title: eCLIP from adrenal gland (ENCLB810OCH)

description:
https://www.encodeproject.org/experiments/ENCSR634MFO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on adrenal gland from the GTEx collection against DGCR8
experiment encode accession: ENCSR634MFO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR217SVF
encode release date: 2017-04-10
lab: Gene Yeo, UCSD
library encode accession: ENCLB810OCH
fragmentation methods: see document
size range: 175-300

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

value: adrenal gland

value: tissue

value: Adrenal Gland GTEx tissue aliquot

value: adult

value: male

value: 37 year

value: ENCBS168TDE at ENCODE; https://www.encodeproject.org/ENCBS168TDE/

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


title: total RNA-seq from macrophage (ENCLB178XCG)

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/ENCSR434TXU/
***************
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 40 minute.
experiment encode accession: ENCSR434TXU
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB178XCG
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

value: macrophage

value: primary cell

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: unknown

tag: age

tag: lab

value: Alexander Hoffmann, UCLA

tag: source

value: Alexander Hoffmann

tag: subcellular fraction term name

value: chromatin

tag: link

value: ENCBS881RYG at ENCODE; https://www.encodeproject.org/ENCBS881RYG/

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


title: TF ChIP-seq from SK-N-SH (ENCLB676GQN)

description:
https://www.encodeproject.org/experiments/ENCSR641XWH/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TOX ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR641XWH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR513QXU, ENCSR593IWN
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB676GQN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

value: TOX

tag: line

value: SK-N-SH

value: cell line

value: female

tag: health state

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: Michael Snyder, Stanford

value: ATCC

tag: treatments

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

value: ENCBS795FSX at ENCODE; https://www.encodeproject.org/ENCBS795FSX/

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


title: total RNA-seq from macrophage (ENCLB391GFA)

description:
https://www.encodeproject.org/experiments/ENCSR314GIF/
***************
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 30 minute.
experiment encode accession: ENCSR314GIF
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB391GFA
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: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: nucleus

value: ENCBS947WYW at ENCODE; https://www.encodeproject.org/ENCBS947WYW/


title: eCLIP from HepG2 (ENCLB639DFA)

description:
https://www.encodeproject.org/experiments/ENCSR766FAC/
***************
biological replicate number: 1
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: ENCLB639DFA
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: cell line

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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

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: TF ChIP-seq from SK-N-SH (ENCLB426YOY)

description:
https://www.encodeproject.org/experiments/ENCSR641XWH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TOX ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR641XWH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR513QXU, ENCSR593IWN
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB426YOY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: TOX

value: SK-N-SH

value: female

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: ENCBS796QER at ENCODE; https://www.encodeproject.org/ENCBS796QER/

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


title: total RNA-seq from macrophage (ENCLB552XHR)

description:
https://www.encodeproject.org/experiments/ENCSR515LYM/
***************
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 25 minute.
experiment encode accession: ENCSR515LYM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB552XHR
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: ENCBS585QGX at ENCODE; https://www.encodeproject.org/ENCBS585QGX/

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


title: Control eCLIP from HepG2 (ENCLB772QSV)

description:
https://www.encodeproject.org/experiments/ENCSR745BIL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against RPS3
experiment encode accession: ENCSR745BIL
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB772QSV
fragmentation methods: see document
size range: 175-300

value: cell line

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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

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 (ENCLB519DEK)

description:
https://www.encodeproject.org/experiments/ENCSR311OMP/
***************
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 10 minute.
experiment encode accession: ENCSR311OMP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB519DEK
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: nucleus

value: ENCBS897NEH at ENCODE; https://www.encodeproject.org/ENCBS897NEH/


title: total RNA-seq from macrophage (ENCLB462BVW)

description:
https://www.encodeproject.org/experiments/ENCSR247QSE/
***************
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 120 minute.
experiment encode accession: ENCSR247QSE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB462BVW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS191VTS at ENCODE; https://www.encodeproject.org/ENCBS191VTS/


title: TF ChIP-seq from K562 (ENCLB239HSM)

description:
https://www.encodeproject.org/experiments/ENCSR744JJU/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-MYC ChIP-seq on human K562
experiment encode accession: ENCSR744JJU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR425VYE, ENCSR926XXG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB239HSM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: MYC

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS892YFL at ENCODE; https://www.encodeproject.org/ENCBS892YFL/

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


title: polyA plus RNA-seq from macrophage (ENCLB369CRL)

description:
https://www.encodeproject.org/experiments/ENCSR195JXZ/
***************
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 for60 minutes.
experiment encode accession: ENCSR195JXZ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB369CRL
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 60 minutes

value: macrophage

value: primary cell

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

value: ENCBS406JMS at ENCODE; https://www.encodeproject.org/ENCBS406JMS/

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


title: Control eCLIP from HepG2 (ENCLB550RSV)

description:
https://www.encodeproject.org/experiments/ENCSR756NPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against EIF3H
experiment encode accession: ENCSR756NPZ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB550RSV
fragmentation methods: see document
size range: 175-300

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 (ENCLB578HVF)

description:
https://www.encodeproject.org/experiments/ENCSR295PZT/
***************
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 40 minute.
experiment encode accession: ENCSR295PZT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB578HVF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: nucleus

value: ENCBS361DEK at ENCODE; https://www.encodeproject.org/ENCBS361DEK/


title: total RNA-seq from macrophage (ENCLB589DGP)

description:
https://www.encodeproject.org/experiments/ENCSR504QOC/
***************
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 30 minute.
experiment encode accession: ENCSR504QOC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB589DGP
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: ENCBS518CLY at ENCODE; https://www.encodeproject.org/ENCBS518CLY/


title: total RNA-seq from macrophage (ENCLB824BZD)

description:
https://www.encodeproject.org/experiments/ENCSR426AUD/
***************
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 120 minute.
experiment encode accession: ENCSR426AUD
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB824BZD
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: cytosol

value: ENCBS299WKY at ENCODE; https://www.encodeproject.org/ENCBS299WKY/

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


title: TF ChIP-seq from K562 (ENCLB898SRF)

description:
https://www.encodeproject.org/experiments/ENCSR744JJU/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-MYC ChIP-seq on human K562
experiment encode accession: ENCSR744JJU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR425VYE, ENCSR926XXG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB898SRF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: MYC

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS011ZQL at ENCODE; https://www.encodeproject.org/ENCBS011ZQL/

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


title: total RNA-seq from macrophage (ENCLB443RTC)

description:
https://www.encodeproject.org/experiments/ENCSR232TFT/
***************
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 15 minute.
experiment encode accession: ENCSR232TFT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB443RTC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS192QEK at ENCODE; https://www.encodeproject.org/ENCBS192QEK/


title: total RNA-seq from macrophage (ENCLB091DPW)

description:
https://www.encodeproject.org/experiments/ENCSR282JJC/
***************
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 40 minute.
experiment encode accession: ENCSR282JJC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB091DPW
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: cytosol

value: ENCBS276HYP at ENCODE; https://www.encodeproject.org/ENCBS276HYP/


title: eCLIP from adrenal gland (ENCLB601PLB)

description:
https://www.encodeproject.org/experiments/ENCSR634MFO/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on adrenal gland from the GTEx collection against DGCR8
experiment encode accession: ENCSR634MFO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR217SVF
encode release date: 2017-04-10
lab: Gene Yeo, UCSD
library encode accession: ENCLB601PLB
fragmentation methods: see document
size range: 175-300

value: adrenal gland

value: tissue

tag: description

value: Adrenal Gland GTEx tissue aliquot

value: male

value: 37 year

value: Gene Yeo, UCSD

value: ENCBS168TDE at ENCODE; https://www.encodeproject.org/ENCBS168TDE/

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


title: polyA plus RNA-seq from macrophage (ENCLB561FLC)

description:
https://www.encodeproject.org/experiments/ENCSR195JXZ/
***************
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 for60 minutes.
experiment encode accession: ENCSR195JXZ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB561FLC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

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

value: ENCBS445BNC at ENCODE; https://www.encodeproject.org/ENCBS445BNC/

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


title: total RNA-seq from macrophage (ENCLB966CDL)

description:
https://www.encodeproject.org/experiments/ENCSR040LSC/
***************
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 15 minute.
experiment encode accession: ENCSR040LSC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB966CDL
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: chromatin

value: ENCBS041QTN at ENCODE; https://www.encodeproject.org/ENCBS041QTN/


title: total RNA-seq from macrophage (ENCLB721ZSD)

description:
https://www.encodeproject.org/experiments/ENCSR080COL/
***************
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 0 minute.
experiment encode accession: ENCSR080COL
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB721ZSD
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: nucleus

value: ENCBS375PPX at ENCODE; https://www.encodeproject.org/ENCBS375PPX/


title: total RNA-seq from macrophage (ENCLB027CXH)

description:
https://www.encodeproject.org/experiments/ENCSR029TSM/
***************
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 10 minute.
experiment encode accession: ENCSR029TSM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB027CXH
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS134HKE at ENCODE; https://www.encodeproject.org/ENCBS134HKE/


title: total RNA-seq from macrophage (ENCLB898FOH)

description:
https://www.encodeproject.org/experiments/ENCSR219DFA/
***************
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 10 minute.
experiment encode accession: ENCSR219DFA
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB898FOH
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS565OIK at ENCODE; https://www.encodeproject.org/ENCBS565OIK/


title: total RNA-seq from macrophage (ENCLB174LGA)

description:
https://www.encodeproject.org/experiments/ENCSR159CPE/
***************
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 10 minute.
experiment encode accession: ENCSR159CPE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB174LGA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS425VWZ at ENCODE; https://www.encodeproject.org/ENCBS425VWZ/


title: total RNA-seq from macrophage (ENCLB931VOY)

description:
https://www.encodeproject.org/experiments/ENCSR008YAY/
***************
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 30 minute.
experiment encode accession: ENCSR008YAY
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB931VOY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

value: ENCBS445PMC at ENCODE; https://www.encodeproject.org/ENCBS445PMC/


title: total RNA-seq from macrophage (ENCLB999GJP)

description:
https://www.encodeproject.org/experiments/ENCSR107TKJ/
***************
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 90 minute.
experiment encode accession: ENCSR107TKJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB999GJP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS804ZBI at ENCODE; https://www.encodeproject.org/ENCBS804ZBI/


title: TF ChIP-seq from K562 (ENCLB479HFI)

description:
https://www.encodeproject.org/experiments/ENCSR740XMB/
***************
biological replicate number: 1
technical replicate number: 1
description: RBPJ ChIP-seq on human K562
experiment encode accession: ENCSR740XMB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR209ADM, ENCSR233HNT
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB479HFI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: RBPJ

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS939ZCP at ENCODE; https://www.encodeproject.org/ENCBS939ZCP/

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


title: eCLIP from HepG2 (ENCLB563IDV)

description:
https://www.encodeproject.org/experiments/ENCSR735HOK/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against YBX3
experiment encode accession: ENCSR735HOK
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR700UGT
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB563IDV
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/

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 (ENCLB221OIW)

description:
https://www.encodeproject.org/experiments/ENCSR542BJQ/
***************
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 30 minute.
experiment encode accession: ENCSR542BJQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB221OIW
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: ENCBS031VXA at ENCODE; https://www.encodeproject.org/ENCBS031VXA/

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


title: total RNA-seq from macrophage (ENCLB090RSX)

description:
https://www.encodeproject.org/experiments/ENCSR153YLH/
***************
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 50 minute.
experiment encode accession: ENCSR153YLH
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB090RSX
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: chromatin

value: ENCBS084IMI at ENCODE; https://www.encodeproject.org/ENCBS084IMI/


title: total RNA-seq from macrophage (ENCLB016ZPY)

description:
https://www.encodeproject.org/experiments/ENCSR059NPM/
***************
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 0 minute.
experiment encode accession: ENCSR059NPM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB016ZPY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS991JTL at ENCODE; https://www.encodeproject.org/ENCBS991JTL/


title: total RNA-seq from macrophage (ENCLB796TEL)

description:
https://www.encodeproject.org/experiments/ENCSR112SFD/
***************
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 15 minute.
experiment encode accession: ENCSR112SFD
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB796TEL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: nucleus

value: ENCBS312KOY at ENCODE; https://www.encodeproject.org/ENCBS312KOY/


title: total RNA-seq from macrophage (ENCLB187VNP)

description:
https://www.encodeproject.org/experiments/ENCSR294OOK/
***************
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 120 minute.
experiment encode accession: ENCSR294OOK
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB187VNP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS177LDS at ENCODE; https://www.encodeproject.org/ENCBS177LDS/


title: eCLIP from HepG2 (ENCLB220YZM)

description:
https://www.encodeproject.org/experiments/ENCSR724RDN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against HNRNPL
experiment encode accession: ENCSR724RDN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR513UTE
encode release date: 2017-12-04
lab: Gene Yeo, UCSD
library encode accession: ENCLB220YZM
fragmentation methods: see document
size range: 175-300

value: HNRNPL

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


title: Control eCLIP from HepG2 (ENCLB741VUQ)

description:
https://www.encodeproject.org/experiments/ENCSR624CUX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against ZNF800
experiment encode accession: ENCSR624CUX
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB741VUQ
fragmentation methods: see document
size range: 175-300

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

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


title: microRNA-seq from left cardiac atrium (ENCLB710XUS)

description:
https://www.encodeproject.org/experiments/ENCSR314AYC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 left cardiac atrium microRNA-seq from Mortazavi
experiment encode accession: ENCSR314AYC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB710XUS
size range: <30

source_name: Homo sapiens male adult (60 years) left cardiac atrium tissue, preserved by flash-freezing

value: left cardiac atrium

value: tissue

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS401TMR at ENCODE; https://www.encodeproject.org/ENCBS401TMR/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: Control eCLIP from K562 (ENCLB295LHX)

description:
https://www.encodeproject.org/experiments/ENCSR615ZYL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against ZNF800
experiment encode accession: ENCSR615ZYL
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB295LHX
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

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

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: TF ChIP-seq from K562 (ENCLB830BBM)

description:
https://www.encodeproject.org/experiments/ENCSR740XMB/
***************
biological replicate number: 2
technical replicate number: 1
description: RBPJ ChIP-seq on human K562
experiment encode accession: ENCSR740XMB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR209ADM, ENCSR233HNT
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB830BBM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: RBPJ

value: ATCC

value: ENCBS982OXT at ENCODE; https://www.encodeproject.org/ENCBS982OXT/


title: eCLIP from HepG2 (ENCLB360MWN)

description:
https://www.encodeproject.org/experiments/ENCSR735HOK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against YBX3
experiment encode accession: ENCSR735HOK
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR700UGT
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB360MWN
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: male

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 K562 (ENCLB038BHO)

description:
https://www.encodeproject.org/experiments/ENCSR734ZHL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against UTP3
experiment encode accession: ENCSR734ZHL
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR241ALC
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB038BHO
fragmentation methods: see document
size range: 175-300

value: cell line

value: adult

value: 53 year

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


title: total RNA-seq from macrophage (ENCLB324CBY)

description:
https://www.encodeproject.org/experiments/ENCSR140QWR/
***************
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 50 minute.
experiment encode accession: ENCSR140QWR
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB324CBY
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: ENCBS814WIT at ENCODE; https://www.encodeproject.org/ENCBS814WIT/

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


title: eCLIP from K562 (ENCLB769DQY)

description:
https://www.encodeproject.org/experiments/ENCSR739VVT/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against APOBEC3C
experiment encode accession: ENCSR739VVT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR382QLC
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB769DQY
fragmentation methods: see document
size range: 175-300

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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


title: eCLIP from K562 (ENCLB734VED)

description:
https://www.encodeproject.org/experiments/ENCSR606BPV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against AQR
experiment encode accession: ENCSR606BPV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR952RGL
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB734VED
fragmentation methods: see document
size range: 175-300

value: AQR

value: cell line

value: adult

value: 53 year

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

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


title: eCLIP from K562 (ENCLB279NAA)

description:
https://www.encodeproject.org/experiments/ENCSR734ZHL/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against UTP3
experiment encode accession: ENCSR734ZHL
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR241ALC
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB279NAA
fragmentation methods: see document
size range: 175-300

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


title: Control eCLIP from HepG2 (ENCLB441OYG)

description:
https://www.encodeproject.org/experiments/ENCSR722KGI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against WDR43
experiment encode accession: ENCSR722KGI
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB441OYG
fragmentation methods: see document
size range: 175-300

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 (ENCLB256ORC)

description:
https://www.encodeproject.org/experiments/ENCSR603TMB/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-RARB ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR603TMB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR715EHB, ENCSR593IWN
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB256ORC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: RARB

value: SK-N-SH

value: female

value: Metastatic neuroblastoma from bone marrow

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: ENCBS678VYF at ENCODE; https://www.encodeproject.org/ENCBS678VYF/

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


title: eCLIP from HepG2 (ENCLB151JKR)

description:
https://www.encodeproject.org/experiments/ENCSR724RDN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against HNRNPL
experiment encode accession: ENCSR724RDN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR513UTE
encode release date: 2017-12-04
lab: Gene Yeo, UCSD
library encode accession: ENCLB151JKR
fragmentation methods: see document
size range: 175-300

value: HNRNPL

value: cell line

value: child

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: eCLIP from HepG2 (ENCLB423EQB)

description:
https://www.encodeproject.org/experiments/ENCSR721HPX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against G3BP1
experiment encode accession: ENCSR721HPX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR907EBB
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB423EQB
fragmentation methods: see document
size range: 175-300

value: male

value: 15 year

value: hepatocellular carcinoma

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

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: Control eCLIP from HepG2 (ENCLB053AXU)

description:
https://www.encodeproject.org/experiments/ENCSR700UGT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against YBX3
experiment encode accession: ENCSR700UGT
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB053AXU
fragmentation methods: see document
size range: 175-300

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


title: Control eCLIP from K562 (ENCLB567GTS)

description:
https://www.encodeproject.org/experiments/ENCSR716DGM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against ZC3H8
experiment encode accession: ENCSR716DGM
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB567GTS
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: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

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


title: eCLIP from K562 (ENCLB764ZKN)

description:
https://www.encodeproject.org/experiments/ENCSR712IAG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against ZC3H11A
experiment encode accession: ENCSR712IAG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR321GBR
encode release date: 2018-04-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB764ZKN
fragmentation methods: see document
size range: 175-300

value: cell line

value: Gene Yeo, UCSD


title: Control eCLIP from HepG2 (ENCLB696RTY)

description:
https://www.encodeproject.org/experiments/ENCSR701QEP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against STAU2
experiment encode accession: ENCSR701QEP
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB696RTY
fragmentation methods: see document
size range: 175-300

value: child

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

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


title: Control eCLIP from HepG2 (ENCLB485HIE)

description:
https://www.encodeproject.org/experiments/ENCSR716AKC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against AQR
experiment encode accession: ENCSR716AKC
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB485HIE
fragmentation methods: see document
size range: 175-300

value: male

value: 15 year

value: hepatocellular carcinoma


title: eCLIP from HepG2 (ENCLB423UHX)

description:
https://www.encodeproject.org/experiments/ENCSR721HPX/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against G3BP1
experiment encode accession: ENCSR721HPX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR907EBB
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB423UHX
fragmentation methods: see document
size range: 175-300

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


title: TF ChIP-seq from K562 (ENCLB743BRU)

description:
https://www.encodeproject.org/experiments/ENCSR594HXD/
***************
biological replicate number: 1
technical replicate number: 1
description: ELF2 ChIP-seq on human K562
experiment encode accession: ENCSR594HXD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR706XZJ, ENCSR275WKO
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB743BRU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ELF2

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS525TXL at ENCODE; https://www.encodeproject.org/ENCBS525TXL/


title: TF ChIP-seq from K562 (ENCLB776WUM)

description:
https://www.encodeproject.org/experiments/ENCSR597CHL/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF518B ChIP-seq on human K562
experiment encode accession: ENCSR597CHL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR682TOC, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB776WUM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF518B

value: female

value: adult

value: 53 year

value: ENCBS131YWX at ENCODE; https://www.encodeproject.org/ENCBS131YWX/


title: TF ChIP-seq from K562 (ENCLB928CKT)

description:
https://www.encodeproject.org/experiments/ENCSR594HXD/
***************
biological replicate number: 2
technical replicate number: 1
description: ELF2 ChIP-seq on human K562
experiment encode accession: ENCSR594HXD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR706XZJ, ENCSR275WKO
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB928CKT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: chronic myelogenous leukemia (CML)

value: ENCBS867FUV at ENCODE; https://www.encodeproject.org/ENCBS867FUV/

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


title: Control eCLIP from HepG2 (ENCLB789BRX)

description:
https://www.encodeproject.org/experiments/ENCSR705DCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against HLTF
experiment encode accession: ENCSR705DCQ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB789BRX
fragmentation methods: see document
size range: 175-300

value: cell line

value: child

value: Gene Yeo, UCSD

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


title: Control eCLIP from HepG2 (ENCLB832EPM)

description:
https://www.encodeproject.org/experiments/ENCSR599YGK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against TIAL1
experiment encode accession: ENCSR599YGK
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB832EPM
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 cell line

value: male

value: 15 year

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


title: eCLIP from K562 (ENCLB086LMP)

description:
https://www.encodeproject.org/experiments/ENCSR606BPV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against AQR
experiment encode accession: ENCSR606BPV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR952RGL
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB086LMP
fragmentation methods: see document
size range: 175-300

value: AQR

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

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 posterior vena cava (ENCLB196KIH)

description:
https://www.encodeproject.org/experiments/ENCSR407CTE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 posterior vena cava microRNA-seq from Mortazavi
experiment encode accession: ENCSR407CTE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB196KIH
size range: <30

source_name: Homo sapiens female adult (59 years) posterior vena cava tissue, preserved by flash-freezing

value: posterior vena cava

value: tissue

value: female

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS892JRQ at ENCODE; https://www.encodeproject.org/ENCBS892JRQ/

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


title: Control eCLIP from HepG2 (ENCLB836TPS)

description:
https://www.encodeproject.org/experiments/ENCSR592ESN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against FXR2
experiment encode accession: ENCSR592ESN
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB836TPS
fragmentation methods: see document
size range: 175-300

value: cell line

value: child

value: male

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

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

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 K562 (ENCLB441YEA)

description:
https://www.encodeproject.org/experiments/ENCSR597CHL/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF518B ChIP-seq on human K562
experiment encode accession: ENCSR597CHL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR682TOC, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB441YEA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS087MDC at ENCODE; https://www.encodeproject.org/ENCBS087MDC/

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


title: TF ChIP-seq from K562 (ENCLB047NBF)

description:
https://www.encodeproject.org/experiments/ENCSR582EIB/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF830 ChIP-seq on human K562
experiment encode accession: ENCSR582EIB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR233HNT, ENCSR915XAG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB047NBF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF830

value: female

value: adult

value: Michael Snyder, Stanford

value: ENCBS759FXB at ENCODE; https://www.encodeproject.org/ENCBS759FXB/


title: TF ChIP-seq from SK-N-SH (ENCLB360ZUK)

description:
https://www.encodeproject.org/experiments/ENCSR603TMB/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-RARB ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR603TMB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR715EHB, ENCSR593IWN
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB360ZUK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: RARB

value: SK-N-SH

value: cell line

value: Metastatic neuroblastoma from bone marrow

value: 4 year

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

value: ENCBS613IEO at ENCODE; https://www.encodeproject.org/ENCBS613IEO/

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


title: eCLIP from K562 (ENCLB791LSC)

description:
https://www.encodeproject.org/experiments/ENCSR712IAG/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against ZC3H11A
experiment encode accession: ENCSR712IAG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR321GBR
encode release date: 2018-04-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB791LSC
fragmentation methods: see document
size range: 175-300

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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


title: Control eCLIP from K562 (ENCLB976AKI)

description:
https://www.encodeproject.org/experiments/ENCSR389ISM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against FUS
experiment encode accession: ENCSR389ISM
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB976AKI
fragmentation methods: see document
size range: 175-300

value: 53 year

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


title: eCLIP from K562 (ENCLB749FTS)

description:
https://www.encodeproject.org/experiments/ENCSR586DGV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against ZNF800
experiment encode accession: ENCSR586DGV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR615ZYL
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB749FTS
fragmentation methods: see document
size range: 175-300

value: adult

value: female

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

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


title: TF ChIP-seq from K562 (ENCLB388WYS)

description:
https://www.encodeproject.org/experiments/ENCSR582EIB/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF830 ChIP-seq on human K562
experiment encode accession: ENCSR582EIB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR233HNT, ENCSR915XAG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB388WYS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS738EYQ at ENCODE; https://www.encodeproject.org/ENCBS738EYQ/


title: eCLIP from K562 (ENCLB669EPI)

description:
https://www.encodeproject.org/experiments/ENCSR739VVT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against APOBEC3C
experiment encode accession: ENCSR739VVT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR382QLC
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB669EPI
fragmentation methods: see document
size range: 175-300

value: cell line

value: ENCBS831COV at ENCODE; https://www.encodeproject.org/ENCBS831COV/


title: Control eCLIP from K562 (ENCLB815RAP)

description:
https://www.encodeproject.org/experiments/ENCSR494JFR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RPS3
experiment encode accession: ENCSR494JFR
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB815RAP
fragmentation methods: see document
size range: 175-300

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


title: eCLIP from K562 (ENCLB466NAH)

description:
https://www.encodeproject.org/experiments/ENCSR580OFI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SUPV3L1
experiment encode accession: ENCSR580OFI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR328KKB
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB466NAH
fragmentation methods: see document
size range: 175-300


title: eCLIP from K562 (ENCLB211FRC)

description:
https://www.encodeproject.org/experiments/ENCSR580OFI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SUPV3L1
experiment encode accession: ENCSR580OFI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR328KKB
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB211FRC
fragmentation methods: see document
size range: 175-300

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


title: CRISPR RNA-seq from K562 (ENCLB514FXP)

description:
https://www.encodeproject.org/experiments/ENCSR999DVK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NIPBL. (NIPBL-BGKcLV08)
experiment encode accession: ENCSR999DVK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB514FXP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting NIPBL

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3d368b5c-e16b-4fc5-aa08-10de860f0638/@@download/attachment/L-NIPBL-BGKcLV08-43.pdf

value: NIPBL

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NIPBL. (NIPBL-BGKcLV08-43)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS217NYK at ENCODE; https://www.encodeproject.org/ENCBS217NYK/


title: CRISPR RNA-seq from K562 (ENCLB863BTV)

description:
https://www.encodeproject.org/experiments/ENCSR999DVK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NIPBL. (NIPBL-BGKcLV08)
experiment encode accession: ENCSR999DVK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB863BTV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f40efb89-37d4-47bd-ad36-8c7a13c7c680/@@download/attachment/L-NIPBL-BGKcLV08-44.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NIPBL. (NIPBL-BGKcLV08-44)

value: 53 year

value: ENCBS316QHL at ENCODE; https://www.encodeproject.org/ENCBS316QHL/

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


title: CRISPR RNA-seq from K562 (ENCLB299TPF)

description:
https://www.encodeproject.org/experiments/ENCSR994EWL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT3. (ADAT3-BGKcLV23)
experiment encode accession: ENCSR994EWL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB299TPF
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting ADAT3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/919e8fa1-2372-4798-9fb4-dfae10de8abb/@@download/attachment/L-ADAT3-BGKcLV23-8.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT3. (ADAT3-BGKcLV23-8)

value: female

value: adult

value: ENCBS546JGY at ENCODE; https://www.encodeproject.org/ENCBS546JGY/


title: CRISPR RNA-seq from K562 (ENCLB949RDH)

description:
https://www.encodeproject.org/experiments/ENCSR997ACY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL23A. (RPL23A-BGKcLV08)
experiment encode accession: ENCSR997ACY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB949RDH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting RPL23A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e0bb30ae-c30f-4154-8c62-b58c4f473548/@@download/attachment/L-RPL23A-BGKcLV08-60.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL23A. (RPL23A-BGKcLV08-60)

value: ATCC

value: ENCBS693ASC at ENCODE; https://www.encodeproject.org/ENCBS693ASC/


title: CRISPR RNA-seq from K562 (ENCLB185WYY)

description:
https://www.encodeproject.org/experiments/ENCSR994EWL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT3. (ADAT3-BGKcLV23)
experiment encode accession: ENCSR994EWL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB185WYY
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dd96ba9d-76f0-4b79-841a-566b820813eb/@@download/attachment/L-ADAT3-BGKcLV23-7.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT3. (ADAT3-BGKcLV23-7)

value: ENCBS796WSR at ENCODE; https://www.encodeproject.org/ENCBS796WSR/


title: eCLIP from HepG2 (ENCLB269FBK)

description:
https://www.encodeproject.org/experiments/ENCSR488JKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against UTP18
experiment encode accession: ENCSR488JKQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR387OVO
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB269FBK
fragmentation methods: see document
size range: 175-300

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: BruChase-seq from GM12878 (ENCLB801PVM)

description:
https://www.encodeproject.org/experiments/ENCSR993ASV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR993ASV
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR267RPG
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB801PVM
size range: 400-500

source_name: Homo sapiens GM12878 cell line, subjected to a 6 hour pulse-chase

value: female

value: unknown

value: adult

value: not collected

value: Mats Ljungman, UMichigan

value: Coriell

value: ENCBS857RVA at ENCODE; https://www.encodeproject.org/ENCBS857RVA/

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


title: eCLIP from K562 (ENCLB525YFQ)

description:
https://www.encodeproject.org/experiments/ENCSR586DGV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against ZNF800
experiment encode accession: ENCSR586DGV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR615ZYL
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB525YFQ
fragmentation methods: see document
size range: 175-300

value: cell line

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/


title: Control eCLIP from HepG2 (ENCLB180AJD)

description:
https://www.encodeproject.org/experiments/ENCSR387OVO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against UTP18
experiment encode accession: ENCSR387OVO
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB180AJD
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized 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/


title: CRISPR RNA-seq from K562 (ENCLB750LGG)

description:
https://www.encodeproject.org/experiments/ENCSR990DKW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against MORC2. (MORC2-BGKcLV19)
experiment encode accession: ENCSR990DKW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB750LGG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting MORC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/77753843-b78c-4b1f-b833-eea5b21a3200/@@download/attachment/L-MORC2-BGKcLV19-24.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against MORC2. (MORC2-BGKcLV19-24)

value: female

value: adult

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS715XCC at ENCODE; https://www.encodeproject.org/ENCBS715XCC/


title: CRISPR RNA-seq from HepG2 (ENCLB000AGN)

description:
https://www.encodeproject.org/experiments/ENCSR999MAE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGHcLV16)
experiment encode accession: ENCSR999MAE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB000AGN
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting EIF4A3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c4ed9620-e127-48cc-97f4-419ec0138cae/@@download/attachment/L-EIF4A3-BGHcLV16-25.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGHcLV16-25)

value: ENCBS338PVK at ENCODE; https://www.encodeproject.org/ENCBS338PVK/

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


title: CRISPR RNA-seq from HepG2 (ENCLB062YJT)

description:
https://www.encodeproject.org/experiments/ENCSR989GNV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMYD3. (SMYD3-BGHcLV20)
experiment encode accession: ENCSR989GNV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB062YJT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting SMYD3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/25436e20-d0d3-48fa-88d3-d49306116474/@@download/attachment/L-SMYD3-BGHcLV20-35.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMYD3. (SMYD3-BGHcLV20-35)

value: ENCBS310PBV at ENCODE; https://www.encodeproject.org/ENCBS310PBV/


title: eCLIP from HepG2 (ENCLB766JEO)

description:
https://www.encodeproject.org/experiments/ENCSR489ABS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against RBM5
experiment encode accession: ENCSR489ABS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR414RME
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB766JEO
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

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

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: TF ChIP-seq from K562 (ENCLB449WYC)

description:
https://www.encodeproject.org/experiments/ENCSR568YNC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF655 ChIP-seq on human K562
experiment encode accession: ENCSR568YNC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR816YLP, ENCSR426BBS
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB449WYC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF655

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS355ZFG at ENCODE; https://www.encodeproject.org/ENCBS355ZFG/

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


title: eCLIP from HepG2 (ENCLB890FUB)

description:
https://www.encodeproject.org/experiments/ENCSR488JKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against UTP18
experiment encode accession: ENCSR488JKQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR387OVO
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB890FUB
fragmentation methods: see document
size range: 175-300

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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


title: BruChase-seq from GM12878 (ENCLB271LZO)

description:
https://www.encodeproject.org/experiments/ENCSR993ASV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR993ASV
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR267RPG
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB271LZO
size range: 400-500

value: cell line

value: female

value: unknown

value: adult

value: not collected

value: Mats Ljungman, UMichigan

value: Coriell

value: ENCBS130TEM at ENCODE; https://www.encodeproject.org/ENCBS130TEM/

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


title: CRISPR RNA-seq from K562 (ENCLB902VRH)

description:
https://www.encodeproject.org/experiments/ENCSR990DKW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against MORC2. (MORC2-BGKcLV19)
experiment encode accession: ENCSR990DKW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB902VRH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7881be0a-a223-4b0f-98e7-2841b6125dfb/@@download/attachment/L-MORC2-BGKcLV19-23.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against MORC2. (MORC2-BGKcLV19-23)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS293GUO at ENCODE; https://www.encodeproject.org/ENCBS293GUO/


title: CRISPR RNA-seq from K562 (ENCLB348LJW)

description:
https://www.encodeproject.org/experiments/ENCSR897BYR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV11)
experiment encode accession: ENCSR897BYR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB348LJW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting RBM25

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/75e6ae6d-2239-4c7e-973e-40fc9f69237b/@@download/attachment/L-RBM25-BGKcLV11-84.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV11-84)

value: ENCBS339ZLL at ENCODE; https://www.encodeproject.org/ENCBS339ZLL/

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


title: TF ChIP-seq from K562 (ENCLB189BEK)

description:
https://www.encodeproject.org/experiments/ENCSR568YNC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF655 ChIP-seq on human K562
experiment encode accession: ENCSR568YNC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR816YLP, ENCSR426BBS
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB189BEK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: female

value: Michael Snyder, Stanford

value: ENCBS654WXR at ENCODE; https://www.encodeproject.org/ENCBS654WXR/


title: CRISPR RNA-seq from K562 (ENCLB185GRI)

description:
https://www.encodeproject.org/experiments/ENCSR989ZNZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against APEX1. (APEX1-BGKcLV13)
experiment encode accession: ENCSR989ZNZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB185GRI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting APEX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a05018ad-c905-4d78-b268-00fe38dd6c6c/@@download/attachment/L-APEX1-BGKcLV13-4.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against APEX1. (APEX1-BGKcLV13-4)

value: adult

value: ENCBS099GWR at ENCODE; https://www.encodeproject.org/ENCBS099GWR/


title: CRISPR RNA-seq from K562 (ENCLB317NYX)

description:
https://www.encodeproject.org/experiments/ENCSR989ZNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against APEX1. (APEX1-BGKcLV13)
experiment encode accession: ENCSR989ZNZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB317NYX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e60da03a-bb98-4df4-931f-4939d88fe8d2/@@download/attachment/L-APEX1-BGKcLV13-3.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against APEX1. (APEX1-BGKcLV13-3)

value: ENCBS298FYO at ENCODE; https://www.encodeproject.org/ENCBS298FYO/


title: CRISPR RNA-seq from HepG2 (ENCLB995GUI)

description:
https://www.encodeproject.org/experiments/ENCSR884REL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against METTL3. (METTL3-BGHcLV22)
experiment encode accession: ENCSR884REL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB995GUI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting METTL3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a2867963-feb0-4464-84d7-2e24964ac9ca/@@download/attachment/L-METTL3-BGHcLV22-31.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against METTL3. (METTL3-BGHcLV22-31)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS025VCL at ENCODE; https://www.encodeproject.org/ENCBS025VCL/

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


title: Control eCLIP from K562 (ENCLB308KEY)

description:
https://www.encodeproject.org/experiments/ENCSR382QLC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against APOBEC3C
experiment encode accession: ENCSR382QLC
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB308KEY
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS831COV at ENCODE; https://www.encodeproject.org/ENCBS831COV/

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 HepG2 (ENCLB651GRE)

description:
https://www.encodeproject.org/experiments/ENCSR489ABS/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against RBM5
experiment encode accession: ENCSR489ABS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR414RME
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB651GRE
fragmentation methods: see document
size range: 175-300

value: cell line

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

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


title: microRNA-seq from Panc1 (ENCLB404OQY)

description:
https://www.encodeproject.org/experiments/ENCSR086DQY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation Panc1 microRNA-seq from Mortazavi
experiment encode accession: ENCSR086DQY
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB404OQY
size range: <30

source_name: Homo sapiens Panc1 cell line

value: adult

value: 56 year

value: Mats Ljungman, UMichigan

value: ATCC

value: pancreatic carcinoma

value: ENCBS777OZT at ENCODE; https://www.encodeproject.org/ENCBS777OZT/

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


title: eCLIP from K562 (ENCLB544WSP)

description:
https://www.encodeproject.org/experiments/ENCSR484LAB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SAFB
experiment encode accession: ENCSR484LAB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR111USM
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB544WSP
fragmentation methods: see document
size range: 175-300

value: SAFB

value: female

value: 53 year

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


title: CRISPR RNA-seq from HepG2 (ENCLB373KGK)

description:
https://www.encodeproject.org/experiments/ENCSR989GNV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMYD3. (SMYD3-BGHcLV20)
experiment encode accession: ENCSR989GNV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB373KGK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ee966739-9a57-4ec1-a426-be4aca562454/@@download/attachment/L-SMYD3-BGHcLV20-36.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMYD3. (SMYD3-BGHcLV20-36)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS521JYS at ENCODE; https://www.encodeproject.org/ENCBS521JYS/

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


title: eCLIP from K562 (ENCLB693IZD)

description:
https://www.encodeproject.org/experiments/ENCSR484LAB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SAFB
experiment encode accession: ENCSR484LAB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR111USM
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB693IZD
fragmentation methods: see document
size range: 175-300

value: cell line

value: adult

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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: CRISPR RNA-seq from K562 (ENCLB213KES)

description:
https://www.encodeproject.org/experiments/ENCSR898KNS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGKcLV11)
experiment encode accession: ENCSR898KNS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB213KES
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting STAU2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d27d9a80-b4d7-4ac0-8ae0-aff869ed7b15/@@download/attachment/L-STAU2-BGKcLV11-101.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGKcLV11-101)

value: female

value: 53 year

value: ATCC

value: ENCBS185CCE at ENCODE; https://www.encodeproject.org/ENCBS185CCE/


title: TF ChIP-seq from K562 (ENCLB848ETL)

description:
https://www.encodeproject.org/experiments/ENCSR551KXD/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-RHOXF2B ChIP-seq on human K562
experiment encode accession: ENCSR551KXD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR706RMI, ENCSR532WSQ
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB848ETL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting RHOXF2B

value: Michael Snyder, Stanford

value: ENCBS341XYK at ENCODE; https://www.encodeproject.org/ENCBS341XYK/


title: CRISPR RNA-seq from K562 (ENCLB649XWC)

description:
https://www.encodeproject.org/experiments/ENCSR897BYR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV11)
experiment encode accession: ENCSR897BYR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB649XWC
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d182cf74-d582-4581-9f6f-32922ebbcca2/@@download/attachment/L-RBM25-BGKcLV11-83.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV11-83)

value: Brenton Graveley, UConn

value: ENCBS697TKR at ENCODE; https://www.encodeproject.org/ENCBS697TKR/


title: CRISPR RNA-seq from K562 (ENCLB694SGM)

description:
https://www.encodeproject.org/experiments/ENCSR883MTV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX39B. (DDX39B-BGKcLV17)
experiment encode accession: ENCSR883MTV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB694SGM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting DDX39B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5047dc89-0afe-4b08-bb2a-98816a921776/@@download/attachment/L-DDX39B-BGKcLV17-10.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX39B. (DDX39B-BGKcLV17-9)

value: ENCBS725UBT at ENCODE; https://www.encodeproject.org/ENCBS725UBT/


title: CRISPR RNA-seq from K562 (ENCLB079ZXF)

description:
https://www.encodeproject.org/experiments/ENCSR883MTV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX39B. (DDX39B-BGKcLV17)
experiment encode accession: ENCSR883MTV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB079ZXF
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1b648b6d-0c0a-48b1-86bf-15a200cb7063/@@download/attachment/L-DDX39B-BGKcLV17-9.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX39B. (DDX39B-BGKcLV17-10)

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS356QKB at ENCODE; https://www.encodeproject.org/ENCBS356QKB/


title: CRISPR RNA-seq from HepG2 (ENCLB728FZE)

description:
https://www.encodeproject.org/experiments/ENCSR999MAE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGHcLV16)
experiment encode accession: ENCSR999MAE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB728FZE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d10b7f29-bb0d-4538-bc17-eac27d009b1e/@@download/attachment/L-EIF4A3-BGHcLV16-26.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGHcLV16-26)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS837RAQ at ENCODE; https://www.encodeproject.org/ENCBS837RAQ/

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


title: CRISPR RNA-seq from K562 (ENCLB973BEL)

description:
https://www.encodeproject.org/experiments/ENCSR898KNS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGKcLV11)
experiment encode accession: ENCSR898KNS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB973BEL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7ea2af1b-0f06-4d7a-845f-65a9e9a9237f/@@download/attachment/L-STAU2-BGKcLV11-102.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGKcLV11-102)

value: female

value: 53 year

value: ATCC

value: ENCBS029ZJF at ENCODE; https://www.encodeproject.org/ENCBS029ZJF/

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


title: CRISPR RNA-seq from HepG2 (ENCLB110DIL)

description:
https://www.encodeproject.org/experiments/ENCSR884REL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against METTL3. (METTL3-BGHcLV22)
experiment encode accession: ENCSR884REL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB110DIL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e3e4b89e-2766-4c71-a224-b28765ddc61f/@@download/attachment/L-METTL3-BGHcLV22-32.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against METTL3. (METTL3-BGHcLV22-32)

value: Brenton Graveley, UConn

value: ENCBS280DNN at ENCODE; https://www.encodeproject.org/ENCBS280DNN/


title: CRISPR RNA-seq from K562 (ENCLB483FFL)

description:
https://www.encodeproject.org/experiments/ENCSR978MMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV19)
experiment encode accession: ENCSR978MMZ
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB483FFL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/05e63b5f-298c-48fb-a103-26328048a1a5/@@download/attachment/L-NT-BGKcLV19-2.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV19-2)

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS866YOW at ENCODE; https://www.encodeproject.org/ENCBS866YOW/


title: CRISPR RNA-seq from K562 (ENCLB891XEO)

description:
https://www.encodeproject.org/experiments/ENCSR877JEM/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV23)
experiment encode accession: ENCSR877JEM
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB891XEO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ed47bf39-2d65-4295-aca8-cd593ed012a0/@@download/attachment/L-NT-BGKcLV23-2.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV23-2)

value: ENCBS571XPD at ENCODE; https://www.encodeproject.org/ENCBS571XPD/


title: CRISPR RNA-seq from K562 (ENCLB524MAE)

description:
https://www.encodeproject.org/experiments/ENCSR997ACY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL23A. (RPL23A-BGKcLV08)
experiment encode accession: ENCSR997ACY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB524MAE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting RPL23A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/991aede0-d7a8-4408-ad3d-166deda74ced/@@download/attachment/L-RPL23A-BGKcLV08-59.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL23A. (RPL23A-BGKcLV08-59)

value: ENCBS759JGW at ENCODE; https://www.encodeproject.org/ENCBS759JGW/