title: TF ChIP-seq from K562 (ENCLB626MZP)

description:
https://www.encodeproject.org/experiments/ENCSR879HUU/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GABPB2 ChIP-seq on human K562
experiment encode accession: ENCSR879HUU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR673WPR, ENCSR532WSQ
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB626MZP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting GABPB2

value: female

value: ENCBS924JQP at ENCODE; https://www.encodeproject.org/ENCBS924JQP/


title: eCLIP from HepG2 (ENCLB676TYH)

status: Public on Jun 15 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR979EWD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against STAU2
experiment encode accession: ENCSR979EWD
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR701QEP
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB676TYH
fragmentation methods: see document
size range: 175-300

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 immortalized cell line

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: dev stage

value: child

tag: age

value: 15 year

tag: Sex

value: male

tag: passage number

tag: lab

value: Gene Yeo, UCSD

tag: health state

value: hepatocellular carcinoma

tag: link

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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

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

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


title: eCLIP from HepG2 (ENCLB695ZJB)

description:
https://www.encodeproject.org/experiments/ENCSR876EYA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against BCLAF1
experiment encode accession: ENCSR876EYA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR128BUO
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB695ZJB
fragmentation methods: see document
size range: 175-300


title: eCLIP from HepG2 (ENCLB886IVQ)

description:
https://www.encodeproject.org/experiments/ENCSR973HOJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against FXR2
experiment encode accession: ENCSR973HOJ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR592ESN
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB886IVQ
fragmentation methods: see document
size range: 175-300

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/


title: eCLIP from HepG2 (ENCLB219RTK)

description:
https://www.encodeproject.org/experiments/ENCSR970FEW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against DDX52
experiment encode accession: ENCSR970FEW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR991LWQ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB219RTK
fragmentation methods: see document
size range: 175-300


title: Control eCLIP from HepG2 (ENCLB018RGO)

description:
https://www.encodeproject.org/experiments/ENCSR991LWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DDX52
experiment encode accession: ENCSR991LWQ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB018RGO
fragmentation methods: see document
size range: 175-300


title: eCLIP from HepG2 (ENCLB539UCR)

description:
https://www.encodeproject.org/experiments/ENCSR979EWD/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against STAU2
experiment encode accession: ENCSR979EWD
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR701QEP
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB539UCR
fragmentation methods: see document
size range: 175-300

value: ENCBS492SDY at ENCODE; https://www.encodeproject.org/ENCBS492SDY/


title: TF ChIP-seq from K562 (ENCLB381DPN)

description:
https://www.encodeproject.org/experiments/ENCSR987KYK/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF717 ChIP-seq on human K562
experiment encode accession: ENCSR987KYK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR501CEJ, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB381DPN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF717

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

tag: source

value: ATCC

value: ENCBS935SUO at ENCODE; https://www.encodeproject.org/ENCBS935SUO/

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


title: Control eCLIP from K562 (ENCLB466VBI)

description:
https://www.encodeproject.org/experiments/ENCSR960OKV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against HNRNPC
experiment encode accession: ENCSR960OKV
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB466VBI
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: cell line

value: female

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/


title: eCLIP from HepG2 (ENCLB041ILA)

description:
https://www.encodeproject.org/experiments/ENCSR970FEW/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against DDX52
experiment encode accession: ENCSR970FEW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR991LWQ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB041ILA
fragmentation methods: see document
size range: 175-300

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

value: ENCBS074YUC at ENCODE; https://www.encodeproject.org/ENCBS074YUC/


title: eCLIP from HepG2 (ENCLB958BNW)

description:
https://www.encodeproject.org/experiments/ENCSR876EYA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against BCLAF1
experiment encode accession: ENCSR876EYA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR128BUO
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB958BNW
fragmentation methods: see document
size range: 175-300

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

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

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


title: eCLIP from HepG2 (ENCLB712LWB)

description:
https://www.encodeproject.org/experiments/ENCSR973HOJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against FXR2
experiment encode accession: ENCSR973HOJ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR592ESN
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB712LWB
fragmentation methods: see document
size range: 175-300


title: Control eCLIP from HepG2 (ENCLB957XQS)

description:
https://www.encodeproject.org/experiments/ENCSR986HXA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against FUS
experiment encode accession: ENCSR986HXA
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB957XQS
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 cell line

value: ENCBS768GCL at ENCODE; https://www.encodeproject.org/ENCBS768GCL/


title: TF ChIP-seq from SK-N-SH (ENCLB009HGN)

description:
https://www.encodeproject.org/experiments/ENCSR835VBH/
***************
biological replicate number: 1
technical replicate number: 2
description: CSRNP3 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR835VBH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR921JGF, ENCSR042UCB
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB009HGN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting CSRNP3 treated with 6 uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: Metastatic neuroblastoma from bone marrow

value: 4 year

value: Michael Snyder, Stanford

tag: treatments

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

value: ENCBS312EAU at ENCODE; https://www.encodeproject.org/ENCBS312EAU/

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


title: TF ChIP-seq from K562 (ENCLB926NDF)

description:
https://www.encodeproject.org/experiments/ENCSR879HUU/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GABPB2 ChIP-seq on human K562
experiment encode accession: ENCSR879HUU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR673WPR, ENCSR532WSQ
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB926NDF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS474SSO at ENCODE; https://www.encodeproject.org/ENCBS474SSO/

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


title: eCLIP from K562 (ENCLB599SHT)

description:
https://www.encodeproject.org/experiments/ENCSR958FKZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against PABPC4
experiment encode accession: ENCSR958FKZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR192TPA
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB599SHT
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS489LOC at ENCODE; https://www.encodeproject.org/ENCBS489LOC/

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

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


title: microRNA-seq from left cardiac atrium (ENCLB571TRB)

description:
https://www.encodeproject.org/experiments/ENCSR454RTD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 left cardiac atrium microRNA-seq from Mortazavi
experiment encode accession: ENCSR454RTD
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB571TRB
size range: <30

source_name: Homo sapiens female adult (59 years) left cardiac atrium tissue, preserved by flash-freezing

value: left cardiac atrium

value: tissue

value: 59 year

value: Yiing Lin, MD, PhD

value: DM:yes; HTN:yes; CAD:no

value: ENCBS034QSD at ENCODE; https://www.encodeproject.org/ENCBS034QSD/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: eCLIP from HepG2 (ENCLB563IZS)

description:
https://www.encodeproject.org/experiments/ENCSR977OXG/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against PRPF4
experiment encode accession: ENCSR977OXG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR367ACZ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB563IZS
fragmentation methods: see document
size range: 175-300

value: cell line

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/

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


title: Control eCLIP from K562 (ENCLB859DBB)

description:
https://www.encodeproject.org/experiments/ENCSR952RGL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against AQR
experiment encode accession: ENCSR952RGL
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB859DBB
fragmentation methods: see document
size range: 175-300

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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


title: eCLIP from K562 (ENCLB425TEI)

description:
https://www.encodeproject.org/experiments/ENCSR964VOX/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against UTP18
experiment encode accession: ENCSR964VOX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR255PGS
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB425TEI
fragmentation methods: see document
size range: 175-300

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/

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


title: eCLIP from HepG2 (ENCLB058IYX)

description:
https://www.encodeproject.org/experiments/ENCSR834YLD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against DROSHA
experiment encode accession: ENCSR834YLD
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR785VKF
encode release date: 2018-04-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB058IYX
fragmentation methods: see document
size range: 175-300

value: DROSHA

value: ENCBS492SDY at ENCODE; https://www.encodeproject.org/ENCBS492SDY/

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


title: TF ChIP-seq from SK-N-SH (ENCLB612VWM)

description:
https://www.encodeproject.org/experiments/ENCSR835VBH/
***************
biological replicate number: 2
technical replicate number: 1
description: CSRNP3 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR835VBH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR921JGF, ENCSR042UCB
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB612VWM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: SK-N-SH

value: cell line

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: Michael Snyder, Stanford

value: ATCC

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

value: ENCBS804WLT at ENCODE; https://www.encodeproject.org/ENCBS804WLT/

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


title: Control eCLIP from K562 (ENCLB425VFA)

description:
https://www.encodeproject.org/experiments/ENCSR864XNB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX52
experiment encode accession: ENCSR864XNB
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB425VFA
fragmentation methods: see document
size range: 175-300

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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


title: eCLIP from K562 (ENCLB365HGS)

description:
https://www.encodeproject.org/experiments/ENCSR964VOX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against UTP18
experiment encode accession: ENCSR964VOX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR255PGS
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB365HGS
fragmentation methods: see document
size range: 175-300

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

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

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


title: eCLIP from HepG2 (ENCLB583RAS)

description:
https://www.encodeproject.org/experiments/ENCSR834YLD/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against DROSHA
experiment encode accession: ENCSR834YLD
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR785VKF
encode release date: 2018-04-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB583RAS
fragmentation methods: see document
size range: 175-300

value: DROSHA

value: cell line

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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

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


title: eCLIP from HepG2 (ENCLB846WBO)

description:
https://www.encodeproject.org/experiments/ENCSR977OXG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against PRPF4
experiment encode accession: ENCSR977OXG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR367ACZ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB846WBO
fragmentation methods: see document
size range: 175-300

value: ATCC

value: ENCBS768GCL at ENCODE; https://www.encodeproject.org/ENCBS768GCL/


title: Control eCLIP from HepG2 (ENCLB128TMZ)

description:
https://www.encodeproject.org/experiments/ENCSR831WYG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against EXOSC5
experiment encode accession: ENCSR831WYG
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB128TMZ
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS074YUC at ENCODE; https://www.encodeproject.org/ENCBS074YUC/


title: Control eCLIP from K562 (ENCLB406IPB)

description:
https://www.encodeproject.org/experiments/ENCSR832DWW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against PUM1
experiment encode accession: ENCSR832DWW
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB406IPB
fragmentation methods: see document
size range: 175-300

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/


title: eCLIP from K562 (ENCLB407STO)

description:
https://www.encodeproject.org/experiments/ENCSR958FKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against PABPC4
experiment encode accession: ENCSR958FKZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR192TPA
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB407STO
fragmentation methods: see document
size range: 175-300

value: cell line

value: ENCBS931MQO at ENCODE; https://www.encodeproject.org/ENCBS931MQO/

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

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

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


title: TF ChIP-seq from K562 (ENCLB730ZKR)

description:
https://www.encodeproject.org/experiments/ENCSR934RJP/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF3 ChIP-seq on human K562
experiment encode accession: ENCSR934RJP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR825BVU, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB730ZKR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF3

value: Michael Snyder, Stanford

value: ENCBS647WKF at ENCODE; https://www.encodeproject.org/ENCBS647WKF/


title: Control eCLIP from K562 (ENCLB838KJY)

description:
https://www.encodeproject.org/experiments/ENCSR857ORY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against ABCF1
experiment encode accession: ENCSR857ORY
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB838KJY
fragmentation methods: see document
size range: 175-300

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/


title: eCLIP from K562 (ENCLB606AKV)

description:
https://www.encodeproject.org/experiments/ENCSR922WJV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against PCBP1
experiment encode accession: ENCSR922WJV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR322KLN
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB606AKV
fragmentation methods: see document
size range: 175-300

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/


title: eCLIP from HepG2 (ENCLB646INW)

description:
https://www.encodeproject.org/experiments/ENCSR820UYE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against PABPN1
experiment encode accession: ENCSR820UYE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR310WYE
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB646INW
fragmentation methods: see document
size range: 175-300

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS768GCL at ENCODE; https://www.encodeproject.org/ENCBS768GCL/

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


title: eCLIP from HepG2 (ENCLB123NMA)

description:
https://www.encodeproject.org/experiments/ENCSR820WHR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against POLR2G
experiment encode accession: ENCSR820WHR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR129SCO
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB123NMA
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS362ASG at ENCODE; https://www.encodeproject.org/ENCBS362ASG/

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


title: TF ChIP-seq from SK-N-SH (ENCLB437BKB)

description:
https://www.encodeproject.org/experiments/ENCSR922RFY/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TCF4 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR922RFY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR593IWN, ENCSR088LKY
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB437BKB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting TCF4 treated with 6 uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: cell line

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 year

value: Michael Snyder

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

value: ENCBS112TOL at ENCODE; https://www.encodeproject.org/ENCBS112TOL/

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


title: eCLIP from K562 (ENCLB000JYH)

description:
https://www.encodeproject.org/experiments/ENCSR819XBT/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against AATF
experiment encode accession: ENCSR819XBT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR290JPJ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB000JYH
fragmentation methods: see document
size range: 175-300

value: AATF

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS517UIR at ENCODE; https://www.encodeproject.org/ENCBS517UIR/

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

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

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


title: eCLIP from K562 (ENCLB646KDC)

description:
https://www.encodeproject.org/experiments/ENCSR922WJV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against PCBP1
experiment encode accession: ENCSR922WJV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR322KLN
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB646KDC
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/


title: eCLIP from HepG2 (ENCLB398WTG)

description:
https://www.encodeproject.org/experiments/ENCSR916XIV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against EIF3H
experiment encode accession: ENCSR916XIV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR756NPZ
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB398WTG
fragmentation methods: see document
size range: 175-300

value: cell line

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS881CIF at ENCODE; https://www.encodeproject.org/ENCBS881CIF/

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

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


title: TF ChIP-seq from SK-N-SH (ENCLB802IJC)

description:
https://www.encodeproject.org/experiments/ENCSR922RFY/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TCF4 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR922RFY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR593IWN, ENCSR088LKY
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB802IJC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: SK-N-SH

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

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

value: ENCBS999FVL at ENCODE; https://www.encodeproject.org/ENCBS999FVL/

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


title: eCLIP from HepG2 (ENCLB911RVR)

description:
https://www.encodeproject.org/experiments/ENCSR916XIV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against EIF3H
experiment encode accession: ENCSR916XIV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR756NPZ
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB911RVR
fragmentation methods: see document
size range: 175-300

value: cell line

value: Gene Yeo, UCSD

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/

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


title: microRNA-seq from HCT116 (ENCLB847MTT)

description:
https://www.encodeproject.org/experiments/ENCSR436ZRS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HCT116 microRNA-seq from Mortazavi
experiment encode accession: ENCSR436ZRS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB847MTT
size range: <30

source_name: Homo sapiens HCT116 cell line

value: male

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

value: ATCC

value: colorectal carcinoma

value: ENCBS375FZQ at ENCODE; https://www.encodeproject.org/ENCBS375FZQ/

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


title: TF ChIP-seq from K562 (ENCLB093SLH)

description:
https://www.encodeproject.org/experiments/ENCSR934RJP/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF3 ChIP-seq on human K562
experiment encode accession: ENCSR934RJP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR825BVU, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB093SLH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS721VER at ENCODE; https://www.encodeproject.org/ENCBS721VER/

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


title: eCLIP from K562 (ENCLB790TIX)

description:
https://www.encodeproject.org/experiments/ENCSR819XBT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against AATF
experiment encode accession: ENCSR819XBT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR290JPJ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB790TIX
fragmentation methods: see document
size range: 175-300

value: AATF

value: cell line

value: Gene Yeo, UCSD

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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


title: eCLIP from HepG2 (ENCLB995NHC)

description:
https://www.encodeproject.org/experiments/ENCSR820UYE/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against PABPN1
experiment encode accession: ENCSR820UYE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR310WYE
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB995NHC
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/

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

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


title: Control eCLIP from K562 (ENCLB915LFT)

description:
https://www.encodeproject.org/experiments/ENCSR925ZRV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against WRN
experiment encode accession: ENCSR925ZRV
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB915LFT
fragmentation methods: see document
size range: 175-300

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS931MQO at ENCODE; https://www.encodeproject.org/ENCBS931MQO/


title: eCLIP from K562 (ENCLB811QYA)

description:
https://www.encodeproject.org/experiments/ENCSR906ZJF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SDAD1
experiment encode accession: ENCSR906ZJF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR155XOS
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB811QYA
fragmentation methods: see document
size range: 175-300

value: 53 year

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

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


title: Control eCLIP from K562 (ENCLB112XSX)

description:
https://www.encodeproject.org/experiments/ENCSR816NVJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against NIPBL
experiment encode accession: ENCSR816NVJ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB112XSX
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 cell line

value: cell line

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/


title: eCLIP from HepG2 (ENCLB718WLY)

description:
https://www.encodeproject.org/experiments/ENCSR903PRV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against FTO
experiment encode accession: ENCSR903PRV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR343MKJ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB718WLY
fragmentation methods: see document
size range: 175-300

value: FTO

value: child

value: 15 year

value: ENCBS074YUC at ENCODE; https://www.encodeproject.org/ENCBS074YUC/

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


title: Control eCLIP from HepG2 (ENCLB267WJE)

description:
https://www.encodeproject.org/experiments/ENCSR825FTY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against PCBP1
experiment encode accession: ENCSR825FTY
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB267WJE
fragmentation methods: see document
size range: 175-300

value: male

value: hepatocellular carcinoma

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

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


title: eCLIP from HepG2 (ENCLB602RZC)

description:
https://www.encodeproject.org/experiments/ENCSR903PRV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against FTO
experiment encode accession: ENCSR903PRV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR343MKJ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB602RZC
fragmentation methods: see document
size range: 175-300

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/


title: eCLIP from HepG2 (ENCLB217FWL)

description:
https://www.encodeproject.org/experiments/ENCSR693JWP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against EXOSC5
experiment encode accession: ENCSR693JWP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR831WYG
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB217FWL
fragmentation methods: see document
size range: 175-300


title: Control eCLIP from HepG2 (ENCLB103YZP)

description:
https://www.encodeproject.org/experiments/ENCSR902XTJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against AKAP1
experiment encode accession: ENCSR902XTJ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB103YZP
fragmentation methods: see document
size range: 175-300


title: eCLIP from HepG2 (ENCLB195YGJ)

description:
https://www.encodeproject.org/experiments/ENCSR820WHR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against POLR2G
experiment encode accession: ENCSR820WHR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR129SCO
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB195YGJ
fragmentation methods: see document
size range: 175-300

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/


title: Control eCLIP from HepG2 (ENCLB772YTI)

description:
https://www.encodeproject.org/experiments/ENCSR907EBB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against G3BP1
experiment encode accession: ENCSR907EBB
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB772YTI
fragmentation methods: see document
size range: 175-300


title: Control eCLIP from K562 (ENCLB162RUZ)

description:
https://www.encodeproject.org/experiments/ENCSR680HYD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SSB
experiment encode accession: ENCSR680HYD
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB162RUZ
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

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


title: eCLIP from HepG2 (ENCLB239DMS)

description:
https://www.encodeproject.org/experiments/ENCSR907GUB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against ZC3H11A
experiment encode accession: ENCSR907GUB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR098VKQ
encode release date: 2018-04-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB239DMS
fragmentation methods: see document
size range: 175-300

value: cell line

value: Gene Yeo, UCSD


title: eCLIP from HepG2 (ENCLB756WIQ)

description:
https://www.encodeproject.org/experiments/ENCSR907GUB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against ZC3H11A
experiment encode accession: ENCSR907GUB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR098VKQ
encode release date: 2018-04-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB756WIQ
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/


title: total RNA-seq from macrophage (ENCLB576TNX)

description:
https://www.encodeproject.org/experiments/ENCSR998WNE/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 10 minute.
experiment encode accession: ENCSR998WNE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB576TNX
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

organism: Mus musculus

source_name: Mus musculus strain C57BL/6J macrophage primary cell cytosolic fraction

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

tag: subcellular fraction term name

value: cytosol

value: ENCBS500MQX at ENCODE; https://www.encodeproject.org/ENCBS500MQX/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: eCLIP from K562 (ENCLB414PJC)

description:
https://www.encodeproject.org/experiments/ENCSR906ZJF/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SDAD1
experiment encode accession: ENCSR906ZJF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR155XOS
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB414PJC
fragmentation methods: see document
size range: 175-300

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/

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

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


title: eCLIP from K562 (ENCLB460IOL)

description:
https://www.encodeproject.org/experiments/ENCSR795CAI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPL
experiment encode accession: ENCSR795CAI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR299AAB
encode release date: 2017-12-04
lab: Gene Yeo, UCSD
library encode accession: ENCLB460IOL
fragmentation methods: see document
size range: 175-300

value: HNRNPL

value: cell line

value: Gene Yeo, UCSD

value: ENCBS517UIR at ENCODE; https://www.encodeproject.org/ENCBS517UIR/

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


title: eCLIP from HepG2 (ENCLB049WZO)

description:
https://www.encodeproject.org/experiments/ENCSR693JWP/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against EXOSC5
experiment encode accession: ENCSR693JWP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR831WYG
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB049WZO
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/

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


title: total RNA-seq from macrophage (ENCLB908ZZX)

description:
https://www.encodeproject.org/experiments/ENCSR864RGP/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR864RGP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB908ZZX
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell chromatin fraction

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: chromatin

value: ENCBS108OFM at ENCODE; https://www.encodeproject.org/ENCBS108OFM/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: eCLIP from K562 (ENCLB757VFG)

description:
https://www.encodeproject.org/experiments/ENCSR795CAI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPL
experiment encode accession: ENCSR795CAI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR299AAB
encode release date: 2017-12-04
lab: Gene Yeo, UCSD
library encode accession: ENCLB757VFG
fragmentation methods: see document
size range: 175-300

value: HNRNPL

value: cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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

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


title: eCLIP from HepG2 (ENCLB500ATO)

description:
https://www.encodeproject.org/experiments/ENCSR685AUR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against ZNF800
experiment encode accession: ENCSR685AUR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR624CUX
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB500ATO
fragmentation methods: see document
size range: 175-300

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS768GCL at ENCODE; https://www.encodeproject.org/ENCBS768GCL/

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


title: total RNA-seq from macrophage (ENCLB568QMQ)

description:
https://www.encodeproject.org/experiments/ENCSR896LKP/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 15 minute.
experiment encode accession: ENCSR896LKP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB568QMQ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: cytosol

value: ENCBS556SXR at ENCODE; https://www.encodeproject.org/ENCBS556SXR/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB262KYO)

description:
https://www.encodeproject.org/experiments/ENCSR839GBV/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 35 minute.
experiment encode accession: ENCSR839GBV
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB262KYO
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: chromatin

value: ENCBS622JSV at ENCODE; https://www.encodeproject.org/ENCBS622JSV/


title: total RNA-seq from macrophage (ENCLB768LQC)

description:
https://www.encodeproject.org/experiments/ENCSR837DAP/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 0 minute.
experiment encode accession: ENCSR837DAP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB768LQC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS885WPU at ENCODE; https://www.encodeproject.org/ENCBS885WPU/


title: TF ChIP-seq from K562 (ENCLB150CQR)

description:
https://www.encodeproject.org/experiments/ENCSR674WPB/
***************
biological replicate number: 1
technical replicate number: 1
description: TFAM ChIP-seq on human K562
experiment encode accession: ENCSR674WPB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR315TRH, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB150CQR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting TFAM

value: TFAM

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS968SXK at ENCODE; https://www.encodeproject.org/ENCBS968SXK/

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


title: polyA plus RNA-seq from macrophage (ENCLB132ZDG)

description:
https://www.encodeproject.org/experiments/ENCSR822FMG/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for180 minutes.
experiment encode accession: ENCSR822FMG
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB132ZDG
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 180 minutes

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:180; duration_units:minute;

value: ENCBS131RKT at ENCODE; https://www.encodeproject.org/ENCBS131RKT/


title: polyA plus RNA-seq from macrophage (ENCLB945UNF)

description:
https://www.encodeproject.org/experiments/ENCSR917CGF/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 0 minutes.
experiment encode accession: ENCSR917CGF
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB945UNF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours

value: Alexander Hoffmann

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour;

value: ENCBS204KQW at ENCODE; https://www.encodeproject.org/ENCBS204KQW/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB237UQO)

description:
https://www.encodeproject.org/experiments/ENCSR940IMN/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 10 minute.
experiment encode accession: ENCSR940IMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB237UQO
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: chromatin

value: ENCBS472UHG at ENCODE; https://www.encodeproject.org/ENCBS472UHG/


title: total RNA-seq from macrophage (ENCLB819STU)

description:
https://www.encodeproject.org/experiments/ENCSR814INP/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR814INP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB819STU
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell nuclear fraction

value: nucleus

value: ENCBS630NCI at ENCODE; https://www.encodeproject.org/ENCBS630NCI/


title: TF ChIP-seq from K562 (ENCLB487PFM)

description:
https://www.encodeproject.org/experiments/ENCSR674WPB/
***************
biological replicate number: 2
technical replicate number: 1
description: TFAM ChIP-seq on human K562
experiment encode accession: ENCSR674WPB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR315TRH, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB487PFM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: TFAM

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS257JHG at ENCODE; https://www.encodeproject.org/ENCBS257JHG/


title: total RNA-seq from macrophage (ENCLB504HQP)

description:
https://www.encodeproject.org/experiments/ENCSR803TDA/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 40 minute.
experiment encode accession: ENCSR803TDA
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB504HQP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS734QQG at ENCODE; https://www.encodeproject.org/ENCBS734QQG/


title: polyA plus RNA-seq from macrophage (ENCLB617DNW)

description:
https://www.encodeproject.org/experiments/ENCSR906KGC/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 180 minutes.
experiment encode accession: ENCSR906KGC
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB617DNW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours, 100 ng/mL lipoprotein A for 180 minutes

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:180; duration_units:minute;

value: ENCBS536YPG at ENCODE; https://www.encodeproject.org/ENCBS536YPG/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA plus RNA-seq from macrophage (ENCLB552DGA)

description:
https://www.encodeproject.org/experiments/ENCSR917CGF/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 0 minutes.
experiment encode accession: ENCSR917CGF
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB552DGA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour;

value: ENCBS893ZEF at ENCODE; https://www.encodeproject.org/ENCBS893ZEF/


title: total RNA-seq from macrophage (ENCLB241SIZ)

description:
https://www.encodeproject.org/experiments/ENCSR671DQW/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR671DQW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB241SIZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS310YNB at ENCODE; https://www.encodeproject.org/ENCBS310YNB/


title: total RNA-seq from macrophage (ENCLB454IDL)

description:
https://www.encodeproject.org/experiments/ENCSR820OHO/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR820OHO
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB454IDL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: chromatin

value: ENCBS730ZYN at ENCODE; https://www.encodeproject.org/ENCBS730ZYN/


title: Control eCLIP from HepG2 (ENCLB855VXV)

description:
https://www.encodeproject.org/experiments/ENCSR785VKF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DROSHA
experiment encode accession: ENCSR785VKF
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-12-03
lab: Gene Yeo, UCSD
library encode accession: ENCLB855VXV
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: cell line

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS492SDY at ENCODE; https://www.encodeproject.org/ENCBS492SDY/

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

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

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


title: total RNA-seq from macrophage (ENCLB935OQZ)

description:
https://www.encodeproject.org/experiments/ENCSR663YJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR663YJQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB935OQZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS849RBF at ENCODE; https://www.encodeproject.org/ENCBS849RBF/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB474PRF)

description:
https://www.encodeproject.org/experiments/ENCSR664IMK/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 30 minute.
experiment encode accession: ENCSR664IMK
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB474PRF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: chromatin

value: ENCBS189GEB at ENCODE; https://www.encodeproject.org/ENCBS189GEB/


title: TF ChIP-seq from K562 (ENCLB915UWS)

description:
https://www.encodeproject.org/experiments/ENCSR653WFU/
***************
biological replicate number: 1
technical replicate number: 1
description: GTF2I ChIP-seq on human K562
experiment encode accession: ENCSR653WFU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR275WKO, ENCSR906GHW
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB915UWS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting GTF2I

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS589YYO at ENCODE; https://www.encodeproject.org/ENCBS589YYO/

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


title: total RNA-seq from macrophage (ENCLB026TBC)

description:
https://www.encodeproject.org/experiments/ENCSR839HSB/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR839HSB
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB026TBC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: cytosol

value: ENCBS873NZI at ENCODE; https://www.encodeproject.org/ENCBS873NZI/


title: total RNA-seq from macrophage (ENCLB322WWP)

description:
https://www.encodeproject.org/experiments/ENCSR992IIX/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 40 minute.
experiment encode accession: ENCSR992IIX
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB322WWP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS870VUY at ENCODE; https://www.encodeproject.org/ENCBS870VUY/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB719WSB)

description:
https://www.encodeproject.org/experiments/ENCSR811YTU/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR811YTU
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB719WSB
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: nucleus

value: ENCBS131YWE at ENCODE; https://www.encodeproject.org/ENCBS131YWE/


title: microRNA-seq from astrocyte (ENCLB717LVB)

description:
https://www.encodeproject.org/experiments/ENCSR527FYM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation PGP1-derived astrocytes microRNA-seq from Mortazavi
experiment encode accession: ENCSR527FYM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB717LVB
size range: <30

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

value: astrocyte

value: in vitro differentiated cells

tag: description

value: PGP1 derived astrocytes

value: male

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS100HNS at ENCODE; https://www.encodeproject.org/ENCBS100HNS/

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


title: TF ChIP-seq from K562 (ENCLB381ZDN)

description:
https://www.encodeproject.org/experiments/ENCSR653WFU/
***************
biological replicate number: 2
technical replicate number: 1
description: GTF2I ChIP-seq on human K562
experiment encode accession: ENCSR653WFU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR275WKO, ENCSR906GHW
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB381ZDN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS980QND at ENCODE; https://www.encodeproject.org/ENCBS980QND/

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


title: total RNA-seq from macrophage (ENCLB966USJ)

description:
https://www.encodeproject.org/experiments/ENCSR771ODD/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR771ODD
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB966USJ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: chromatin

value: ENCBS078CSI at ENCODE; https://www.encodeproject.org/ENCBS078CSI/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB903PAC)

description:
https://www.encodeproject.org/experiments/ENCSR911EZW/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 15 minute.
experiment encode accession: ENCSR911EZW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB903PAC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS251IMB at ENCODE; https://www.encodeproject.org/ENCBS251IMB/


title: total RNA-seq from macrophage (ENCLB848RXG)

description:
https://www.encodeproject.org/experiments/ENCSR616IPE/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR616IPE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB848RXG
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS795KSZ at ENCODE; https://www.encodeproject.org/ENCBS795KSZ/


title: total RNA-seq from macrophage (ENCLB101ZLM)

description:
https://www.encodeproject.org/experiments/ENCSR771BCK/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR771BCK
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB101ZLM
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS641GOZ at ENCODE; https://www.encodeproject.org/ENCBS641GOZ/


title: TF ChIP-seq from K562 (ENCLB640JCC)

description:
https://www.encodeproject.org/experiments/ENCSR775FSH/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF280B ChIP-seq on human K562
experiment encode accession: ENCSR775FSH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR502CWG, ENCSR275WKO
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB640JCC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF280B

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS493YCB at ENCODE; https://www.encodeproject.org/ENCBS493YCB/


title: polyA plus RNA-seq from macrophage (ENCLB378GJX)

description:
https://www.encodeproject.org/experiments/ENCSR614KOV/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for480 minutes.
experiment encode accession: ENCSR614KOV
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB378GJX
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 480 minutes

value: macrophage

value: primary cell

value: not collected

value: unknown

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:480; duration_units:minute;

value: ENCBS743ZFO at ENCODE; https://www.encodeproject.org/ENCBS743ZFO/


title: total RNA-seq from macrophage (ENCLB123XKW)

description:
https://www.encodeproject.org/experiments/ENCSR726YJC/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR726YJC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB123XKW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: nucleus

value: ENCBS290JOW at ENCODE; https://www.encodeproject.org/ENCBS290JOW/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB629MFV)

description:
https://www.encodeproject.org/experiments/ENCSR596SMN/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR596SMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB629MFV
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS616DMC at ENCODE; https://www.encodeproject.org/ENCBS616DMC/


title: TF ChIP-seq from K562 (ENCLB455IUD)

description:
https://www.encodeproject.org/experiments/ENCSR650AWW/
***************
biological replicate number: 2
technical replicate number: 1
description: PHB ChIP-seq on human K562
experiment encode accession: ENCSR650AWW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR276WUU, ENCSR275WKO
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB455IUD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting PHB

value: PHB

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS255HKM at ENCODE; https://www.encodeproject.org/ENCBS255HKM/

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


title: total RNA-seq from macrophage (ENCLB250GPS)

description:
https://www.encodeproject.org/experiments/ENCSR584FVS/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 0 minute.
experiment encode accession: ENCSR584FVS
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB250GPS
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: cytosol

value: ENCBS833JSS at ENCODE; https://www.encodeproject.org/ENCBS833JSS/


title: polyA plus RNA-seq from macrophage (ENCLB276PBK)

description:
https://www.encodeproject.org/experiments/ENCSR614DLJ/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for0 minutes.
experiment encode accession: ENCSR614DLJ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB276PBK
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS249YNJ at ENCODE; https://www.encodeproject.org/ENCBS249YNJ/


title: total RNA-seq from macrophage (ENCLB698MUE)

description:
https://www.encodeproject.org/experiments/ENCSR857KZU/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 120 minute.
experiment encode accession: ENCSR857KZU
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB698MUE
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS168IUK at ENCODE; https://www.encodeproject.org/ENCBS168IUK/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB474VZY)

description:
https://www.encodeproject.org/experiments/ENCSR737BTH/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 40 minute.
experiment encode accession: ENCSR737BTH
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB474VZY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS373WDK at ENCODE; https://www.encodeproject.org/ENCBS373WDK/


title: eCLIP from HepG2 (ENCLB792EAF)

description:
https://www.encodeproject.org/experiments/ENCSR647HOX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against HLTF
experiment encode accession: ENCSR647HOX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR705DCQ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB792EAF
fragmentation methods: see document
size range: 175-300

value: HLTF

value: cell line

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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

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

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


title: polyA plus RNA-seq from macrophage (ENCLB397IJD)

description:
https://www.encodeproject.org/experiments/ENCSR590GUK/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 480 minutes.
experiment encode accession: ENCSR590GUK
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB397IJD
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours, 100 ng/mL lipoprotein A for 480 minutes

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:480; duration_units:minute;

value: ENCBS447UBW at ENCODE; https://www.encodeproject.org/ENCBS447UBW/


title: total RNA-seq from macrophage (ENCLB408ZIL)

description:
https://www.encodeproject.org/experiments/ENCSR489PYT/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR489PYT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB408ZIL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann

value: cytosol

value: ENCBS002OWX at ENCODE; https://www.encodeproject.org/ENCBS002OWX/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB587CED)

description:
https://www.encodeproject.org/experiments/ENCSR719VAW/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR719VAW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB587CED
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: nucleus

value: ENCBS176PQF at ENCODE; https://www.encodeproject.org/ENCBS176PQF/


title: polyA plus RNA-seq from macrophage (ENCLB642ANK)

description:
https://www.encodeproject.org/experiments/ENCSR614DLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for0 minutes.
experiment encode accession: ENCSR614DLJ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB642ANK
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS899OWM at ENCODE; https://www.encodeproject.org/ENCBS899OWM/


title: total RNA-seq from macrophage (ENCLB925PXU)

description:
https://www.encodeproject.org/experiments/ENCSR498KKO/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR498KKO
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB925PXU
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: chromatin

value: ENCBS434SSN at ENCODE; https://www.encodeproject.org/ENCBS434SSN/


title: microRNA-seq from adrenal gland (ENCLB564XVL)

description:
https://www.encodeproject.org/experiments/ENCSR333JBN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 adrenal gland microRNA-seq from Mortazavi
experiment encode accession: ENCSR333JBN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-03-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB564XVL
size range: <30

source_name: Homo sapiens female adult (41 years) adrenal gland tissue, preserved by flash-freezing

value: adrenal gland

value: tissue

value: female

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:no; CAD:no

value: ENCBS629ZGV at ENCODE; https://www.encodeproject.org/ENCBS629ZGV/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: total RNA-seq from macrophage (ENCLB052GNS)

description:
https://www.encodeproject.org/experiments/ENCSR499CRL/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 120 minute.
experiment encode accession: ENCSR499CRL
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB052GNS
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS630NFR at ENCODE; https://www.encodeproject.org/ENCBS630NFR/


title: TF ChIP-seq from K562 (ENCLB564GGH)

description:
https://www.encodeproject.org/experiments/ENCSR650AWW/
***************
biological replicate number: 1
technical replicate number: 1
description: PHB ChIP-seq on human K562
experiment encode accession: ENCSR650AWW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR276WUU, ENCSR275WKO
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB564GGH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: PHB

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS183NQU at ENCODE; https://www.encodeproject.org/ENCBS183NQU/

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


title: microRNA-seq from astrocyte (ENCLB711NSN)

description:
https://www.encodeproject.org/experiments/ENCSR527FYM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation PGP1-derived astrocytes microRNA-seq from Mortazavi
experiment encode accession: ENCSR527FYM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB711NSN
size range: <30

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: male

value: adult

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS372XQF at ENCODE; https://www.encodeproject.org/ENCBS372XQF/

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


title: eCLIP from HepG2 (ENCLB475YKU)

description:
https://www.encodeproject.org/experiments/ENCSR685AUR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against ZNF800
experiment encode accession: ENCSR685AUR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR624CUX
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB475YKU
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/

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

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


title: eCLIP from HepG2 (ENCLB485JLL)

description:
https://www.encodeproject.org/experiments/ENCSR647HOX/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against HLTF
experiment encode accession: ENCSR647HOX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR705DCQ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB485JLL
fragmentation methods: see document
size range: 175-300

value: HLTF

value: cell line

value: ENCBS074YUC at ENCODE; https://www.encodeproject.org/ENCBS074YUC/

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


title: total RNA-seq from macrophage (ENCLB413LDF)

description:
https://www.encodeproject.org/experiments/ENCSR465TWT/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 25 minute.
experiment encode accession: ENCSR465TWT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB413LDF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: chromatin

value: ENCBS182RLC at ENCODE; https://www.encodeproject.org/ENCBS182RLC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: TF ChIP-seq from K562 (ENCLB596AVH)

description:
https://www.encodeproject.org/experiments/ENCSR775FSH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF280B ChIP-seq on human K562
experiment encode accession: ENCSR775FSH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR502CWG, ENCSR275WKO
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB596AVH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS673XEY at ENCODE; https://www.encodeproject.org/ENCBS673XEY/

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


title: polyA plus RNA-seq from macrophage (ENCLB527FTI)

description:
https://www.encodeproject.org/experiments/ENCSR577EOP/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minutes.
experiment encode accession: ENCSR577EOP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB527FTI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours, 100 ng/mL lipoprotein A for 60 minutes

value: macrophage

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:60; duration_units:minute;

value: ENCBS584TTR at ENCODE; https://www.encodeproject.org/ENCBS584TTR/


title: total RNA-seq from macrophage (ENCLB991OUT)

description:
https://www.encodeproject.org/experiments/ENCSR460HQN/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 120 minute.
experiment encode accession: ENCSR460HQN
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB991OUT
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: primary cell

value: not collected

value: unknown

value: nucleus

value: ENCBS606RRH at ENCODE; https://www.encodeproject.org/ENCBS606RRH/


title: eCLIP from HepG2 (ENCLB636HXE)

description:
https://www.encodeproject.org/experiments/ENCSR766FAC/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against RPS3
experiment encode accession: ENCSR766FAC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR745BIL
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB636HXE
fragmentation methods: see document
size range: 175-300

value: cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/

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

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

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


title: total RNA-seq from macrophage (ENCLB445TQA)

description:
https://www.encodeproject.org/experiments/ENCSR460RCF/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR460RCF
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB445TQA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell cytosolic fraction

value: macrophage

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: cytosol

value: ENCBS571VNB at ENCODE; https://www.encodeproject.org/ENCBS571VNB/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA plus RNA-seq from macrophage (ENCLB714JOB)

description:
https://www.encodeproject.org/experiments/ENCSR577EOP/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minutes.
experiment encode accession: ENCSR577EOP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB714JOB
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: primary cell

value: not collected

value: unknown

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:60; duration_units:minute;

value: ENCBS580BLO at ENCODE; https://www.encodeproject.org/ENCBS580BLO/


title: total RNA-seq from macrophage (ENCLB434OXT)

description:
https://www.encodeproject.org/experiments/ENCSR330ILI/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 30 minute.
experiment encode accession: ENCSR330ILI
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB434OXT
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell chromatin fraction

value: chromatin

value: ENCBS895JGX at ENCODE; https://www.encodeproject.org/ENCBS895JGX/


title: Control eCLIP from K562 (ENCLB291YBV)

description:
https://www.encodeproject.org/experiments/ENCSR761AJD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against EIF3G
experiment encode accession: ENCSR761AJD
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB291YBV
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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

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


title: total RNA-seq from macrophage (ENCLB996AQG)

description:
https://www.encodeproject.org/experiments/ENCSR403ING/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR403ING
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB996AQG
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: cytosol

value: ENCBS012HEC at ENCODE; https://www.encodeproject.org/ENCBS012HEC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from macrophage (ENCLB769DCL)

description:
https://www.encodeproject.org/experiments/ENCSR507OWX/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 15 minute.
experiment encode accession: ENCSR507OWX
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB769DCL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: primary cell

value: not collected

value: unknown

value: nucleus

value: ENCBS755ZMO at ENCODE; https://www.encodeproject.org/ENCBS755ZMO/