title: ChIA-PET from GM12891 (ENCLB388OVY)

description:
https://www.encodeproject.org/experiments/ENCSR299VMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in GM12891
experiment encode accession: ENCSR299VMZ
assay title: ChIA-PET
encode release date: 2016-10-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB388OVY
size range: 200-500

source_name: Homo sapiens GM12891 cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: male

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000ACA; https://www.encodeproject.org/ENCDO000ACA/

value: ENCBS041WYJ at ENCODE; https://www.encodeproject.org/ENCBS041WYJ/

value: ENCODE dbxrefs Cellosaurus CVCL_9630; https://web.expasy.org/cellosaurus/CVCL_9630


title: ChIA-PET from K562 (ENCLB779ZWL)

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/ENCSR338WUS/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in human K562 cells
experiment encode accession: ENCSR338WUS
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB779ZWL
size range: 450-650

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

tag: link

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

value: ENCBS521IJY at ENCODE; https://www.encodeproject.org/ENCBS521IJY/

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


title: ChIA-PET from GM19240 (ENCLB369IUI)

description:
https://www.encodeproject.org/experiments/ENCSR312TUD/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in GM19240
experiment encode accession: ENCSR312TUD
assay title: ChIA-PET
encode release date: 2016-10-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB369IUI
size range: 200-500

source_name: Homo sapiens GM19240 cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/a0261bf8-009c-4c0b-98ed-9bad4ec0e490/@@download/attachment/Snyder_lab_ChIA-PET_protocol_for_dataset_ENCSR727WCB.pdf
extraction method: see document

tag: description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: unknown

value: Derived from ENCODE donor ENCDO000ACN; https://www.encodeproject.org/ENCDO000ACN/

value: ENCBS760NLE at ENCODE; https://www.encodeproject.org/ENCBS760NLE/

value: ENCODE dbxrefs Cellosaurus CVCL_9635; https://web.expasy.org/cellosaurus/CVCL_9635


title: CRISPRi RNA-seq from K562 (ENCLB054DAI)

description:
https://www.encodeproject.org/experiments/ENCSR650QAK/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SP1.
experiment encode accession: ENCSR650QAK
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB054DAI
size range: >200

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting SP1

value: Michael Snyder, Stanford

value: ENCBS062HQW at ENCODE; https://www.encodeproject.org/ENCBS062HQW/


title: ChIA-PET from GM12891 (ENCLB978NMK)

description:
https://www.encodeproject.org/experiments/ENCSR299VMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIA-PET in GM12891
experiment encode accession: ENCSR299VMZ
assay title: ChIA-PET
encode release date: 2016-10-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB978NMK
size range: 200-500

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: male

value: Derived from ENCODE donor ENCDO000ACA; https://www.encodeproject.org/ENCDO000ACA/

value: ENCBS270GPL at ENCODE; https://www.encodeproject.org/ENCBS270GPL/


title: CRISPRi RNA-seq from K562 (ENCLB249IBX)

description:
https://www.encodeproject.org/experiments/ENCSR650QAK/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SP1.
experiment encode accession: ENCSR650QAK
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB249IBX
size range: >200

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS790JVO at ENCODE; https://www.encodeproject.org/ENCBS790JVO/


title: CRISPRi RNA-seq from K562 (ENCLB668WNY)

description:
https://www.encodeproject.org/experiments/ENCSR620DOP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting KLF2.
experiment encode accession: ENCSR620DOP
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB668WNY
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting KLF2

value: adult

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS022YEG at ENCODE; https://www.encodeproject.org/ENCBS022YEG/


title: CRISPRi RNA-seq from K562 (ENCLB954PCI)

description:
https://www.encodeproject.org/experiments/ENCSR620DOP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting KLF2.
experiment encode accession: ENCSR620DOP
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB954PCI
size range: >200

value: ENCBS560YKU at ENCODE; https://www.encodeproject.org/ENCBS560YKU/

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


title: ChIA-PET from MCF-7 (ENCLB816UCJ)

description:
https://www.encodeproject.org/experiments/ENCSR255XYX/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIA-PET in human MCF-7 cells
experiment encode accession: ENCSR255XYX
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB816UCJ
size range: 450-650

source_name: Homo sapiens MCF-7 cell line

value: breast cancer (adenocarcinoma)

value: 69 year

value: Michael Snyder, Stanford

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

value: ENCBS035QUK at ENCODE; https://www.encodeproject.org/ENCBS035QUK/

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


title: CRISPRi RNA-seq from K562 (ENCLB764SDJ)

description:
https://www.encodeproject.org/experiments/ENCSR819PCU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SETDB1.
experiment encode accession: ENCSR819PCU
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB764SDJ
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting SETDB1

value: cell line

value: ENCBS764XDY at ENCODE; https://www.encodeproject.org/ENCBS764XDY/


title: CRISPRi RNA-seq from K562 (ENCLB059XLG)

description:
https://www.encodeproject.org/experiments/ENCSR650QAK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SP1.
experiment encode accession: ENCSR650QAK
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB059XLG
size range: >200

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS252TPF at ENCODE; https://www.encodeproject.org/ENCBS252TPF/


title: ChIA-PET from neural progenitor cell (ENCLB489IKA)

description:
https://www.encodeproject.org/experiments/ENCSR247RGI/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIA-PET in human neural progenitor cells
experiment encode accession: ENCSR247RGI
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB489IKA
size range: 450-650

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

value: neural progenitor cell

value: in vitro differentiated cells

value: healthy

value: embryonic

value: 5 day

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

value: ENCBS895MZN at ENCODE; https://www.encodeproject.org/ENCBS895MZN/


title: CRISPRi RNA-seq from K562 (ENCLB704TBH)

description:
https://www.encodeproject.org/experiments/ENCSR619EYC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RFX5.
experiment encode accession: ENCSR619EYC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB704TBH
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting RFX5

value: adult

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS440LRV at ENCODE; https://www.encodeproject.org/ENCBS440LRV/

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


title: ChIA-PET from neural progenitor cell (ENCLB296SPB)

description:
https://www.encodeproject.org/experiments/ENCSR247RGI/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in human neural progenitor cells
experiment encode accession: ENCSR247RGI
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB296SPB
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS731HKD at ENCODE; https://www.encodeproject.org/ENCBS731HKD/


title: CRISPRi RNA-seq from K562 (ENCLB950YVW)

description:
https://www.encodeproject.org/experiments/ENCSR619EYC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RFX5.
experiment encode accession: ENCSR619EYC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB950YVW
size range: >200

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS033LKY at ENCODE; https://www.encodeproject.org/ENCBS033LKY/


title: CRISPRi RNA-seq from K562 (ENCLB005UBJ)

description:
https://www.encodeproject.org/experiments/ENCSR608ORR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting UBTF.
experiment encode accession: ENCSR608ORR
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB005UBJ
size range: >200

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

value: UBTF

value: ENCBS898GYH at ENCODE; https://www.encodeproject.org/ENCBS898GYH/


title: CRISPRi RNA-seq from K562 (ENCLB063NDQ)

description:
https://www.encodeproject.org/experiments/ENCSR608ORR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting UBTF.
experiment encode accession: ENCSR608ORR
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB063NDQ
size range: >200

value: ENCBS938ECK at ENCODE; https://www.encodeproject.org/ENCBS938ECK/


title: ChIA-PET from GM19240 (ENCLB248ENV)

description:
https://www.encodeproject.org/experiments/ENCSR130SRF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIA-PET in GM19240
experiment encode accession: ENCSR130SRF
assay title: ChIA-PET
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB248ENV
size range: 200-500

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: unknown

value: Derived from ENCODE donor ENCDO000ACN; https://www.encodeproject.org/ENCDO000ACN/

value: ENCBS338PQB at ENCODE; https://www.encodeproject.org/ENCBS338PQB/

value: ENCODE dbxrefs Cellosaurus CVCL_9635; https://web.expasy.org/cellosaurus/CVCL_9635


title: ChIA-PET from SU-DHL-2 (ENCLB968CCF)

description:
https://www.encodeproject.org/experiments/ENCSR128RPG/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in human SU-DHL-2 cells
experiment encode accession: ENCSR128RPG
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB968CCF
size range: 450-650

source_name: Homo sapiens SU-DHL-2 cell line

value: large cell lymphoma; diffuse histiocytic lymphoma

value: adult

value: 75 year

value: Derived from ENCODE donor ENCDO852AAX; https://www.encodeproject.org/ENCDO852AAX/

value: ENCBS621PAH at ENCODE; https://www.encodeproject.org/ENCBS621PAH/

value: ENCODE dbxrefs Cellosaurus CVCL_9550; https://web.expasy.org/cellosaurus/CVCL_9550


title: ChIA-PET from GM19240 (ENCLB881BFL)

description:
https://www.encodeproject.org/experiments/ENCSR130SRF/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIA-PET in GM19240
experiment encode accession: ENCSR130SRF
assay title: ChIA-PET
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB881BFL
size range: 200-500

value: cell line

value: female

value: Michael Snyder, Stanford

value: ENCBS760NLE at ENCODE; https://www.encodeproject.org/ENCBS760NLE/


title: ChIA-PET from LNCAP (ENCLB742HAJ)

description:
https://www.encodeproject.org/experiments/ENCSR113OIR/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIA-PET in human LNCAP cells
experiment encode accession: ENCSR113OIR
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB742HAJ
size range: 450-650

source_name: Homo sapiens LNCAP cell line

value: LNCAP

value: male

value: prostate adenocarcinoma

value: 50 year

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

value: ENCBS849SWQ at ENCODE; https://www.encodeproject.org/ENCBS849SWQ/

value: ENCODE dbxrefs Cellosaurus CVCL_0395; https://web.expasy.org/cellosaurus/CVCL_0395


title: CRISPRi RNA-seq from K562 (ENCLB635CHZ)

description:
https://www.encodeproject.org/experiments/ENCSR591QYK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TRIM28.
experiment encode accession: ENCSR591QYK
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB635CHZ
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting TRIM28

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS180EYO at ENCODE; https://www.encodeproject.org/ENCBS180EYO/

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


title: ChIA-PET from MCF-7 (ENCLB133DKJ)

description:
https://www.encodeproject.org/experiments/ENCSR255XYX/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in human MCF-7 cells
experiment encode accession: ENCSR255XYX
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB133DKJ
size range: 450-650

value: cell line

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

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

value: ENCBS746EOD at ENCODE; https://www.encodeproject.org/ENCBS746EOD/

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


title: CRISPRi RNA-seq from K562 (ENCLB076YKR)

description:
https://www.encodeproject.org/experiments/ENCSR557BMX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting GATA2.
experiment encode accession: ENCSR557BMX
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB076YKR
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting GATA2

value: female

value: ENCBS993XPI at ENCODE; https://www.encodeproject.org/ENCBS993XPI/


title: CRISPRi RNA-seq from K562 (ENCLB074XVL)

description:
https://www.encodeproject.org/experiments/ENCSR552HTC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TFDP1.
experiment encode accession: ENCSR552HTC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB074XVL
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting TFDP1

value: ENCBS650AIV at ENCODE; https://www.encodeproject.org/ENCBS650AIV/


title: ChIA-PET from ARPE-19 (ENCLB279GFE)

description:
https://www.encodeproject.org/experiments/ENCSR110JOO/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIA-PET in human ARPE-19 cells
experiment encode accession: ENCSR110JOO
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB279GFE
size range: 450-650

source_name: Homo sapiens ARPE-19 cell line

value: male

value: Healthy

value: 19 year

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO917IRX; https://www.encodeproject.org/ENCDO917IRX/

value: ENCBS534TJM at ENCODE; https://www.encodeproject.org/ENCBS534TJM/

value: ENCODE dbxrefs Cellosaurus CVCL_0145; https://web.expasy.org/cellosaurus/CVCL_0145


title: ChIA-PET from LNCAP (ENCLB135RIE)

description:
https://www.encodeproject.org/experiments/ENCSR113OIR/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in human LNCAP cells
experiment encode accession: ENCSR113OIR
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB135RIE
size range: 450-650

value: LNCAP

value: cell line

value: prostate adenocarcinoma

value: 50 year

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

value: ENCBS687TQL at ENCODE; https://www.encodeproject.org/ENCBS687TQL/

value: ENCODE dbxrefs Cellosaurus CVCL_0395; https://web.expasy.org/cellosaurus/CVCL_0395


title: CRISPRi RNA-seq from K562 (ENCLB210ZET)

description:
https://www.encodeproject.org/experiments/ENCSR552HTC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TFDP1.
experiment encode accession: ENCSR552HTC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB210ZET
size range: >200

value: female

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: ENCBS461XSF at ENCODE; https://www.encodeproject.org/ENCBS461XSF/

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


title: CRISPRi RNA-seq from K562 (ENCLB435NGH)

description:
https://www.encodeproject.org/experiments/ENCSR557BMX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting GATA2.
experiment encode accession: ENCSR557BMX
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB435NGH
size range: >200

value: ENCBS946UFP at ENCODE; https://www.encodeproject.org/ENCBS946UFP/


title: CRISPRi RNA-seq from K562 (ENCLB495LOU)

description:
https://www.encodeproject.org/experiments/ENCSR550FIL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TEAD4.
experiment encode accession: ENCSR550FIL
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB495LOU
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting TEAD4

value: ENCBS327TGR at ENCODE; https://www.encodeproject.org/ENCBS327TGR/


title: ChIA-PET from ARPE-19 (ENCLB150LFT)

description:
https://www.encodeproject.org/experiments/ENCSR110JOO/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in human ARPE-19 cells
experiment encode accession: ENCSR110JOO
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB150LFT
size range: 450-650

value: male

value: Healthy

value: 19 year

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO917IRX; https://www.encodeproject.org/ENCDO917IRX/

value: ENCBS054LTE at ENCODE; https://www.encodeproject.org/ENCBS054LTE/

value: ENCODE dbxrefs Cellosaurus CVCL_0145; https://web.expasy.org/cellosaurus/CVCL_0145


title: ChIA-PET from GM12892 (ENCLB409XUH)

description:
https://www.encodeproject.org/experiments/ENCSR033GUP/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIA-PET in GM12892
experiment encode accession: ENCSR033GUP
assay title: ChIA-PET
encode release date: 2016-10-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB409XUH
size range: 200-500

source_name: Homo sapiens GM12892 cell line

value: cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: female

value: unknown

value: Derived from ENCODE donor ENCDO000AAL; https://www.encodeproject.org/ENCDO000AAL/

value: ENCBS698HPL at ENCODE; https://www.encodeproject.org/ENCBS698HPL/

value: ENCODE dbxrefs Cellosaurus CVCL_9631; https://web.expasy.org/cellosaurus/CVCL_9631


title: ChIA-PET from GM12892 (ENCLB687WSC)

description:
https://www.encodeproject.org/experiments/ENCSR033GUP/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in GM12892
experiment encode accession: ENCSR033GUP
assay title: ChIA-PET
encode release date: 2016-10-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB687WSC
size range: 200-500

value: ENCBS813EMP at ENCODE; https://www.encodeproject.org/ENCBS813EMP/


title: ChIA-PET from GM19238 (ENCLB662ASL)

description:
https://www.encodeproject.org/experiments/ENCSR029IXY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIA-PET in GM19238
experiment encode accession: ENCSR029IXY
assay title: ChIA-PET
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB662ASL
size range: 200-500

source_name: Homo sapiens GM19238 cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: Derived from ENCODE donor ENCDO000ACL; https://www.encodeproject.org/ENCDO000ACL/

value: ENCBS594JOC at ENCODE; https://www.encodeproject.org/ENCBS594JOC/

value: ENCODE dbxrefs Cellosaurus CVCL_9633; https://web.expasy.org/cellosaurus/CVCL_9633


title: CRISPRi RNA-seq from K562 (ENCLB074TJB)

description:
https://www.encodeproject.org/experiments/ENCSR550FIL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TEAD4.
experiment encode accession: ENCSR550FIL
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB074TJB
size range: >200

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: ENCBS526FZT at ENCODE; https://www.encodeproject.org/ENCBS526FZT/

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


title: CRISPRi RNA-seq from K562 (ENCLB605JDN)

description:
https://www.encodeproject.org/experiments/ENCSR545HTM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting USF1.
experiment encode accession: ENCSR545HTM
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB605JDN
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting USF1

value: cell line

value: female

value: ENCBS753CQR at ENCODE; https://www.encodeproject.org/ENCBS753CQR/


title: ChIA-PET from GM19240 (ENCLB147KYD)

description:
https://www.encodeproject.org/experiments/ENCSR025JPD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIA-PET in GM19240
experiment encode accession: ENCSR025JPD
assay title: ChIA-PET
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB147KYD
size range: 200-500

source_name: Homo sapiens GM19240 cell line

value: unknown

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000ACN; https://www.encodeproject.org/ENCDO000ACN/

value: ENCBS760NLE at ENCODE; https://www.encodeproject.org/ENCBS760NLE/

value: ENCODE dbxrefs Cellosaurus CVCL_9635; https://web.expasy.org/cellosaurus/CVCL_9635


title: ChIA-PET from GM19238 (ENCLB562ROH)

description:
https://www.encodeproject.org/experiments/ENCSR029IXY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIA-PET in GM19238
experiment encode accession: ENCSR029IXY
assay title: ChIA-PET
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB562ROH
size range: 200-500

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: Derived from ENCODE donor ENCDO000ACL; https://www.encodeproject.org/ENCDO000ACL/

value: ENCBS332FBI at ENCODE; https://www.encodeproject.org/ENCBS332FBI/


title: CRISPRi RNA-seq from K562 (ENCLB128IOG)

description:
https://www.encodeproject.org/experiments/ENCSR591QYK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TRIM28.
experiment encode accession: ENCSR591QYK
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB128IOG
size range: >200

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS342LZY at ENCODE; https://www.encodeproject.org/ENCBS342LZY/


title: ChIA-PET from SU-DHL-2 (ENCLB706XNX)

description:
https://www.encodeproject.org/experiments/ENCSR128RPG/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIA-PET in human SU-DHL-2 cells
experiment encode accession: ENCSR128RPG
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB706XNX
size range: 450-650

value: large cell lymphoma; diffuse histiocytic lymphoma

value: 75 year

value: Derived from ENCODE donor ENCDO852AAX; https://www.encodeproject.org/ENCDO852AAX/

value: ENCBS354PZC at ENCODE; https://www.encodeproject.org/ENCBS354PZC/

value: ENCODE dbxrefs Cellosaurus CVCL_9550; https://web.expasy.org/cellosaurus/CVCL_9550


title: CRISPRi RNA-seq from K562 (ENCLB528PEP)

description:
https://www.encodeproject.org/experiments/ENCSR545HTM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting USF1.
experiment encode accession: ENCSR545HTM
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB528PEP
size range: >200

value: cell line

value: female

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS132SWD at ENCODE; https://www.encodeproject.org/ENCBS132SWD/

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


title: ChIA-PET from GM19240 (ENCLB384GWJ)

description:
https://www.encodeproject.org/experiments/ENCSR025JPD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIA-PET in GM19240
experiment encode accession: ENCSR025JPD
assay title: ChIA-PET
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB384GWJ
size range: 200-500

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: unknown

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000ACN; https://www.encodeproject.org/ENCDO000ACN/

value: ENCBS338PQB at ENCODE; https://www.encodeproject.org/ENCBS338PQB/

value: ENCODE dbxrefs Cellosaurus CVCL_9635; https://web.expasy.org/cellosaurus/CVCL_9635


title: ChIA-PET from GM19239 (ENCLB890SWG)

description:
https://www.encodeproject.org/experiments/ENCSR018VOS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIA-PET in GM19239
experiment encode accession: ENCSR018VOS
assay title: ChIA-PET
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB890SWG
size range: 200-500

source_name: Homo sapiens GM19239 cell line

value: male

value: Derived from ENCODE donor ENCDO000ACM; https://www.encodeproject.org/ENCDO000ACM/

value: ENCBS513JGI at ENCODE; https://www.encodeproject.org/ENCBS513JGI/

value: ENCODE dbxrefs Cellosaurus CVCL_9634; https://web.expasy.org/cellosaurus/CVCL_9634


title: ChIA-PET from GM19239 (ENCLB624DVY)

description:
https://www.encodeproject.org/experiments/ENCSR018VOS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIA-PET in GM19239
experiment encode accession: ENCSR018VOS
assay title: ChIA-PET
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB624DVY
size range: 200-500

value: cell line

value: ENCBS657HMS at ENCODE; https://www.encodeproject.org/ENCBS657HMS/


title: CRISPRi RNA-seq from K562 (ENCLB704ASE)

description:
https://www.encodeproject.org/experiments/ENCSR469EFL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting STAT2.
experiment encode accession: ENCSR469EFL
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB704ASE
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting STAT2

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS140ZVH at ENCODE; https://www.encodeproject.org/ENCBS140ZVH/


title: CRISPRi RNA-seq from K562 (ENCLB523YQA)

description:
https://www.encodeproject.org/experiments/ENCSR409OFU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SNW1.
experiment encode accession: ENCSR409OFU
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR761AQZ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB523YQA
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting SNW1

value: Sherman Weissman, Yale

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

value: ENCBS174GHJ at ENCODE; https://www.encodeproject.org/ENCBS174GHJ/

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


title: CRISPRi RNA-seq from K562 (ENCLB063WAI)

description:
https://www.encodeproject.org/experiments/ENCSR469EFL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting STAT2.
experiment encode accession: ENCSR469EFL
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB063WAI
size range: >200

value: ENCBS780AML at ENCODE; https://www.encodeproject.org/ENCBS780AML/


title: CRISPRi RNA-seq from K562 (ENCLB515JTL)

description:
https://www.encodeproject.org/experiments/ENCSR399QAP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TLE2.
experiment encode accession: ENCSR399QAP
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB515JTL
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting TLE2

value: ENCBS736DGC at ENCODE; https://www.encodeproject.org/ENCBS736DGC/


title: CRISPRi RNA-seq from K562 (ENCLB318SPP)

description:
https://www.encodeproject.org/experiments/ENCSR399QAP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting TLE2.
experiment encode accession: ENCSR399QAP
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB318SPP
size range: >200

value: ENCBS418CDR at ENCODE; https://www.encodeproject.org/ENCBS418CDR/


title: CRISPRi RNA-seq from K562 (ENCLB512QGV)

description:
https://www.encodeproject.org/experiments/ENCSR409OFU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting SNW1.
experiment encode accession: ENCSR409OFU
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR761AQZ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB512QGV
size range: >200

value: ENCBS970RDW at ENCODE; https://www.encodeproject.org/ENCBS970RDW/


title: ChIA-PET from K562 (ENCLB555ABK)

description:
https://www.encodeproject.org/experiments/ENCSR000FDG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIA-PET in K562
experiment encode accession: ENCSR000FDG
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABK
size range: 200-500

source_name: Homo sapiens K562 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: Michael Snyder, Stanford

tag: passage number

value: ENCBS501AAA at ENCODE; https://www.encodeproject.org/ENCBS501AAA/


title: CRISPRi RNA-seq from K562 (ENCLB311AAK)

description:
https://www.encodeproject.org/experiments/ENCSR389OCD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting JUND.
experiment encode accession: ENCSR389OCD
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB311AAK
size range: >200

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

value: JUND

value: cell line

value: ENCBS649JIJ at ENCODE; https://www.encodeproject.org/ENCBS649JIJ/


title: ChIA-PET from K562 (ENCLB555ABL)

description:
https://www.encodeproject.org/experiments/ENCSR000FDG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIA-PET in K562
experiment encode accession: ENCSR000FDG
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABL
size range: 200-500

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS502AAA at ENCODE; https://www.encodeproject.org/ENCBS502AAA/


title: ChIA-PET from K562 (ENCLB555ABI)

description:
https://www.encodeproject.org/experiments/ENCSR000FDF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIA-PET in K562
experiment encode accession: ENCSR000FDF
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABI
size range: 200-500

value: 53 year

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


title: ChIA-PET from K562 (ENCLB555ABJ)

description:
https://www.encodeproject.org/experiments/ENCSR000FDF/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIA-PET in K562
experiment encode accession: ENCSR000FDF
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABJ
size range: 200-500

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


title: ChIA-PET from K562 (ENCLB555ABH)

description:
https://www.encodeproject.org/experiments/ENCSR000FDE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIA-PET in K562
experiment encode accession: ENCSR000FDE
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABH
size range: 200-500


title: CRISPRi RNA-seq from K562 (ENCLB511KKV)

description:
https://www.encodeproject.org/experiments/ENCSR389OCD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting JUND.
experiment encode accession: ENCSR389OCD
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB511KKV
size range: >200

value: Sherman Weissman, Yale

value: ENCBS725SHQ at ENCODE; https://www.encodeproject.org/ENCBS725SHQ/


title: CRISPRi RNA-seq from K562 (ENCLB925AAI)

description:
https://www.encodeproject.org/experiments/ENCSR385ZTW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFE2L1.
experiment encode accession: ENCSR385ZTW
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB925AAI
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting NFE2L1

value: ENCBS124RUW at ENCODE; https://www.encodeproject.org/ENCBS124RUW/


title: ChIA-PET from K562 (ENCLB555ABG)

description:
https://www.encodeproject.org/experiments/ENCSR000FDE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIA-PET in K562
experiment encode accession: ENCSR000FDE
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABG
size range: 200-500


title: ChIA-PET from K562 (ENCLB555ABF)

description:
https://www.encodeproject.org/experiments/ENCSR000FDD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIA-PET in K562
experiment encode accession: ENCSR000FDD
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABF
size range: 200-500


title: ChIA-PET from K562 (ENCLB555ABC)

description:
https://www.encodeproject.org/experiments/ENCSR000FDC/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIA-PET in K562
experiment encode accession: ENCSR000FDC
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABC
size range: 200-500

value: ENCBS499AAA at ENCODE; https://www.encodeproject.org/ENCBS499AAA/


title: CRISPRi RNA-seq from K562 (ENCLB681OZM)

description:
https://www.encodeproject.org/experiments/ENCSR385ZTW/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFE2L1.
experiment encode accession: ENCSR385ZTW
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB681OZM
size range: >200

value: ENCBS142CAC at ENCODE; https://www.encodeproject.org/ENCBS142CAC/


title: ChIA-PET from K562 (ENCLB555ABE)

description:
https://www.encodeproject.org/experiments/ENCSR000FDD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIA-PET in K562
experiment encode accession: ENCSR000FDD
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABE
size range: 200-500

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: Michael Snyder, Stanford


title: CRISPRi RNA-seq from K562 (ENCLB877WLS)

description:
https://www.encodeproject.org/experiments/ENCSR385ZTW/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFE2L1.
experiment encode accession: ENCSR385ZTW
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB877WLS
size range: >200

value: ENCBS095UXJ at ENCODE; https://www.encodeproject.org/ENCBS095UXJ/


title: CRISPRi RNA-seq from K562 (ENCLB138NID)

description:
https://www.encodeproject.org/experiments/ENCSR385ZTW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFE2L1.
experiment encode accession: ENCSR385ZTW
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB138NID
size range: >200

value: cell line

value: ENCBS506ANY at ENCODE; https://www.encodeproject.org/ENCBS506ANY/


title: CRISPRi RNA-seq from K562 (ENCLB464MPN)

description:
https://www.encodeproject.org/experiments/ENCSR381TNV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFATC1.
experiment encode accession: ENCSR381TNV
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB464MPN
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting NFATC1

value: female

value: ENCBS670WOE at ENCODE; https://www.encodeproject.org/ENCBS670WOE/


title: ChIA-PET from K562 (ENCLB555ABA)

description:
https://www.encodeproject.org/experiments/ENCSR000FDB/
***************
biological replicate number: 1
technical replicate number: 1,2
description: RAD21 ChIA-PET in K562
experiment encode accession: ENCSR000FDB
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABA
size range: 200-500

value: chronic myelogenous leukemia (CML)

value: adult


title: ChIA-PET from K562 (ENCLB555ABB)

description:
https://www.encodeproject.org/experiments/ENCSR000FDB/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in K562
experiment encode accession: ENCSR000FDB
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABB
size range: 200-500

value: 53 year

value: ENCBS500AAA at ENCODE; https://www.encodeproject.org/ENCBS500AAA/


title: CRISPRi RNA-seq from K562 (ENCLB324ZDA)

description:
https://www.encodeproject.org/experiments/ENCSR381TNV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NFATC1.
experiment encode accession: ENCSR381TNV
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB324ZDA
size range: >200

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

value: ENCBS355HGB at ENCODE; https://www.encodeproject.org/ENCBS355HGB/

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


title: CRISPRi RNA-seq from K562 (ENCLB413TNJ)

description:
https://www.encodeproject.org/experiments/ENCSR376CFR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting STAT5A.
experiment encode accession: ENCSR376CFR
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB413TNJ
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting STAT5A

value: Sherman Weissman, Yale

value: ENCBS017OLD at ENCODE; https://www.encodeproject.org/ENCBS017OLD/


title: CRISPRi RNA-seq from K562 (ENCLB217KGU)

description:
https://www.encodeproject.org/experiments/ENCSR376CFR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting STAT5A.
experiment encode accession: ENCSR376CFR
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB217KGU
size range: >200

value: ENCBS597EDW at ENCODE; https://www.encodeproject.org/ENCBS597EDW/


title: ChIA-PET from K562 (ENCLB555ABD)

description:
https://www.encodeproject.org/experiments/ENCSR000FDC/
***************
biological replicate number: 2
technical replicate number: 1,2
description: POLR2A ChIA-PET in K562
experiment encode accession: ENCSR000FDC
assay title: ChIA-PET
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ABD
size range: 200-500

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


title: CRISPRi RNA-seq from K562 (ENCLB989OCM)

description:
https://www.encodeproject.org/experiments/ENCSR369BHC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HDAC8.
experiment encode accession: ENCSR369BHC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB989OCM
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting HDAC8

value: ENCBS935HHK at ENCODE; https://www.encodeproject.org/ENCBS935HHK/


title: Hi-C from THP-1 (ENCLB919ZNJ)

description:
https://www.encodeproject.org/experiments/ENCSR748LQF/
***************
biological replicate number: 2
technical replicate number: 1
description: in situ MboI Hi-C
experiment encode accession: ENCSR748LQF
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB919ZNJ
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

source_name: Homo sapiens THP-1 cell line originated from THP-1

value: in situ Hi-C of human cell line:Transitionary Obejct, THP-1 cells with PMA

value: male

value: acute monocytic leukemia

value: child

value: 1 year

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO303OIJ; https://www.encodeproject.org/ENCDO303OIJ/

value: ENCBS913QYS at ENCODE; https://www.encodeproject.org/ENCBS913QYS/

value: ENCODE dbxrefs Cellosaurus CVCL_0006; https://web.expasy.org/cellosaurus/CVCL_0006


title: CRISPRi RNA-seq from K562 (ENCLB737LRN)

description:
https://www.encodeproject.org/experiments/ENCSR359VJC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HOXB4.
experiment encode accession: ENCSR359VJC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB737LRN
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting HOXB4

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

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

value: ENCBS195REE at ENCODE; https://www.encodeproject.org/ENCBS195REE/


title: Hi-C from THP-1 (ENCLB076DGG)

description:
https://www.encodeproject.org/experiments/ENCSR748LQF/
***************
biological replicate number: 1
technical replicate number: 2
description: in situ MboI Hi-C
experiment encode accession: ENCSR748LQF
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB076DGG
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

value: ENCBS615XLU at ENCODE; https://www.encodeproject.org/ENCBS615XLU/


title: Hi-C from THP-1 (ENCLB546KKI)

description:
https://www.encodeproject.org/experiments/ENCSR748LQF/
***************
biological replicate number: 1
technical replicate number: 3
description: in situ MboI Hi-C
experiment encode accession: ENCSR748LQF
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB546KKI
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

value: in situ Hi-C of human cell line:Transitionary Obejct, THP-1 cells with PMA


title: CRISPRi RNA-seq from K562 (ENCLB581PKH)

description:
https://www.encodeproject.org/experiments/ENCSR359VJC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HOXB4.
experiment encode accession: ENCSR359VJC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB581PKH
size range: >200

value: Sherman Weissman, Yale

value: ENCBS999ADL at ENCODE; https://www.encodeproject.org/ENCBS999ADL/

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


title: Hi-C from THP-1 (ENCLB479SZL)

description:
https://www.encodeproject.org/experiments/ENCSR748LQF/
***************
biological replicate number: 2
technical replicate number: 2
description: in situ MboI Hi-C
experiment encode accession: ENCSR748LQF
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB479SZL
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

value: male

value: acute monocytic leukemia

value: child

value: 1 year


title: CRISPRi RNA-seq from K562 (ENCLB582XDX)

description:
https://www.encodeproject.org/experiments/ENCSR357LVC/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NR4A1.
experiment encode accession: ENCSR357LVC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB582XDX
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting NR4A1

value: Michael Snyder, Stanford

value: ENCBS248RXV at ENCODE; https://www.encodeproject.org/ENCBS248RXV/


title: CRISPRi RNA-seq from K562 (ENCLB280PFL)

description:
https://www.encodeproject.org/experiments/ENCSR357LVC/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NR4A1.
experiment encode accession: ENCSR357LVC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB280PFL
size range: >200

value: cell line

value: female

value: ENCBS345SBC at ENCODE; https://www.encodeproject.org/ENCBS345SBC/


title: CRISPRi RNA-seq from K562 (ENCLB277AYQ)

description:
https://www.encodeproject.org/experiments/ENCSR299HUJ/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NRF1.
experiment encode accession: ENCSR299HUJ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB277AYQ
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting NRF1

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS631OMB at ENCODE; https://www.encodeproject.org/ENCBS631OMB/


title: Hi-C from THP-1 (ENCLB417VRG)

description:
https://www.encodeproject.org/experiments/ENCSR748LQF/
***************
biological replicate number: 1
technical replicate number: 1
description: in situ MboI Hi-C
experiment encode accession: ENCSR748LQF
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB417VRG
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

value: in situ Hi-C of human cell line:Transitionary Obejct, THP-1 cells with PMA

value: Derived from ENCODE donor ENCDO303OIJ; https://www.encodeproject.org/ENCDO303OIJ/

value: ENCBS615XLU at ENCODE; https://www.encodeproject.org/ENCBS615XLU/

value: ENCODE dbxrefs Cellosaurus CVCL_0006; https://web.expasy.org/cellosaurus/CVCL_0006


title: CRISPRi RNA-seq from K562 (ENCLB353WMA)

description:
https://www.encodeproject.org/experiments/ENCSR299HUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NRF1.
experiment encode accession: ENCSR299HUJ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB353WMA
size range: >200

value: Sherman Weissman, Yale

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

value: ENCBS118LXR at ENCODE; https://www.encodeproject.org/ENCBS118LXR/

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


title: CRISPRi RNA-seq from K562 (ENCLB950MCF)

description:
https://www.encodeproject.org/experiments/ENCSR299HUJ/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting NRF1.
experiment encode accession: ENCSR299HUJ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB950MCF
size range: >200

value: Michael Snyder, Stanford

value: ENCBS557XQF at ENCODE; https://www.encodeproject.org/ENCBS557XQF/


title: Hi-C from THP-1 (ENCLB135NTF)

description:
https://www.encodeproject.org/experiments/ENCSR669GJD/
***************
biological replicate number: 1
technical replicate number: 1
description: in situ MboI Hi-C
experiment encode accession: ENCSR669GJD
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB135NTF
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

source_name: Homo sapiens THP-1 cell line originated from THP-1 treated with 35.8 ng/mL phorbol 13-acetate 12-myristate for 72 hours

value: cell line

value: in situ Hi-C of human cell line:THP-1 cells pma-treated

value: male

value: acute monocytic leukemia

value: child

value: 1 year

tag: treatments

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:72; duration_units:hour;

value: ENCBS443IYN at ENCODE; https://www.encodeproject.org/ENCBS443IYN/


title: Hi-C from THP-1 (ENCLB402DRA)

description:
https://www.encodeproject.org/experiments/ENCSR669GJD/
***************
biological replicate number: 2
technical replicate number: 1
description: in situ MboI Hi-C
experiment encode accession: ENCSR669GJD
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB402DRA
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

value: Derived from ENCODE donor ENCDO303OIJ; https://www.encodeproject.org/ENCDO303OIJ/

value: ENCBS248PAQ at ENCODE; https://www.encodeproject.org/ENCBS248PAQ/


title: Hi-C from THP-1 (ENCLB272QBD)

description:
https://www.encodeproject.org/experiments/ENCSR669GJD/
***************
biological replicate number: 1
technical replicate number: 2
description: in situ MboI Hi-C
experiment encode accession: ENCSR669GJD
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB272QBD
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells
instrument models: Illumina HiSeq 2000,Illumina HiSeq 4000


title: Hi-C from THP-1 (ENCLB412KQW)

description:
https://www.encodeproject.org/experiments/ENCSR669GJD/
***************
biological replicate number: 2
technical replicate number: 3
description: in situ MboI Hi-C
experiment encode accession: ENCSR669GJD
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB412KQW
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells


title: Hi-C from THP-1 (ENCLB053TJC)

description:
https://www.encodeproject.org/experiments/ENCSR669GJD/
***************
biological replicate number: 2
technical replicate number: 2
description: in situ MboI Hi-C
experiment encode accession: ENCSR669GJD
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB053TJC
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells


title: CRISPRi RNA-seq from K562 (ENCLB977TGD)

description:
https://www.encodeproject.org/experiments/ENCSR369BHC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HDAC8.
experiment encode accession: ENCSR369BHC
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB977TGD
size range: >200

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS151UTN at ENCODE; https://www.encodeproject.org/ENCBS151UTN/


title: CRISPRi RNA-seq from K562 (ENCLB057VDB)

description:
https://www.encodeproject.org/experiments/ENCSR294ZCD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting THAP1.
experiment encode accession: ENCSR294ZCD
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB057VDB
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting THAP1

value: Sherman Weissman, Yale

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

value: ENCBS311JPS at ENCODE; https://www.encodeproject.org/ENCBS311JPS/

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


title: CRISPRi RNA-seq from K562 (ENCLB935DFY)

description:
https://www.encodeproject.org/experiments/ENCSR294ZCD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting THAP1.
experiment encode accession: ENCSR294ZCD
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB935DFY
size range: >200

value: cell line

value: ENCBS209WHZ at ENCODE; https://www.encodeproject.org/ENCBS209WHZ/


title: Hi-C from THP-1 (ENCLB024DQM)

description:
https://www.encodeproject.org/experiments/ENCSR748LQF/
***************
biological replicate number: 2
technical replicate number: 3
description: in situ MboI Hi-C
experiment encode accession: ENCSR748LQF
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB024DQM
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

value: in situ Hi-C of human cell line:Transitionary Obejct, THP-1 cells with PMA

value: male

value: acute monocytic leukemia

value: child

value: Michael Snyder, Stanford

value: ENCBS913QYS at ENCODE; https://www.encodeproject.org/ENCBS913QYS/

value: ENCODE dbxrefs Cellosaurus CVCL_0006; https://web.expasy.org/cellosaurus/CVCL_0006


title: miR-204-transfected mouse articular chondrocytes, rep 4

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
RNA-seq samples were analyzed by Illumina HiSeq 2500 System.
Sequenced reads were processed and aligned to the reference genome (mm10) using TopHat program.
Cufflinks v2.2.1 was used to assemble aligned reads into transcripts and estimate their abundance.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including FPKM values for each sample

organism: Mus musculus

growth_protocol: Primary cultured chondrocytes were maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (Gibco) and antibiotics (penicillin and streptomycin). Cultured cells were maintained in a humidified 37°C, 5% CO2, and 3% O2 atmosphere.

extract_protocol:
Total RNA was extracted using the TRI reagent (Molecular Research enter, Inc.).
One microgram of total RNA (RIN > 9.5) was used to obtain cDNA libraries using Truseq Stranded mRNA LT Sample Prep kit (Illumina). Final cDNA libraries were analyzed for size distribution, quantified by qRT-PCR (Kapa Biosystems) using Agilent 2100 Bioanalyzer, and normalized to 2 nM for sequencing.

treatment_protocol: Mouse articular chondrocytes were transfected with 50 nM of miR-Ctrl or miR-204 for 24 h. The cells were harvested 24 h after completion of transfection.

tag: strain background

value: ICR

tag: genotype/variation

value: miR-204 transfection

tag: cell type

value: articular chondrocytes


title: CRISPRi RNA-seq from K562 (ENCLB504SDP)

description:
https://www.encodeproject.org/experiments/ENCSR267BHU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ZNF395.
experiment encode accession: ENCSR267BHU
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB504SDP
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting ZNF395

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS928QPS at ENCODE; https://www.encodeproject.org/ENCBS928QPS/


title: CRISPRi RNA-seq from K562 (ENCLB181BON)

description:
https://www.encodeproject.org/experiments/ENCSR268DNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ERF.
experiment encode accession: ENCSR268DNJ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB181BON
size range: >200

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

value: ERF

value: cell line

value: Sherman Weissman, Yale

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

value: ENCBS566CFZ at ENCODE; https://www.encodeproject.org/ENCBS566CFZ/

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


title: CRISPRi RNA-seq from K562 (ENCLB818EIU)

description:
https://www.encodeproject.org/experiments/ENCSR263IOO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGB2.
experiment encode accession: ENCSR263IOO
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB818EIU
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting HMGB2

value: ENCBS936ASP at ENCODE; https://www.encodeproject.org/ENCBS936ASP/


title: miR-204-transfected mouse articular chondrocytes, rep 2


title: miR-204-transfected mouse articular chondrocytes, rep 3


title: CRISPRi RNA-seq from K562 (ENCLB206CAL)

description:
https://www.encodeproject.org/experiments/ENCSR267BHU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ZNF395.
experiment encode accession: ENCSR267BHU
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB206CAL
size range: >200

value: ENCBS929SKV at ENCODE; https://www.encodeproject.org/ENCBS929SKV/


title: siRNA RNA-seq from C4-2B (ENCLB069PAC)

description:
https://www.encodeproject.org/experiments/ENCSR244ZVP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on CB-24 cells treated with siRNA targeting ZFX.
experiment encode accession: ENCSR244ZVP
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR142YZV
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB069PAC
size range: >200

source_name: Homo sapiens C4-2B cell line expressing RNAi targeting ZFX

value: ZFX

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

value: male

value: prostate adenocarcinoma

value: 50 year

value: Peggy Farnham, USC

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

value: ENCBS108UKE at ENCODE; https://www.encodeproject.org/ENCBS108UKE/

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


title: miR-204-transfected mouse articular chondrocytes, rep 1

value: ICR

value: miR-204 transfection

value: articular chondrocytes


title: mESC only

city: Blacksburg

first: M. Cristina

last: Villafranca

state: VA

address: 205 Duckpond Drive

institute: Virginia Polytechnic Institute and State University

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

source_name: 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: control

tag: sampling time after fusion

value: mouse embryonic stem cell


title: CRISPRi RNA-seq from K562 (ENCLB793YXR)

description:
https://www.encodeproject.org/experiments/ENCSR268DNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ERF.
experiment encode accession: ENCSR268DNJ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB793YXR
size range: >200

tag: antibody

value: ERF

tag: line

value: cell line

value: female

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: ENCBS689WZM at ENCODE; https://www.encodeproject.org/ENCBS689WZM/

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


title: siRNA RNA-seq from C4-2B (ENCLB471LFR)

description:
https://www.encodeproject.org/experiments/ENCSR244ZVP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on CB-24 cells treated with siRNA targeting ZFX.
experiment encode accession: ENCSR244ZVP
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR142YZV
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB471LFR
size range: >200

value: ZFX

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

tag: biosample encode accession

tag: Sex

value: male

value: prostate adenocarcinoma

value: 50 year

value: Peggy Farnham, USC

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

value: ENCBS159HRH at ENCODE; https://www.encodeproject.org/ENCBS159HRH/


title: miR-Ctrl-transfected mouse articular chondrocytes, rep 4

value: ICR

value: miR-Ctrl transfection

value: articular chondrocytes


title: siRNA RNA-seq from C4-2B (ENCLB288ZVP)

description:
https://www.encodeproject.org/experiments/ENCSR244ZVP/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on CB-24 cells treated with siRNA targeting ZFX.
experiment encode accession: ENCSR244ZVP
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR142YZV
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB288ZVP
size range: >200

value: cell line

tag: health state

tag: dev stage

value: adult

value: ENCBS328CYG at ENCODE; https://www.encodeproject.org/ENCBS328CYG/

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


title: miR-Ctrl-transfected mouse articular chondrocytes, rep 2


title: CRISPRi RNA-seq from K562 (ENCLB646WHD)

description:
https://www.encodeproject.org/experiments/ENCSR243VNX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGN2.
experiment encode accession: ENCSR243VNX
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB646WHD
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting HMGN2

value: female

value: chronic myelogenous leukemia (CML)

tag: age

value: 53 year

tag: lab

value: Sherman Weissman, Yale

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

value: ENCBS848BRU at ENCODE; https://www.encodeproject.org/ENCBS848BRU/


title: Subject 4 anti-CD3

city: Saint Louis

first: Anil

middle: Kumar

last: Chauhan

state: MO

address: 1402 South grant

department: Medicine

institute: Saint Louis University

data_processing:
Sequencing was performed in Ion Torrent Proton
Reads were aligned to the hg19 Transcriptome
Normalization was performed based on total reads
Genome_build: hg 19
Supplementary_files_format_and_content: Excel spreadsheet, Target, Transcript Reads, NCBI name, HGNC_SYMBOL_ACC, ENTREZ_GENES_ID, V133PLUS2_PSID

source_name: Naïve CD4 T cells

growth_protocol: Grown at 37 degree in CO2 incubator at 5% CO2.

extract_protocol:
As per Clontech RNA extraction kit.
The libray was contructed using Ion AmpliSeq Transcriptome Human  Gene Expression Kit (Life Technologies)
A total of 20 ng of RNA purified was used to contruct libraries.

treatment_protocol: anti-CD3 (0.25 microgram/ml); anti-CD28 (2.0 microgram/ml), and ICs (10 microgram/ml) for each one million cells.

value: Naive CD4 T cells

tag: agent


title: CRISPRi RNA-seq from K562 (ENCLB937JVD)

description:
https://www.encodeproject.org/experiments/ENCSR243VNX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGN2.
experiment encode accession: ENCSR243VNX
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB937JVD
size range: >200

tag: link

value: ENCBS307TAZ at ENCODE; https://www.encodeproject.org/ENCBS307TAZ/

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


title: Hi-C from THP-1 (ENCLB648VTO)

description:
https://www.encodeproject.org/experiments/ENCSR669GJD/
***************
biological replicate number: 1
technical replicate number: 3
description: in situ MboI Hi-C
experiment encode accession: ENCSR669GJD
assay title: Hi-C
assembly: hg19
encode release date: 2018-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB648VTO
size range: 300-500
nucleic acid starting quantity: 6000000
nucleic acid starting quantity units: cells

tag: description

value: in situ Hi-C of human cell line:THP-1 cells pma-treated

value: male

value: acute monocytic leukemia

value: child

value: 1 year

value: Michael Snyder, Stanford

tag: treatments

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:72; duration_units:hour;

value: Derived from ENCODE donor ENCDO303OIJ; https://www.encodeproject.org/ENCDO303OIJ/

value: ENCBS443IYN at ENCODE; https://www.encodeproject.org/ENCBS443IYN/


title: CRISPRi RNA-seq from K562 (ENCLB763SEC)

description:
https://www.encodeproject.org/experiments/ENCSR235ZEI/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RBBP7.
experiment encode accession: ENCSR235ZEI
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB763SEC
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting RBBP7

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS016PHF at ENCODE; https://www.encodeproject.org/ENCBS016PHF/


title: Subject 4 anti-CD3 + ICs

value: Naive CD4 T cells

value: anti-CD3 + ICs


title: CRISPRi RNA-seq from K562 (ENCLB500HGP)

description:
https://www.encodeproject.org/experiments/ENCSR235ZEI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RBBP7.
experiment encode accession: ENCSR235ZEI
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB500HGP
size range: >200

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS628LPZ at ENCODE; https://www.encodeproject.org/ENCBS628LPZ/

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


title: Subject 3 anti-CD3


title: CRISPRi RNA-seq from K562 (ENCLB707XOX)

description:
https://www.encodeproject.org/experiments/ENCSR263IOO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting HMGB2.
experiment encode accession: ENCSR263IOO
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB707XOX
size range: >200

value: ENCBS134NXZ at ENCODE; https://www.encodeproject.org/ENCBS134NXZ/


title: Subject 4 anti-CD3 + anti-CD28

value: anti-CD3 + anti-CD28


title: Subject 3 anti-CD3 + anti CD28


title: CRISPRi RNA-seq from K562 (ENCLB406ECL)

description:
https://www.encodeproject.org/experiments/ENCSR223QTD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ZBTB33.
experiment encode accession: ENCSR223QTD
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB406ECL
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting ZBTB33

value: ENCBS189ORA at ENCODE; https://www.encodeproject.org/ENCBS189ORA/


title: Subject 2 anti-CD3 +anti-CD28


title: CRISPRi RNA-seq from K562 (ENCLB712BZW)

description:
https://www.encodeproject.org/experiments/ENCSR200UDS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting CITED2.
experiment encode accession: ENCSR200UDS
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB712BZW
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting CITED2

value: ENCBS156YIS at ENCODE; https://www.encodeproject.org/ENCBS156YIS/


title: Subject 2 anti-CD3


title: CRISPRi RNA-seq from K562 (ENCLB462MEY)

description:
https://www.encodeproject.org/experiments/ENCSR184VVN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting STAT1.
experiment encode accession: ENCSR184VVN
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2018-01-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB462MEY
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting STAT1

value: ENCBS554LPK at ENCODE; https://www.encodeproject.org/ENCBS554LPK/


title: Subject 1 anti-CD3


title: CRISPRi RNA-seq from K562 (ENCLB864WAC)

description:
https://www.encodeproject.org/experiments/ENCSR200UDS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting CITED2.
experiment encode accession: ENCSR200UDS
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB864WAC
size range: >200

value: cell line

value: ENCBS846JUN at ENCODE; https://www.encodeproject.org/ENCBS846JUN/


title: Subject 3 anti-CD3 + ICs


title: miR-Ctrl-transfected mouse articular chondrocytes, rep 3

tag: strain background

value: ICR

tag: genotype/variation

value: miR-Ctrl transfection

value: articular chondrocytes


title: Subject 2 anti-CD3 + ICs

tag: cell type

value: Naive CD4 T cells


title: miR-Ctrl-transfected mouse articular chondrocytes, rep 1


title: CRISPRi RNA-seq from K562 (ENCLB708DUS)

description:
https://www.encodeproject.org/experiments/ENCSR190RZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting BACH1.
experiment encode accession: ENCSR190RZZ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB708DUS
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting BACH1

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS347VOS at ENCODE; https://www.encodeproject.org/ENCBS347VOS/


title: Subject 1 anti-CD3 + ICs

value: anti-CD3 + ICs


title: CRISPRi RNA-seq from K562 (ENCLB970TUL)

description:
https://www.encodeproject.org/experiments/ENCSR181WYS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting WHSC1.
experiment encode accession: ENCSR181WYS
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB970TUL
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting WHSC1

value: 53 year

value: Sherman Weissman, Yale

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

value: ENCBS279DUW at ENCODE; https://www.encodeproject.org/ENCBS279DUW/

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


title: CRISPRi RNA-seq from K562 (ENCLB556CJW)

description:
https://www.encodeproject.org/experiments/ENCSR190RZZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting BACH1.
experiment encode accession: ENCSR190RZZ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB556CJW
size range: >200

value: ENCBS020BQK at ENCODE; https://www.encodeproject.org/ENCBS020BQK/


title: Subject 1 anti-CD3 + anti-CD28

value: anti-CD3 + anti-CD28


title: CRISPRi RNA-seq from K562 (ENCLB029MPB)

description:
https://www.encodeproject.org/experiments/ENCSR181WYS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting WHSC1.
experiment encode accession: ENCSR181WYS
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB029MPB
size range: >200

value: cell line

value: ENCBS392DZH at ENCODE; https://www.encodeproject.org/ENCBS392DZH/


title: CRISPRi RNA-seq from K562 (ENCLB020JNI)

description:
https://www.encodeproject.org/experiments/ENCSR223QTD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting ZBTB33.
experiment encode accession: ENCSR223QTD
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB020JNI
size range: >200

value: ENCBS493JKJ at ENCODE; https://www.encodeproject.org/ENCBS493JKJ/


title: OCT6Flag_input

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

country: China

institute: tongji university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to hg19 reference genome using bowtie2 (v 2.2.9) with default parameters.
ChIP peaks were called using macs14(v 1.4.2) with parameter: macs14 –t Sample.bam –c input.bam –g hs –p 1e-7 –n name.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig and macs2 with parameter --SPRM.

source_name: reprogramming cells

extract_protocol:
DNA was extracted by reverse crosslinking at 65 °C overnight with proteinase K (20 μg/μl) and RNaseA (20 ug/ul) and purified using phenol/chloroform extraction.
Sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB).

treatment_protocol: The cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125 M glycine for 5 min at at room temperature. The cross-linked cells were incubated with lysis buffer 1 (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM 0.5 M EDTA, 10% glycerol, 0.5% IGEPAL CA630, 0.25% Triton X-100, and 1 ´ Complete Protease inhibitor) for 30 min at 4 °C and washed in lysis buffer 2 (10 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 1 ´ Complete Protease inhibitor) for 10 min at 4 °C. The cells were then resuspended in sonication buffer and sonicated using the Diagenode Bioruptor (high power, 30 cycles of 30 s on and 30 s off). 100 μg of sonicated chromatin was then incubated with Dynabeads protein G (Invitrogen) coupled to 15 μg of FLAG antibody (Sigma) in 4 ´ volume of ChIP dilution buffer at 4 °C overnight. Beads were washed once with low-salt buffer, twice with high-salt buffer, twice with RIPA buffer, and once with TE containing 50 mM NaCl. Elution was done with elution buffer for 15 min at 65 °C.

tag: reprogramming factor

tag: reprogramming day


title: OCT4Flag_ChIP

tag: antibody

value: anti-Flag


title: CRISPRi RNA-seq from K562 (ENCLB286MTD)

description:
https://www.encodeproject.org/experiments/ENCSR181WYS/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting WHSC1.
experiment encode accession: ENCSR181WYS
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB286MTD
size range: >200

tag: line

value: Michael Snyder, Stanford

value: ENCBS428QGT at ENCODE; https://www.encodeproject.org/ENCBS428QGT/


title: CRISPRi RNA-seq from K562 (ENCLB539UGM)

description:
https://www.encodeproject.org/experiments/ENCSR184VVN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting STAT1.
experiment encode accession: ENCSR184VVN
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR016WFQ
encode release date: 2018-01-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB539UGM
size range: >200

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS304WSL at ENCODE; https://www.encodeproject.org/ENCBS304WSL/


title: CRISPRi RNA-seq from K562 (ENCLB016THV)

description:
https://www.encodeproject.org/experiments/ENCSR235ZEI/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting RBBP7.
experiment encode accession: ENCSR235ZEI
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB016THV
size range: >200

tag: Sex

value: adult

value: ENCBS366UYB at ENCODE; https://www.encodeproject.org/ENCBS366UYB/


title: CRISPRi RNA-seq from K562 (ENCLB827LGF)

description:
https://www.encodeproject.org/experiments/ENCSR181WYS/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting WHSC1.
experiment encode accession: ENCSR181WYS
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB827LGF
size range: >200

tag: health state

value: 53 year

value: ENCBS989PGE at ENCODE; https://www.encodeproject.org/ENCBS989PGE/


title: OCT4Flag_input


title: OCT6Flag_ChIP


title: CRISPRi RNA-seq from K562 (ENCLB199EZM)

description:
https://www.encodeproject.org/experiments/ENCSR171KMM/
***************
biological replicate number: 3
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: ENCLB199EZM
size range: >200

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

value: NFYB

tag: dev stage

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

value: ENCBS721IWW at ENCODE; https://www.encodeproject.org/ENCBS721IWW/


title: CRISPRi RNA-seq from K562 (ENCLB371XCO)

description:
https://www.encodeproject.org/experiments/ENCSR171KMM/
***************
biological replicate number: 2
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: ENCLB371XCO
size range: >200

tag: age

value: Sherman Weissman, Yale

value: ENCBS259LHA at ENCODE; https://www.encodeproject.org/ENCBS259LHA/

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


title: CRISPRi RNA-seq from K562 (ENCLB300DYC)

description:
https://www.encodeproject.org/experiments/ENCSR171RTN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting CTBP1.
experiment encode accession: ENCSR171RTN
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB300DYC
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting CTBP1

value: cell line

tag: lab

value: ENCBS658SHA at ENCODE; https://www.encodeproject.org/ENCBS658SHA/


title: CRISPRi RNA-seq from K562 (ENCLB314OUR)

description:
https://www.encodeproject.org/experiments/ENCSR171RTN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference targeting CTBP1.
experiment encode accession: ENCSR171RTN
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR095PIC
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB314OUR
size range: >200

value: ENCBS419JRM at ENCODE; https://www.encodeproject.org/ENCBS419JRM/


title: CRISPRi RNA-seq from K562 (ENCLB795NDL)

description:
https://www.encodeproject.org/experiments/ENCSR160YSN/
***************
biological replicate number: 2
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: ENCLB795NDL
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting HMGN3

value: ENCBS673RQY at ENCODE; https://www.encodeproject.org/ENCBS673RQY/