)

description:
https://www.encodeproject.org/experiments/ENCSR184MFH/
***************
biological replicate number: 1
technical replicate number: 1
description: ZFP36 ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR184MFH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB397WWM
size range: 150-350

source_name: Homo sapiens HeLa-S3 cell line

value: cell line

value: cervical adenocarcinoma

value: 31 year

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCBS199XIN at ENCODE; https://www.encodeproject.org/ENCBS199XIN/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; https://web.expasy.org/cellosaurus/CVCL_0058


title: CRISPRi RNA-seq from K562 (ENCLB968BOI)

description:
https://www.encodeproject.org/experiments/ENCSR024HAR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting STAT6.
experiment encode accession: ENCSR024HAR
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB968BOI
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting STAT6

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Sherman Weissman, Yale

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

value: ENCBS407GFZ at ENCODE; https://www.encodeproject.org/ENCBS407GFZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from SK-N-SH (ENCLB406PIZ)

description:
https://www.encodeproject.org/experiments/ENCSR145HNT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR145HNT
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-13
lab: Richard Myers, HAIB
library encode accession: ENCLB406PIZ

value: SK-N-SH

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

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

value: ENCBS439KOM at ENCODE; https://www.encodeproject.org/ENCBS439KOM/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; https://web.expasy.org/cellosaurus/CVCL_0531


title: CRISPRi RNA-seq from K562 (ENCLB715OBN)

description:
https://www.encodeproject.org/experiments/ENCSR024HAR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting STAT6.
experiment encode accession: ENCSR024HAR
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB715OBN
size range: >200

value: cell line

value: 53 year

value: ENCBS851CQU at ENCODE; https://www.encodeproject.org/ENCBS851CQU/


title: WGBS from right lobe of liver (ENCLB516XAY)

description:
https://www.encodeproject.org/experiments/ENCSR108ESU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR108ESU
assay title: WGBS
encode release date: 2018-12-22
lab: Richard Myers, HAIB
library encode accession: ENCLB516XAY

value: right lobe of liver

value: tissue

value: female

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS992RNI at ENCODE; https://www.encodeproject.org/ENCBS992RNI/


title: ChIP-seq from HepG2 (ENCLB304LPY)

description:
https://www.encodeproject.org/experiments/ENCSR681WHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ETS1 ChIP-seq on human HepG2
experiment encode accession: ENCSR681WHQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB304LPY
size range: 150-350

value: 15 year

value: male

value: Michael Snyder, Stanford

value: hepatocellular carcinoma

value: ENCBS546FZO at ENCODE; https://www.encodeproject.org/ENCBS546FZO/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from HepG2 (ENCLB501CDX)

description:
https://www.encodeproject.org/experiments/ENCSR681WHQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ETS1 ChIP-seq on human HepG2
experiment encode accession: ENCSR681WHQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB501CDX
size range: 150-350

value: Hepatocellular carcinoma

value: child

value: ENCBS523AAA at ENCODE; https://www.encodeproject.org/ENCBS523AAA/

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: CRISPRi RNA-seq from K562 (ENCLB620RBM)

description:
https://www.encodeproject.org/experiments/ENCSR016WFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference for a non-specific target (batch C control).
experiment encode accession: ENCSR016WFQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB620RBM
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting Non-specific target control

value: Control

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS861OYO at ENCODE; https://www.encodeproject.org/ENCBS861OYO/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from smooth muscle cell (ENCLB101NNR)

description:
https://www.encodeproject.org/experiments/ENCSR076OHG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR076OHG
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-09
lab: Richard Myers, HAIB
library encode accession: ENCLB101NNR

source_name: Homo sapiens female embryo (5 days) smooth muscle in vitro differentiated cells originated from H9

value: smooth muscle cell

value: in vitro differentiated cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Richard Myers, HAIB

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

value: ENCBS095OTG at ENCODE; https://www.encodeproject.org/ENCBS095OTG/


title: human_MAb_polyclonal_recomb_IgG1

type: protein

city: Cleveland

first: Christopher

middle: L

last: King

state: Ohio

address: 2109 Adelbert Road 4th Floor

department: Center for Global Health & Diseases

institute: Case Western Reserve University

hyb_protocol: Monoclonal antibodies prepared at 10 ng/ml in protein array blocking buffer (Maine Manufacturing, Sanford, ME). Serum sample was diluted 1:100 in protein array blocking buffer supplemented with E. coli lysate (GenScript, Piscataway, NJ) to a final concentration of 10mg/ml, and pre-incubated at room temperature (RT) for 30 min. Concurrently, arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking buffer was removed, and arrays were probed with samples using sealed chambers to ensure no cross-contamination of sample between pads. Arrays were incubated over-night at 4 °C with gentle agitation. Arrays were then washed at RT five times with TBS-0.05% Tween 20 (T-TBS), followed by incubation with biotin-conjugated goat anti-human IgG (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer for 1 h at RT. After incubation in secondary antibodies, arrays were then washed three times with T-TBS, followed by incubation with QDot® 800 Streptavidin Conjugate (Molecular Probes by Life Technologies, Eugene, Oregon, USA,) for 45 min at RT protected from light. Arrays were washed three times with T-TBS, and once with water. Chips were air dried by centrifugation at 1,000 g for 5 min and scanned on ArrayCam™ 400-S Microarray Imaging System from Grace Bio-Labs (Bend, OR). Spot and background intensities were measured using an annotated grid (.gal) file. ArrayCam™settings were set at 50 gain, and the exposure time 50ms.

scan_protocol: ArrayCam 400-S Microarray Imaging System from Grace Bio-Labs (Bend, OR), settings were set at 50 gain, and the exposure time 50 (ms). Spot and background intensities were measured using an annotated grid (.gal) file. single wavelength excitation at 800nm, automated software  provides spot finding and data.

data_processing: the mean background signal of antibody binding to 24 control spots of in vitro transcription/translation reaction without DNA template (noDNA spots) were removed from each samples raw values of antibody binding measured as the mean pixel intensity of spots of printed protein

molecule: protein

source_name: recombinant antibody,IgG1

label_protocol: The primary antibody used for arrays was biotin-conjugated goat anti-human IgG from Jackson Immunoresearch (872 W Baltimore Pike, West Grove, PA 19390 USA). Detection by QDot 800 Streptavidin Conjugate.

growth_protocol: H+L plasmids PEI transient transfection using Expi293 (Life Technologies) cells in suspension

extract_protocol: Protein A column purification of epi293 cell supernatant

tag: human antibody

value: polyclonal

tag: h+l transfection

value: produced by transient transfection using Expi293 (Life Technologies) cells in suspension

tag: country origin h+l

value: Cambodia


title: ChIP-seq from HeLa-S3 (ENCLB420IME)

description:
https://www.encodeproject.org/experiments/ENCSR680OFU/
***************
biological replicate number: 1
technical replicate number: 1
description: EP300 ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR680OFU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB420IME
size range: 150-350

value: cell line

value: Cervical adenocarcinoma

value: adult

value: 31 year

value: cervical adenocarcinoma

value: Michael Snyder, Stanford

value: ENCBS061SJE at ENCODE; https://www.encodeproject.org/ENCBS061SJE/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-2.2.aspx


title: CRISPRi RNA-seq from K562 (ENCLB178VAV)

description:
https://www.encodeproject.org/experiments/ENCSR011GAO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGN1.
experiment encode accession: ENCSR011GAO
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB178VAV
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting HMGN1

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS296ZGL at ENCODE; https://www.encodeproject.org/ENCBS296ZGL/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: human_MAb_PvDBPII_specific_recomb_IgG1 (099100)

value: monoclonal

value: produced by transient transfection using Expi293 (Life Technologies) cells in suspension

value: Cambodia


title: WGBS from lower leg skin (ENCLB672LGT)

description:
https://www.encodeproject.org/experiments/ENCSR128RMY/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on skin tissue
experiment encode accession: ENCSR128RMY
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-22
lab: Richard Myers, HAIB
library encode accession: ENCLB672LGT

source_name: Homo sapiens male adult (37 years) lower leg skin tissue

value: lower leg skin

value: tissue

value: male

value: adult

value: 37 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS215WEN at ENCODE; https://www.encodeproject.org/ENCBS215WEN/


title: siRNA RNA-seq from MCF-7 (ENCLB386YWF)

description:
https://www.encodeproject.org/experiments/ENCSR005AHI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on MCF-7 cells treated with siRNA targeting ZFX.
experiment encode accession: ENCSR005AHI
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR783OQM
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB386YWF
size range: >200

source_name: Homo sapiens MCF-7 cell line expressing RNAi targeting ZFX

value: ZFX

value: cell line

value: MCF-7 cells treated with a siRNA knockdown against ZFX, used in RNA-seq experiments.

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: Peggy Farnham, USC

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

value: ENCBS227IDP at ENCODE; https://www.encodeproject.org/ENCBS227IDP/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; https://web.expasy.org/cellosaurus/CVCL_0031


title: CRISPRi RNA-seq from K562 (ENCLB866NWC)

description:
https://www.encodeproject.org/experiments/ENCSR011GAO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGN1.
experiment encode accession: ENCSR011GAO
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB866NWC
size range: >200

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS765ASV at ENCODE; https://www.encodeproject.org/ENCBS765ASV/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: WGBS from smooth muscle cell (ENCLB753MSX)

description:
https://www.encodeproject.org/experiments/ENCSR076OHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR076OHG
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-09
lab: Richard Myers, HAIB
library encode accession: ENCLB753MSX

value: smooth muscle cell

value: in vitro differentiated cells

value: healthy

value: embryonic

value: 5 day

value: Richard Myers, HAIB

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

value: ENCBS971VGF at ENCODE; https://www.encodeproject.org/ENCBS971VGF/


title: WGBS from adrenal gland (ENCLB206OWW)

description:
https://www.encodeproject.org/experiments/ENCSR042LOG/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS sequencing from adrenal gland tissue
experiment encode accession: ENCSR042LOG
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB206OWW

source_name: Homo sapiens male adult (54 years) adrenal gland tissue

value: adrenal gland

value: tissue

value: male

value: adult

value: 54 year

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS517DMY at ENCODE; https://www.encodeproject.org/ENCBS517DMY/


title: ChIP-seq from HeLa-S3 (ENCLB487WKY)

description:
https://www.encodeproject.org/experiments/ENCSR680OFU/
***************
biological replicate number: 2
technical replicate number: 1
description: EP300 ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR680OFU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB487WKY
size range: 150-350

value: cell line

value: Cervical adenocarcinoma

value: 31 year

value: female

value: Michael Snyder, Stanford

value: cervical adenocarcinoma

value: ENCBS577WSP at ENCODE; https://www.encodeproject.org/ENCBS577WSP/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-2.2.aspx


title: human_MAb_PvDBPII_specific_recomb_IgG1 (094083)

value: monoclonal

value: produced by transient transfection using Expi293 (Life Technologies) cells in suspension

value: Cambodia


title: human_pooled plasma (Papua New Guinea)

description: pool Papua New Guinea

source_name: plasma

value: plasma

value: Papua New Guinea


title: human_MAb_PvDBPII_specific_recomb_IgG1 (092096)


title: siRNA RNA-seq from MCF-7 (ENCLB367KER)

description:
https://www.encodeproject.org/experiments/ENCSR005AHI/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on MCF-7 cells treated with siRNA targeting ZFX.
experiment encode accession: ENCSR005AHI
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR783OQM
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB367KER
size range: >200

value: ZFX

value: MCF-7 cells treated with a siRNA knockdown against ZFX, used in RNA-seq experiments.

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

value: Peggy Farnham, USC

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

value: ENCBS705AVG at ENCODE; https://www.encodeproject.org/ENCBS705AVG/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; https://web.expasy.org/cellosaurus/CVCL_0031


title: ChIP-seq from H1-hESC (ENCLB548QER)

description:
https://www.encodeproject.org/experiments/ENCSR633XNG/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR633XNG
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB548QER
size range: 150-350

source_name: Homo sapiens H1-hESC cell line

value: Control

value: cell line

value: male

value: healthy

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCBS019EUF at ENCODE; https://www.encodeproject.org/ENCBS019EUF/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; https://web.expasy.org/cellosaurus/CVCL_9771


title: Heterokaryon 72h

city: Blacksburg

first: M. Cristina

last: Villafranca

state: VA

address: 205 Duckpond Drive

institute: Virginia Polytechnic Institute and State University

description:
Final_BovineReads_bFF_24_48_72.xlsx
Final_MouseReads_mESC_24_48_72.xlsx

data_processing:
MiSeq Fastq files uploaded to Geneious version 8.
Geneious used to align all reads to the bovine and mouse NCBI Reference Sequence (NCBI RefSeq NM_ and NR_ genes only (35,814 mouse genes and 14,234 Cow genes); retrieved on June 2017), using the “Map to Reference” option (with a custom setting allowing for 2% error, and the “Map Multiple Matches” option set to “random”.
Number of reads aligning to each gene (by species) exported to Microsoft Excel, resulting in one spreadsheet for mouse reads, and one for bovine reads.
Read counts were normalized to reads per million mapped reads (RPM).
Genome_build: Bovine assembly UMD_3.1.1/bosTau8
Genome_build: Mouse assembly GRCm38/mm10
Supplementary_files_format_and_content: Two .xlsx files containing read counts by species (mouse and bovine). Each file contains gene name, gene ID, read counts, and normalized expression (RPM).

molecule: polyA RNA

organism:
Bos taurus
Mus musculus

source_name: bovine fetal fibroblast,mouse embryonic stem cell C57BL

growth_protocol: Bovine fetal fibroblasts (bFFs) were isolated from an abattoir-obtained male fetus of unknown genetic background at approximately gestation day 60, and cultured in fibroblast medium consisting of Dulbecco's Modified Eagle's Medium (DMEM; Gibco) with 10% fetal bovine serum (FBS; HyClone) and 50 ug/ml Gentamycin (Lonza) in a 5% CO2 in air incubator at 38.5°C. Mouse embryonic stem (mES) cells from the line C57BL/6 were purchased from ATCC (CRL-1002) and cultured on a monolayer of gamma irradiated mouse embryonic fibroblasts (IRR-MEFs, StemGent) in mES cell medium: DMEM with 15% ESC-qualified FBS (Gibco), 1X Non-Essential Amino Acids (HyClone), 1X Glutamax (Gibco), 1,500 U/ml of ESGRO (Millipore), 0.55 mM beta-mercaptoethanol (Sigma), 1 µM PD0325901 (PD; Cayman chemical company), 3 µM CHIR99021 (CHIR; Cayman chemical company), and 50 µg/ml Gentamycin (Lonza) in a 5% CO2 in air incubator at 37°C. After fusion, co-cultured bFFs and mES cells were incubated in basic ES cell medium: DMEM with 15% ESC-qualified FBS (Gibco), 1X Non-Essential Amino Acids (HyClone), 1X Glutamax (Gibco), 1,500 U/ml of ESGRO (Millipore), 0.55 mM beta-mercaptoethanol (Sigma), and 50 µg/ml Gentamycin (Lonza) in a 5% CO2 in air incubator at 37°C until analysis.

extract_protocol:
For each sample, 200 cells of the respective type were isolated using ImageStream and FACS. cDNA was generated from intact cells, using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following the manufacturer’s instructions for cDNA production using cells as starting material. We used 14 cycles for cDNA amplification.
Libraries were prepared using the Accel-NGS® 2S Plus DNA Library Kit (Swift biosciences).

treatment_protocol: A total of 2x10e5 bFFs were seeded in one well of a 24-well plate in basic ES cell medium, and 2 h later 6x10e5 mES cells were seeded in the same well. Cells were co-cultured for 4h before fusion. Fusion was performed by adding a mixture of 280 µl PEG with 20 µl DMSO, pre-warmed to 37°C to each well during exactly 2 min at room temperature, followed by 2 washes with DPBS and 1 wash with basic ES cell medium. Cells were cultured at 37°C in basic ES cell medium until isolation and analysis.

tag: strain

tag: treatment

value: fused

tag: sampling time after fusion

tag: cell type

value: bi-species (mouse/bovine) heterokaryon