title: Bru-seq from PC-3 (ENCLB085CIW)

description:
https://www.encodeproject.org/experiments/ENCSR916VGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR916VGW
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR622SUM
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB085CIW
size range: 400-500

value: male

value: ENCBS975ZEX at ENCODE; https://www.encodeproject.org/ENCBS975ZEX/


title: eCLIP from HepG2 (ENCLB014HZJ)

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/ENCSR322HHA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against TIAL1
experiment encode accession: ENCSR322HHA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR599YGK
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB014HZJ
fragmentation methods: see document
size range: 175-300

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 immortalized cell line

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: dev stage

value: child

tag: age

value: 15 year

tag: Sex

tag: passage number

tag: lab

value: Gene Yeo, UCSD

tag: health state

value: hepatocellular carcinoma

tag: link

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

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

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


title: eCLIP from HepG2 (ENCLB573KAQ)

description:
https://www.encodeproject.org/experiments/ENCSR337XGI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against SAFB
experiment encode accession: ENCSR337XGI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR451BRX
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB573KAQ
fragmentation methods: see document
size range: 175-300

value: SAFB

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

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


title: CRISPR RNA-seq from K562 (ENCLB391DMF)

description:
https://www.encodeproject.org/experiments/ENCSR914IEV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF3. (SRSF3-BGKcLV08)
experiment encode accession: ENCSR914IEV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB391DMF
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 SRSF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9060d783-6d45-4be5-99b3-a2cb915a8262/@@download/attachment/L-SRSF3-BGKcLV08-76.pdf

tag: description

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF3. (SRSF3-BGKcLV08-76)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

tag: source

value: ATCC

value: ENCBS251FSC at ENCODE; https://www.encodeproject.org/ENCBS251FSC/

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


title: Control eCLIP from K562 (ENCLB647BQI)

description:
https://www.encodeproject.org/experiments/ENCSR328KKB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SUPV3L1
experiment encode accession: ENCSR328KKB
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB647BQI
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: cell line

value: Gene Yeo, UCSD

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

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


title: CRISPR RNA-seq from K562 (ENCLB902ZQT)

description:
https://www.encodeproject.org/experiments/ENCSR965MSX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD4. (SMAD4-BGKcLV17)
experiment encode accession: ENCSR965MSX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB902ZQT
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 SMAD4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f0cb7b26-fedf-40f5-8231-afde2a668872/@@download/attachment/L-SMAD4-BGKcLV17-48.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD4. (SMAD4-BGKcLV17-48)

value: ENCBS242OIJ at ENCODE; https://www.encodeproject.org/ENCBS242OIJ/


title: CRISPR RNA-seq from K562 (ENCLB317XMX)

description:
https://www.encodeproject.org/experiments/ENCSR913OZW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CHTOP. (CHTOP-BGKcLV21)
experiment encode accession: ENCSR913OZW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB317XMX
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 CHTOP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a7691a36-6410-4e63-bba8-76348b0de65d/@@download/attachment/L-CHTOP-BGKcLV21-6.pdf

value: CHTOP

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CHTOP. (CHTOP-BGKcLV21-6)

value: ENCBS608XTN at ENCODE; https://www.encodeproject.org/ENCBS608XTN/


title: CRISPR RNA-seq from K562 (ENCLB762LGN)

description:
https://www.encodeproject.org/experiments/ENCSR921RQX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against THOC1. (THOC1-BGKcLV15)
experiment encode accession: ENCSR921RQX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB762LGN
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 THOC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c166d5f5-49e1-4463-b694-11f7b3970f2c/@@download/attachment/L-THOC1-BGKcLV15-59.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against THOC1. (THOC1-BGKcLV15-59)

value: female

value: ENCBS139TLH at ENCODE; https://www.encodeproject.org/ENCBS139TLH/


title: CRISPR RNA-seq from K562 (ENCLB231CGP)

description:
https://www.encodeproject.org/experiments/ENCSR825EPB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BAZ1A. (BAZ1A-BGKcLV17)
experiment encode accession: ENCSR825EPB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB231CGP
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 BAZ1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8bac0160-8e14-48b9-9d0f-c3ff4285461e/@@download/attachment/L-BAZ1A-BGKcLV17-3.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BAZ1A. (BAZ1A-BGKcLV17-3)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS089LHN at ENCODE; https://www.encodeproject.org/ENCBS089LHN/


title: CRISPR RNA-seq from K562 (ENCLB678HRR)

description:
https://www.encodeproject.org/experiments/ENCSR913OZW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CHTOP. (CHTOP-BGKcLV21)
experiment encode accession: ENCSR913OZW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB678HRR
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/b69182c3-28d5-43ef-8010-ffb06a5b53cb/@@download/attachment/L-CHTOP-BGKcLV21-5.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CHTOP. (CHTOP-BGKcLV21-5)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS278CHX at ENCODE; https://www.encodeproject.org/ENCBS278CHX/

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


title: CRISPR RNA-seq from K562 (ENCLB150APE)

description:
https://www.encodeproject.org/experiments/ENCSR825EPB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BAZ1A. (BAZ1A-BGKcLV17)
experiment encode accession: ENCSR825EPB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB150APE
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/aab7fbf4-0513-4f6e-af42-2e8011bc9710/@@download/attachment/L-BAZ1A-BGKcLV17-4.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BAZ1A. (BAZ1A-BGKcLV17-4)

value: ENCBS287JVX at ENCODE; https://www.encodeproject.org/ENCBS287JVX/


title: Control eCLIP from HepG2 (ENCLB530LHN)

description:
https://www.encodeproject.org/experiments/ENCSR414RME/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against RBM5
experiment encode accession: ENCSR414RME
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB530LHN
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

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

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


title: Control eCLIP from HepG2 (ENCLB590PCH)

description:
https://www.encodeproject.org/experiments/ENCSR513UTE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against HNRNPL
experiment encode accession: ENCSR513UTE
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-12-03
lab: Gene Yeo, UCSD
library encode accession: ENCLB590PCH
fragmentation methods: see document
size range: 175-300

value: cell line

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


title: Control eCLIP from K562 (ENCLB938FOD)

description:
https://www.encodeproject.org/experiments/ENCSR321GBR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against ZC3H11A
experiment encode accession: ENCSR321GBR
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-12-03
lab: Gene Yeo, UCSD
library encode accession: ENCLB938FOD
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB929ICY)

description:
https://www.encodeproject.org/experiments/ENCSR909TFJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PRPF3. (PRPF3-BGHcLV22)
experiment encode accession: ENCSR909TFJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB929ICY
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 PRPF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/314693c0-2780-4954-adb6-1817cf059e49/@@download/attachment/L-PRPF3-BGHcLV22-40.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PRPF3. (PRPF3-BGHcLV22-40)

value: child

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS607OAV at ENCODE; https://www.encodeproject.org/ENCBS607OAV/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB965ITQ)

description:
https://www.encodeproject.org/experiments/ENCSR175IGC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR175IGC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR934ZBY
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB965ITQ
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

library_source: genomic

molecule: genomic DNA

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

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

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: eCLIP from HepG2 (ENCLB008ULQ)

description:
https://www.encodeproject.org/experiments/ENCSR322HHA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against TIAL1
experiment encode accession: ENCSR322HHA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR599YGK
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB008ULQ
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 cell line

value: cell line

value: male

value: hepatocellular carcinoma

value: 15 year

value: Gene Yeo, UCSD

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

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


title: microRNA-seq from heart left ventricle (ENCLB515MQX)

description:
https://www.encodeproject.org/experiments/ENCSR249SPI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W76 heart left ventricle microRNA-seq from Mortazavi
experiment encode accession: ENCSR249SPI
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB515MQX
size range: <30

source_name: Homo sapiens male adult (40 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: adult

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS756BZF at ENCODE; https://www.encodeproject.org/ENCBS756BZF/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: CRISPR RNA-seq from HepG2 (ENCLB054VXK)

description:
https://www.encodeproject.org/experiments/ENCSR814JQP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF9. (SRSF9-BGHcLV09)
experiment encode accession: ENCSR814JQP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB054VXK
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 SRSF9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1180b78e-4282-40f2-8a1f-74856a2d0f6d/@@download/attachment/L-SRSF9-BGHcLV09-22.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF9. (SRSF9-BGHcLV09-22)

value: child

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS151QTT at ENCODE; https://www.encodeproject.org/ENCBS151QTT/


title: CRISPR RNA-seq from HepG2 (ENCLB193JDP)

description:
https://www.encodeproject.org/experiments/ENCSR695RQF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PPP1R10. (PPP1R10-BGHcLV18)
experiment encode accession: ENCSR695RQF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB193JDP
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 PPP1R10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/917007d2-48cc-4cce-bbc7-dbe74289bec0/@@download/attachment/L-PPP1R10-BGHcLV18-33.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PPP1R10. (PPP1R10-BGHcLV18-33)

value: male

value: hepatocellular carcinoma

value: 15 year

value: ENCBS537VXF at ENCODE; https://www.encodeproject.org/ENCBS537VXF/


title: CRISPR RNA-seq from HepG2 (ENCLB224DHA)

description:
https://www.encodeproject.org/experiments/ENCSR695RQF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PPP1R10. (PPP1R10-BGHcLV18)
experiment encode accession: ENCSR695RQF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB224DHA
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/4462528b-37f3-4007-b90a-e6d9ab8d8c9a/@@download/attachment/L-PPP1R10-BGHcLV18-34.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PPP1R10. (PPP1R10-BGHcLV18-34)

value: ENCBS611YBI at ENCODE; https://www.encodeproject.org/ENCBS611YBI/

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


title: CRISPR RNA-seq from K562 (ENCLB535XLP)

description:
https://www.encodeproject.org/experiments/ENCSR816LHY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL11. (RPL11-BGKcLV15)
experiment encode accession: ENCSR816LHY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB535XLP
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 RPL11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b9ea8bf6-d7a8-4d83-9c19-05a44a61aa08/@@download/attachment/L-RPL11-BGKcLV15-52.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL11. (RPL11-BGKcLV15-52)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS432KQK at ENCODE; https://www.encodeproject.org/ENCBS432KQK/

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


title: eCLIP from K562 (ENCLB554ZYW)

description:
https://www.encodeproject.org/experiments/ENCSR308YNT/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against PUM1
experiment encode accession: ENCSR308YNT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR832DWW
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB554ZYW
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

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: Control eCLIP from HepG2 (ENCLB473HYJ)

description:
https://www.encodeproject.org/experiments/ENCSR310WYE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against PABPN1
experiment encode accession: ENCSR310WYE
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB473HYJ
fragmentation methods: see document
size range: 175-300

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: ATCC

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


title: BruChase-seq from IMR-90 (ENCLB935SLN)

description:
https://www.encodeproject.org/experiments/ENCSR809IJG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR809IJG
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR103IHW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB935SLN
size range: 400-500

source_name: Homo sapiens IMR-90 cell line, subjected to a 6 hour pulse-chase

value: unknown

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ENCBS987NHY at ENCODE; https://www.encodeproject.org/ENCBS987NHY/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: CRISPR RNA-seq from HepG2 (ENCLB188NOL)

description:
https://www.encodeproject.org/experiments/ENCSR687ITW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL28. (RPL28-BGHcLV18)
experiment encode accession: ENCSR687ITW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB188NOL
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 RPL28

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2a256f5e-9078-4fbf-acee-edee1efb6648/@@download/attachment/L-RPL28-BGHcLV18-42.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL28. (RPL28-BGHcLV18-42)

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS282WMO at ENCODE; https://www.encodeproject.org/ENCBS282WMO/

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


title: CRISPR RNA-seq from HepG2 (ENCLB302UCC)

description:
https://www.encodeproject.org/experiments/ENCSR814JQP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF9. (SRSF9-BGHcLV09)
experiment encode accession: ENCSR814JQP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB302UCC
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/1fd84bbf-d4bd-4f5a-bf49-2c9adb03f075/@@download/attachment/L-SRSF9-BGHcLV09-21.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF9. (SRSF9-BGHcLV09-21)

value: ENCBS986HKN at ENCODE; https://www.encodeproject.org/ENCBS986HKN/


title: CRISPR RNA-seq from K562 (ENCLB124FWX)

description:
https://www.encodeproject.org/experiments/ENCSR816LHY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL11. (RPL11-BGKcLV15)
experiment encode accession: ENCSR816LHY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB124FWX
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/d479fe03-2026-4218-a44c-638c66988ca1/@@download/attachment/L-RPL11-BGKcLV15-51.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL11. (RPL11-BGKcLV15-51)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS600KIV at ENCODE; https://www.encodeproject.org/ENCBS600KIV/

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


title: CRISPR RNA-seq from K562 (ENCLB795YCM)

description:
https://www.encodeproject.org/experiments/ENCSR914IEV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF3. (SRSF3-BGKcLV08)
experiment encode accession: ENCSR914IEV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB795YCM
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/4478e96c-ecdd-4aef-bb4a-e65d76914006/@@download/attachment/L-SRSF3-BGKcLV08-75.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF3. (SRSF3-BGKcLV08-75)

value: ATCC

value: ENCBS978SXT at ENCODE; https://www.encodeproject.org/ENCBS978SXT/


title: eCLIP from K562 (ENCLB428AQN)

description:
https://www.encodeproject.org/experiments/ENCSR308YNT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against PUM1
experiment encode accession: ENCSR308YNT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR832DWW
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB428AQN
fragmentation methods: see document
size range: 175-300

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: BruChase-seq from IMR-90 (ENCLB657JGB)

description:
https://www.encodeproject.org/experiments/ENCSR809IJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR809IJG
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR103IHW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB657JGB
size range: 400-500

value: unknown

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ENCBS663QIP at ENCODE; https://www.encodeproject.org/ENCBS663QIP/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: BruChase-seq from GM12878 (ENCLB060KPP)

description:
https://www.encodeproject.org/experiments/ENCSR685SOS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR685SOS
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR267RPG
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB060KPP
size range: 400-500

source_name: Homo sapiens GM12878 cell line, subjected to a 2 hour pulse-chase

value: cell line

value: female

value: not collected

value: Coriell

value: ENCBS358DDF at ENCODE; https://www.encodeproject.org/ENCBS358DDF/

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


title: Mint-ChIP-seq from immature natural killer cell (ENCLB705BTM)

description:
https://www.encodeproject.org/experiments/ENCSR806HUT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR806HUT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR169WAD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB705BTM
fragmentation methods: none

source_name: Homo sapiens immature natural killer primary cell with multiple sclerosis

value: immature natural killer cell

value: primary cell

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

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS911UEN at ENCODE; https://www.encodeproject.org/ENCBS911UEN/

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


title: BruChase-seq from GM12878 (ENCLB667HHY)

description:
https://www.encodeproject.org/experiments/ENCSR685SOS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR685SOS
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR267RPG
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB667HHY
size range: 400-500

value: unknown

value: adult

value: Mats Ljungman, UMichigan

value: ENCBS237THJ at ENCODE; https://www.encodeproject.org/ENCBS237THJ/


title: CRISPR RNA-seq from K562 (ENCLB128JEB)

description:
https://www.encodeproject.org/experiments/ENCSR916PCG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against E4F1. (E4F1-BGKcLV17)
experiment encode accession: ENCSR916PCG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB128JEB
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 E4F1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7f992dbd-65bc-41de-94f4-baf4b208e347/@@download/attachment/L-E4F1-BGKcLV17-16.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against E4F1. (E4F1-BGKcLV17-16)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS805LKE at ENCODE; https://www.encodeproject.org/ENCBS805LKE/

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


title: CRISPR RNA-seq from K562 (ENCLB605DQW)

description:
https://www.encodeproject.org/experiments/ENCSR681ELF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PRPF3. (PRPF3-BGKcLV23)
experiment encode accession: ENCSR681ELF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB605DQW
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 PRPF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/be74fc6e-ca0a-4014-b0ad-4a7ae1c8e248/@@download/attachment/L-PRPF3-BGKcLV23-56.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PRPF3. (PRPF3-BGKcLV23-56)

value: ENCBS212CME at ENCODE; https://www.encodeproject.org/ENCBS212CME/


title: CRISPR RNA-seq from K562 (ENCLB223OQN)

description:
https://www.encodeproject.org/experiments/ENCSR681ELF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PRPF3. (PRPF3-BGKcLV23)
experiment encode accession: ENCSR681ELF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB223OQN
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/34b46887-d775-45eb-bbbc-66b15b326301/@@download/attachment/L-PRPF3-BGKcLV23-55.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PRPF3. (PRPF3-BGKcLV23-55)

value: ENCBS248THI at ENCODE; https://www.encodeproject.org/ENCBS248THI/


title: Bru-seq from HCT116 (ENCLB730XDS)

description:
https://www.encodeproject.org/experiments/ENCSR799MPW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR799MPW
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB730XDS
size range: 400-500

source_name: Homo sapiens HCT116 cell line

value: male

value: colorectal carcinoma

value: 48 year

value: ENCBS422PTE at ENCODE; https://www.encodeproject.org/ENCBS422PTE/

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


title: Control eCLIP from K562 (ENCLB272OWM)

description:
https://www.encodeproject.org/experiments/ENCSR404ABA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against WDR43
experiment encode accession: ENCSR404ABA
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB272OWM
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: cell line

value: adult

value: Gene Yeo, UCSD

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

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

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


title: Control eCLIP from K562 (ENCLB724LCD)

description:
https://www.encodeproject.org/experiments/ENCSR299AAB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against HNRNPL
experiment encode accession: ENCSR299AAB
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-28
lab: Gene Yeo, UCSD
library encode accession: ENCLB724LCD
fragmentation methods: see document
size range: 175-300

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)


title: eCLIP from HepG2 (ENCLB985KTR)

description:
https://www.encodeproject.org/experiments/ENCSR290VLT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against MATR3
experiment encode accession: ENCSR290VLT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR438XYI
encode release date: 2018-04-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB985KTR
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: child

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: CRISPR RNA-seq from HepG2 (ENCLB249WNR)

description:
https://www.encodeproject.org/experiments/ENCSR909TFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PRPF3. (PRPF3-BGHcLV22)
experiment encode accession: ENCSR909TFJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB249WNR
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/f3f46b44-e31b-4349-9f13-8956f1b5a0a0/@@download/attachment/L-PRPF3-BGHcLV22-39.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PRPF3. (PRPF3-BGHcLV22-39)

value: male

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS615UGH at ENCODE; https://www.encodeproject.org/ENCBS615UGH/


title: eCLIP from HepG2 (ENCLB984MLU)

description:
https://www.encodeproject.org/experiments/ENCSR290VLT/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against MATR3
experiment encode accession: ENCSR290VLT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR438XYI
encode release date: 2018-04-24
lab: Gene Yeo, UCSD
library encode accession: ENCLB984MLU
fragmentation methods: see document
size range: 175-300

value: cell line

value: Gene Yeo, UCSD

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


title: CRISPR RNA-seq from HepG2 (ENCLB922EXY)

description:
https://www.encodeproject.org/experiments/ENCSR670KAS/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV18)
experiment encode accession: ENCSR670KAS
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB922EXY
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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6100f80c-3034-4221-a6e4-d597466d68b6/@@download/attachment/L-NT-BGHcLV18-1.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV18-1)

value: ENCBS876GKI at ENCODE; https://www.encodeproject.org/ENCBS876GKI/


title: CRISPR RNA-seq from HepG2 (ENCLB502SZZ)

description:
https://www.encodeproject.org/experiments/ENCSR670KAS/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV18)
experiment encode accession: ENCSR670KAS
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB502SZZ
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/6c1b04c3-4d46-43c8-a997-e6bc514fd31b/@@download/attachment/L-NT-BGHcLV18-2.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV18-2)

value: ENCBS742NFJ at ENCODE; https://www.encodeproject.org/ENCBS742NFJ/


title: Bru-seq from HCT116 (ENCLB735LTZ)

description:
https://www.encodeproject.org/experiments/ENCSR799MPW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR799MPW
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB735LTZ
size range: 400-500

value: colorectal carcinoma

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

value: ENCBS186IVF at ENCODE; https://www.encodeproject.org/ENCBS186IVF/

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


title: CRISPR RNA-seq from K562 (ENCLB194UJD)

description:
https://www.encodeproject.org/experiments/ENCSR682DZY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SUZ12. (SUZ12-BGKcLV17)
experiment encode accession: ENCSR682DZY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB194UJD
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 SUZ12

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/31331a85-db37-4fb1-bd41-1136471e73fb/@@download/attachment/L-SUZ12-BGKcLV17-49.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SUZ12. (SUZ12-BGKcLV17-49)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS159DJP at ENCODE; https://www.encodeproject.org/ENCBS159DJP/

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


title: CRISPR RNA-seq from K562 (ENCLB999PPX)

description:
https://www.encodeproject.org/experiments/ENCSR682DZY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SUZ12. (SUZ12-BGKcLV17)
experiment encode accession: ENCSR682DZY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB999PPX
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/a6dec87b-b6b0-4a01-97af-91b11de09bfb/@@download/attachment/L-SUZ12-BGKcLV17-50.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SUZ12. (SUZ12-BGKcLV17-50)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS930MOC at ENCODE; https://www.encodeproject.org/ENCBS930MOC/


title: CRISPR RNA-seq from HepG2 (ENCLB135EOF)

description:
https://www.encodeproject.org/experiments/ENCSR796HOP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against FBL. (FBL-BGHcLV18)
experiment encode accession: ENCSR796HOP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB135EOF
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 FBL

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2f971f3c-9cb9-45ac-9ba6-1415c7baedb3/@@download/attachment/L-FBL-BGHcLV18-19.pdf

value: FBL

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against FBL. (FBL-BGHcLV18-19)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS141JHO at ENCODE; https://www.encodeproject.org/ENCBS141JHO/

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


title: Control eCLIP from HepG2 (ENCLB122ZTE)

description:
https://www.encodeproject.org/experiments/ENCSR098VKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against ZC3H11A
experiment encode accession: ENCSR098VKQ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-28
lab: Gene Yeo, UCSD
library encode accession: ENCLB122ZTE
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

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

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: Mint-ChIP-seq from immature natural killer cell (ENCLB101USM)

description:
https://www.encodeproject.org/experiments/ENCSR667HUI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR667HUI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR169WAD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB101USM
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: immature natural killer cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS911UEN at ENCODE; https://www.encodeproject.org/ENCBS911UEN/

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


title: CRISPR RNA-seq from HepG2 (ENCLB930MCV)

description:
https://www.encodeproject.org/experiments/ENCSR687ITW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL28. (RPL28-BGHcLV18)
experiment encode accession: ENCSR687ITW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB930MCV
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/7e9c0fa9-f165-4a4a-96b5-10a1c2bf082c/@@download/attachment/L-RPL28-BGHcLV18-41.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL28. (RPL28-BGHcLV18-41)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS484PMS at ENCODE; https://www.encodeproject.org/ENCBS484PMS/


title: microRNA-seq from Right ventricle myocardium superior (ENCLB535CWS)

description:
https://www.encodeproject.org/experiments/ENCSR064DFT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 right ventricle myocardium superior microRNA-seq from Mortazavi
experiment encode accession: ENCSR064DFT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB535CWS
size range: <30

source_name: Homo sapiens male adult (60 years) Right ventricle myocardium superior tissue, preserved by flash-freezing

value: Right ventricle myocardium superior

value: tissue

value: Superior wall of right ventricle.

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: ENCBS580WTV at ENCODE; https://www.encodeproject.org/ENCBS580WTV/

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


title: TF ChIP-seq from WTC11 (ENCLB964KBL)

description:
https://www.encodeproject.org/experiments/ENCSR281VWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GTF2I ChIP-seq on human WTC11
experiment encode accession: ENCSR281VWZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR325SCU, ENCSR712UWN
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB964KBL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting GTF2I

value: cell line

value: male

value: 30 year

value: Kevin White

value: ENCBS771ODO at ENCODE; https://www.encodeproject.org/ENCBS771ODO/

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


title: Control eCLIP from K562 (ENCLB045QID)

description:
https://www.encodeproject.org/experiments/ENCSR308RMD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against EXOSC5
experiment encode accession: ENCSR308RMD
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB045QID
fragmentation methods: see document
size range: 175-300

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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: CRISPR RNA-seq from HepG2 (ENCLB381VPB)

description:
https://www.encodeproject.org/experiments/ENCSR796HOP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against FBL. (FBL-BGHcLV18)
experiment encode accession: ENCSR796HOP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB381VPB
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/960d387d-fed6-48ae-9ad4-06de2ef35158/@@download/attachment/L-FBL-BGHcLV18-20.pdf

value: FBL

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against FBL. (FBL-BGHcLV18-20)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS145TEI at ENCODE; https://www.encodeproject.org/ENCBS145TEI/

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


title: CRISPR RNA-seq from K562 (ENCLB512NHN)

description:
https://www.encodeproject.org/experiments/ENCSR671OGO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against IFIT2. (IFIT2-BGKcLV17)
experiment encode accession: ENCSR671OGO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB512NHN
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 IFIT2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/20f75456-7787-458c-a507-9b823684360b/@@download/attachment/L-IFIT2-BGKcLV17-32.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against IFIT2. (IFIT2-BGKcLV17-32)

value: female

value: adult

value: ENCBS662ZVC at ENCODE; https://www.encodeproject.org/ENCBS662ZVC/


title: TF ChIP-seq from WTC11 (ENCLB592RFP)

description:
https://www.encodeproject.org/experiments/ENCSR281VWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GTF2I ChIP-seq on human WTC11
experiment encode accession: ENCSR281VWZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR325SCU, ENCSR712UWN
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB592RFP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS496TRA at ENCODE; https://www.encodeproject.org/ENCBS496TRA/

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


title: CRISPR RNA-seq from K562 (ENCLB294ORG)

description:
https://www.encodeproject.org/experiments/ENCSR667WZB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2AK1. (EIF2AK1-BGKcLV15)
experiment encode accession: ENCSR667WZB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB294ORG
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 EIF2AK1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/eeeb85ff-1fe9-4a9b-8dde-f499e94a0257/@@download/attachment/L-EIF2AK1-BGKcLV15-24.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2AK1. (EIF2AK1-BGKcLV15-24)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS403NOH at ENCODE; https://www.encodeproject.org/ENCBS403NOH/

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


title: BruChase-seq from IMR-90 (ENCLB161TEC)

description:
https://www.encodeproject.org/experiments/ENCSR797SWY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR797SWY
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR103IHW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB161TEC
size range: 400-500

source_name: Homo sapiens IMR-90 cell line, subjected to a 2 hour pulse-chase

value: unknown

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS694MVQ at ENCODE; https://www.encodeproject.org/ENCBS694MVQ/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: BruChase-seq from IMR-90 (ENCLB183CDX)

description:
https://www.encodeproject.org/experiments/ENCSR797SWY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR797SWY
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR103IHW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB183CDX
size range: 400-500

value: cell line

value: female

value: ENCBS055HAM at ENCODE; https://www.encodeproject.org/ENCBS055HAM/


title: CRISPR RNA-seq from HepG2 (ENCLB653BOA)

description:
https://www.encodeproject.org/experiments/ENCSR666FOS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CXXC1. (CXXC1-BGHcLV18)
experiment encode accession: ENCSR666FOS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB653BOA
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 CXXC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0ffb1342-c8c6-4cbc-be6e-928fe869a210/@@download/attachment/L-CXXC1-BGHcLV18-7.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CXXC1. (CXXC1-BGHcLV18-7)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS285GCD at ENCODE; https://www.encodeproject.org/ENCBS285GCD/

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


title: microRNA-seq from MCF-7 (ENCLB488YTB)

description:
https://www.encodeproject.org/experiments/ENCSR155IQU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation MCF7 microRNA-seq from Mortazavi
experiment encode accession: ENCSR155IQU
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB488YTB
size range: <30

source_name: Homo sapiens MCF-7 cell line

value: adult

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS734JMT at ENCODE; https://www.encodeproject.org/ENCBS734JMT/

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


title: CRISPR RNA-seq from K562 (ENCLB946ISK)

description:
https://www.encodeproject.org/experiments/ENCSR667WZB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2AK1. (EIF2AK1-BGKcLV15)
experiment encode accession: ENCSR667WZB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB946ISK
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/a24f7b0b-8807-4b41-af90-b4ecb36831e4/@@download/attachment/L-EIF2AK1-BGKcLV15-23.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2AK1. (EIF2AK1-BGKcLV15-23)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS902FGA at ENCODE; https://www.encodeproject.org/ENCBS902FGA/

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


title: CRISPR RNA-seq from K562 (ENCLB938DOP)

description:
https://www.encodeproject.org/experiments/ENCSR667FZF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against KPNB1. (KPNB1-BGKcLV13)
experiment encode accession: ENCSR667FZF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB938DOP
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 KPNB1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/09c7d4a5-09c6-4c08-8208-8f7983a5e1d0/@@download/attachment/L-KPNB1-BGKcLV13-46.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against KPNB1. (KPNB1-BGKcLV13-46)

value: female

value: ENCBS352MSE at ENCODE; https://www.encodeproject.org/ENCBS352MSE/


title: microRNA-seq from chondrocyte (ENCLB671JIW)

description:
https://www.encodeproject.org/experiments/ENCSR153MHB/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation WA09-derived chondrocytes microRNA-seq from Mortazavi
experiment encode accession: ENCSR153MHB
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB671JIW
size range: <30

source_name: Homo sapiens female embryo (5 days) chondrocyte in vitro differentiated cells

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS668AFC at ENCODE; https://www.encodeproject.org/ENCBS668AFC/

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


title: microRNA-seq from right lobe of liver (ENCLB094TUZ)

description:
https://www.encodeproject.org/experiments/ENCSR155HYM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W62 right lobe liver microRNA-seq from Mortazavi
experiment encode accession: ENCSR155HYM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-03-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB094TUZ
size range: <30

source_name: Homo sapiens female child (16 years) right lobe of liver tissue, preserved by flash-freezing

value: right lobe of liver

value: tissue

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS949OWB at ENCODE; https://www.encodeproject.org/ENCBS949OWB/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: CRISPR RNA-seq from K562 (ENCLB213UQE)

description:
https://www.encodeproject.org/experiments/ENCSR665DMA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against MECP2. (MECP2-BGKcLV15)
experiment encode accession: ENCSR665DMA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB213UQE
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 MECP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c08f998b-209d-4945-b1c2-c548a201b3e6/@@download/attachment/L-GSK3B-BGKcLV15-38.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against MECP2. (MECP2-BGKcLV15-40)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS786QAW at ENCODE; https://www.encodeproject.org/ENCBS786QAW/

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


title: CRISPR RNA-seq from K562 (ENCLB876JWM)

description:
https://www.encodeproject.org/experiments/ENCSR667FZF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against KPNB1. (KPNB1-BGKcLV13)
experiment encode accession: ENCSR667FZF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB876JWM
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/0c8ec4cc-0c11-41d1-81cf-94f781f3b3af/@@download/attachment/L-KPNB1-BGKcLV13-45.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against KPNB1. (KPNB1-BGKcLV13-45)

value: ENCBS488XRL at ENCODE; https://www.encodeproject.org/ENCBS488XRL/


title: CRISPR RNA-seq from K562 (ENCLB754LHH)

description:
https://www.encodeproject.org/experiments/ENCSR665CVU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NCL. (NCL-BGKcLV19)
experiment encode accession: ENCSR665CVU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB754LHH
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 NCL

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/74038f3f-a5dc-44c1-9dcd-69e689bccac9/@@download/attachment/L-NCL-BGKcLV19-25.pdf

value: NCL

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NCL. (NCL-BGKcLV19-25)

value: ENCBS383YWT at ENCODE; https://www.encodeproject.org/ENCBS383YWT/


title: CRISPR RNA-seq from K562 (ENCLB719ENY)

description:
https://www.encodeproject.org/experiments/ENCSR671OGO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against IFIT2. (IFIT2-BGKcLV17)
experiment encode accession: ENCSR671OGO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB719ENY
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/17f87f12-2bb1-4fcf-8f2c-f77bacb57905/@@download/attachment/L-IFIT2-BGKcLV17-31.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against IFIT2. (IFIT2-BGKcLV17-31)

value: ENCBS101PEX at ENCODE; https://www.encodeproject.org/ENCBS101PEX/


title: CRISPR RNA-seq from K562 (ENCLB140EDP)

description:
https://www.encodeproject.org/experiments/ENCSR665CVU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NCL. (NCL-BGKcLV19)
experiment encode accession: ENCSR665CVU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB140EDP
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/8c5a5e94-5308-4c99-a8aa-939654aa21a5/@@download/attachment/L-NCL-BGKcLV19-26.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NCL. (NCL-BGKcLV19-26)

value: ENCBS298ZDQ at ENCODE; https://www.encodeproject.org/ENCBS298ZDQ/


title: Control eCLIP from HepG2 (ENCLB971TQM)

description:
https://www.encodeproject.org/experiments/ENCSR278BZH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against NOLC1
experiment encode accession: ENCSR278BZH
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB971TQM
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: Control eCLIP from K562 (ENCLB749DJU)

description:
https://www.encodeproject.org/experiments/ENCSR268SKI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX51
experiment encode accession: ENCSR268SKI
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB749DJU
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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

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


title: CRISPR RNA-seq from K562 (ENCLB322DGZ)

description:
https://www.encodeproject.org/experiments/ENCSR665DMA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against MECP2. (MECP2-BGKcLV15)
experiment encode accession: ENCSR665DMA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB322DGZ
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/184c93aa-9909-4745-801b-4e52ea17a05b/@@download/attachment/L-GSK3B-BGKcLV15-37.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against MECP2. (MECP2-BGKcLV15-39)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS691RCG at ENCODE; https://www.encodeproject.org/ENCBS691RCG/


title: eCLIP from HepG2 (ENCLB707GOE)

description:
https://www.encodeproject.org/experiments/ENCSR085JPB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against WDR43
experiment encode accession: ENCSR085JPB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR722KGI
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB707GOE
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: ENCBS492SDY at ENCODE; https://www.encodeproject.org/ENCBS492SDY/


title: CRISPR RNA-seq from K562 (ENCLB532NOM)

description:
https://www.encodeproject.org/experiments/ENCSR786OLN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2B3. (EIF2B3-BGKcLV15)
experiment encode accession: ENCSR786OLN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB532NOM
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 EIF2B3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/db20db71-563a-493b-b74c-d4f8aa1f208e/@@download/attachment/L-EIF2B3-BGKcLV15-27.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2B3. (EIF2B3-BGKcLV15-27)

value: female

value: adult

value: ENCBS422SUU at ENCODE; https://www.encodeproject.org/ENCBS422SUU/


title: CRISPR RNA-seq from K562 (ENCLB505VFF)

description:
https://www.encodeproject.org/experiments/ENCSR786OLN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2B3. (EIF2B3-BGKcLV15)
experiment encode accession: ENCSR786OLN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB505VFF
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/e5da82e6-c270-4ac9-99e2-e76b954cb5ac/@@download/attachment/L-EIF2B3-BGKcLV15-28.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2B3. (EIF2B3-BGKcLV15-28)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS726XNC at ENCODE; https://www.encodeproject.org/ENCBS726XNC/

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


title: microRNA-seq from chondrocyte (ENCLB689NVY)

description:
https://www.encodeproject.org/experiments/ENCSR153MHB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation WA09-derived chondrocytes microRNA-seq from Mortazavi
experiment encode accession: ENCSR153MHB
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB689NVY
size range: <30

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS434FZQ at ENCODE; https://www.encodeproject.org/ENCBS434FZQ/

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


title: Control eCLIP from K562 (ENCLB981SPY)

description:
https://www.encodeproject.org/experiments/ENCSR290JPJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against AATF
experiment encode accession: ENCSR290JPJ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB981SPY
fragmentation methods: see document
size range: 175-300

value: cell line

value: adult

value: female

value: Gene Yeo, UCSD

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

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

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


title: eCLIP from K562 (ENCLB743FZU)

description:
https://www.encodeproject.org/experiments/ENCSR089BXO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against ABCF1
experiment encode accession: ENCSR089BXO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR857ORY
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB743FZU
fragmentation methods: see document
size range: 175-300

value: 53 year

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/


title: microRNA-seq from left colon (ENCLB217SWL)

description:
https://www.encodeproject.org/experiments/ENCSR152XXM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 left colon microRNA-seq from Mortazavi
experiment encode accession: ENCSR152XXM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB217SWL
size range: <30

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

value: left colon

value: tissue

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS908TVF at ENCODE; https://www.encodeproject.org/ENCBS908TVF/

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


title: microRNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB417DEV)

description:
https://www.encodeproject.org/experiments/ENCSR151IFS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human memory CD4+ T cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR151IFS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-06-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB417DEV
size range: <30

source_name: Homo sapiens male adult (43 years) CD4-positive, alpha-beta memory T primary cell

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

value: primary cell

value: memory CD4+ T cell (CD45RO+CCR7+/-)

value: male

value: adult

value: 43 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS009MRL at ENCODE; https://www.encodeproject.org/ENCBS009MRL/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: CRISPR RNA-seq from K562 (ENCLB647YIO)

description:
https://www.encodeproject.org/experiments/ENCSR660WRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZFP106. (ZFP106-BGKcLV08)
experiment encode accession: ENCSR660WRQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB647YIO
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 ZNF106

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/879d421a-0eb1-48d8-8112-f2305a8d8b85/@@download/attachment/L-ZFP106-BGKcLV08-87.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZFP106. (ZFP106-BGKcLV08-87)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS087MOX at ENCODE; https://www.encodeproject.org/ENCBS087MOX/

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


title: CRISPR RNA-seq from K562 (ENCLB207CPD)

description:
https://www.encodeproject.org/experiments/ENCSR660WRQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZFP106. (ZFP106-BGKcLV08)
experiment encode accession: ENCSR660WRQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB207CPD
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/5a2a57e6-a84e-46cb-9045-6de7864f5c66/@@download/attachment/L-ZFP106-BGKcLV08-88.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZFP106. (ZFP106-BGKcLV08-88)

value: ENCBS132FUX at ENCODE; https://www.encodeproject.org/ENCBS132FUX/


title: CRISPR RNA-seq from K562 (ENCLB834XBA)

description:
https://www.encodeproject.org/experiments/ENCSR663BBL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CNOT2. (CNOT2-BGKcLV23)
experiment encode accession: ENCSR663BBL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB834XBA
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 CNOT2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6e65c353-7d1d-4bd2-9cf6-6504e10a5293/@@download/attachment/L-CNOT2-BGKcLV23-29.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CNOT2. (CNOT2-BGKcLV23-29)

value: adult

value: ENCBS721LOQ at ENCODE; https://www.encodeproject.org/ENCBS721LOQ/


title: eCLIP from HepG2 (ENCLB407VOF)

description:
https://www.encodeproject.org/experiments/ENCSR085JPB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against WDR43
experiment encode accession: ENCSR085JPB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR722KGI
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB407VOF
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB465QNE)

description:
https://www.encodeproject.org/experiments/ENCSR666FOS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CXXC1. (CXXC1-BGHcLV18)
experiment encode accession: ENCSR666FOS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB465QNE
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/e5a2d6f8-2c6e-484b-b17b-4694d954a429/@@download/attachment/L-CXXC1-BGHcLV18-8.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CXXC1. (CXXC1-BGHcLV18-8)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS083QAV at ENCODE; https://www.encodeproject.org/ENCBS083QAV/


title: microRNA-seq from chondrocyte (ENCLB183FIS)

description:
https://www.encodeproject.org/experiments/ENCSR153MHB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation WA09-derived chondrocytes microRNA-seq from Mortazavi
experiment encode accession: ENCSR153MHB
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB183FIS
size range: <30

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS524YKH at ENCODE; https://www.encodeproject.org/ENCBS524YKH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB382WZU)

description:
https://www.encodeproject.org/experiments/ENCSR775ZWO/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV10)
experiment encode accession: ENCSR775ZWO
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB382WZU
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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/88c6f001-0f59-4753-946b-83824a571abb/@@download/attachment/L-NT-BGHcLV10-1.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV10-1)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS275IUW at ENCODE; https://www.encodeproject.org/ENCBS275IUW/

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


title: microRNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB133HYE)

description:
https://www.encodeproject.org/experiments/ENCSR151IFS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human memory CD4+ T cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR151IFS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-06-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB133HYE
size range: <30

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

value: primary cell

value: memory CD4+ T cell (CD45RO+CCR7+/-)

value: adult

value: 43 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS010ART at ENCODE; https://www.encodeproject.org/ENCBS010ART/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: CRISPR RNA-seq from K562 (ENCLB207LOE)

description:
https://www.encodeproject.org/experiments/ENCSR663BBL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CNOT2. (CNOT2-BGKcLV23)
experiment encode accession: ENCSR663BBL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB207LOE
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/fcac5bfa-0ffe-4677-9c07-e1c85cf39880/@@download/attachment/L-CNOT2-BGKcLV23-30.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CNOT2. (CNOT2-BGKcLV23-30)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS739YPH at ENCODE; https://www.encodeproject.org/ENCBS739YPH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB607GKN)

description:
https://www.encodeproject.org/experiments/ENCSR659DRE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAVL1. (ELAVL1-BGHcLV14)
experiment encode accession: ENCSR659DRE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB607GKN
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 ELAVL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5f560e20-528a-4712-acbc-17ccc723f851/@@download/attachment/L-ELAVL1-BGHcLV14-39.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAVL1. (ELAVL1-BGHcLV14-39)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS834AUG at ENCODE; https://www.encodeproject.org/ENCBS834AUG/

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


title: CRISPR RNA-seq from K562 (ENCLB212CFZ)

description:
https://www.encodeproject.org/experiments/ENCSR659UXO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against YBX1. (YBX1-BGKcLV15)
experiment encode accession: ENCSR659UXO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB212CFZ
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 YBX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d9732693-089a-4a91-a47f-80185a6f6696/@@download/attachment/L-YBX1-BGKcLV15-63.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against YBX1. (YBX1-BGKcLV15-63)

value: adult

value: ENCBS568TBB at ENCODE; https://www.encodeproject.org/ENCBS568TBB/


title: Control eCLIP from K562 (ENCLB912YUQ)

description:
https://www.encodeproject.org/experiments/ENCSR266XXD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX21
experiment encode accession: ENCSR266XXD
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB912YUQ
fragmentation methods: see document
size range: 175-300

value: cell line

value: female

value: Gene Yeo, UCSD

value: ENCBS126AJR at ENCODE; https://www.encodeproject.org/ENCBS126AJR/

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

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


title: eCLIP from K562 (ENCLB702DKM)

description:
https://www.encodeproject.org/experiments/ENCSR089BXO/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against ABCF1
experiment encode accession: ENCSR089BXO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR857ORY
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB702DKM
fragmentation methods: see document
size range: 175-300

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: eCLIP from HepG2 (ENCLB081AAY)

description:
https://www.encodeproject.org/experiments/ENCSR194HZU/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against NOLC1
experiment encode accession: ENCSR194HZU
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR278BZH
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB081AAY
fragmentation methods: see document
size range: 175-300

value: child

value: male

value: hepatocellular carcinoma

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

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


title: eCLIP from HepG2 (ENCLB788KXR)

description:
https://www.encodeproject.org/experiments/ENCSR194HZU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against NOLC1
experiment encode accession: ENCSR194HZU
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR278BZH
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB788KXR
fragmentation methods: see document
size range: 175-300

value: 15 year

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

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


title: CRISPR RNA-seq from K562 (ENCLB028MCJ)

description:
https://www.encodeproject.org/experiments/ENCSR775USN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMYD3. (SMYD3-BGKcLV19)
experiment encode accession: ENCSR775USN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB028MCJ
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 SMYD3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/710bb577-41fd-4050-b222-f13aedc1bc31/@@download/attachment/L-SMYD3-BGKcLV19-51.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMYD3. (SMYD3-BGKcLV19-51)

value: female

value: adult

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS689KXA at ENCODE; https://www.encodeproject.org/ENCBS689KXA/


title: Control eCLIP from K562 (ENCLB248UAI)

description:
https://www.encodeproject.org/experiments/ENCSR192TPA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against PABPC4
experiment encode accession: ENCSR192TPA
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB248UAI
fragmentation methods: see document
size range: 175-300

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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

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


title: TF ChIP-seq from A549 (ENCLB838WGF)

description:
https://www.encodeproject.org/experiments/ENCSR192SKV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-HMGXB4 ChIP-seq on human A549
experiment encode accession: ENCSR192SKV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR580TXR, ENCSR542LGX
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB838WGF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting HMGXB4

value: male

value: 58 year

value: Michael Snyder, Stanford

value: ENCBS256AQB at ENCODE; https://www.encodeproject.org/ENCBS256AQB/

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


title: CRISPR RNA-seq from K562 (ENCLB945CFI)

description:
https://www.encodeproject.org/experiments/ENCSR659UXO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against YBX1. (YBX1-BGKcLV15)
experiment encode accession: ENCSR659UXO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB945CFI
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/06e7b3b3-b0c2-4ceb-b06c-d88020cc8cf3/@@download/attachment/L-YBX1-BGKcLV15-64.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against YBX1. (YBX1-BGKcLV15-64)

value: ENCBS446AVJ at ENCODE; https://www.encodeproject.org/ENCBS446AVJ/

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