title: BruChase-seq from MCF-7 (ENCLB683WGA)

description:
https://www.encodeproject.org/experiments/ENCSR874VJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR874VJT
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR727IHV
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB683WGA
size range: 400-500

source_name: Homo sapiens MCF-7 cell line, subjected to a 2 hour pulse-chase

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: Mats Ljungman, UMichigan

value: ENCBS497PWR at ENCODE; https://www.encodeproject.org/ENCBS497PWR/

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


title: BruChase-seq from MCF-7 (ENCLB454PQP)

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/ENCSR874VJT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR874VJT
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR727IHV
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB454PQP
size range: 400-500

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

value: adult

tag: age

tag: lab

tag: source

value: ATCC

tag: link

value: ENCBS933FHF at ENCODE; https://www.encodeproject.org/ENCBS933FHF/


title: TF ChIP-seq from K562 (ENCLB177WAF)

description:
https://www.encodeproject.org/experiments/ENCSR451UQX/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF551 ChIP-seq on human K562
experiment encode accession: ENCSR451UQX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR012KTG, ENCSR705NCQ
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB177WAF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF551

tag: antibody

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS098SJG at ENCODE; https://www.encodeproject.org/ENCBS098SJG/

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


title: TF ChIP-seq from K562 (ENCLB328IXD)

description:
https://www.encodeproject.org/experiments/ENCSR451UQX/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF551 ChIP-seq on human K562
experiment encode accession: ENCSR451UQX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR012KTG, ENCSR705NCQ
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB328IXD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ENCBS909WEI at ENCODE; https://www.encodeproject.org/ENCBS909WEI/


title: CRISPR RNA-seq from K562 (ENCLB243KUM)

description:
https://www.encodeproject.org/experiments/ENCSR982XTO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NSUN5. (NSUN5-BGKcLV19)
experiment encode accession: ENCSR982XTO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB243KUM
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 NSUN5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3e8336f9-ce8f-4a08-8635-7875f0d99879/@@download/attachment/L-NSUN5-BGKcLV19-30.pdf

tag: description

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NSUN5. (NSUN5-BGKcLV19-30)

value: Brenton Graveley, UConn

value: ENCBS332GWN at ENCODE; https://www.encodeproject.org/ENCBS332GWN/


title: CRISPR RNA-seq from K562 (ENCLB792KWX)

description:
https://www.encodeproject.org/experiments/ENCSR982XTO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NSUN5. (NSUN5-BGKcLV19)
experiment encode accession: ENCSR982XTO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB792KWX
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/a572882a-b636-41dd-ad1c-af95147ca746/@@download/attachment/L-NSUN5-BGKcLV19-29.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NSUN5. (NSUN5-BGKcLV19-29)

value: female

value: ENCBS660QBK at ENCODE; https://www.encodeproject.org/ENCBS660QBK/


title: CRISPR RNA-seq from HepG2 (ENCLB011VZC)

description:
https://www.encodeproject.org/experiments/ENCSR871XPX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CTCF. (CTCF-BGHcLV18)
experiment encode accession: ENCSR871XPX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB011VZC
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 CTCF

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1479b069-7d88-470f-8052-b5d12a172efc/@@download/attachment/L-CTCF-BGHcLV18-6.pdf

value: CTCF

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CTCF. (CTCF-BGHcLV18-6)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS180SBL at ENCODE; https://www.encodeproject.org/ENCBS180SBL/

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


title: Bru-seq from IMR-90 (ENCLB606PCG)

description:
https://www.encodeproject.org/experiments/ENCSR873ZUO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR873ZUO
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR103IHW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB606PCG
size range: 400-500

source_name: Homo sapiens IMR-90 cell line treated with 500 rad irradiation

value: cell line

value: unknown

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ATCC

tag: treatments

value: ENCBS149YBR at ENCODE; https://www.encodeproject.org/ENCBS149YBR/

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


title: eCLIP from HepG2 (ENCLB577IAD)

description:
https://www.encodeproject.org/experiments/ENCSR464OSH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against FUS
experiment encode accession: ENCSR464OSH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR986HXA
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB577IAD
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 cell line

value: FUS

value: Gene Yeo, UCSD

tag: passage number

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


title: eCLIP from HepG2 (ENCLB100OQN)

description:
https://www.encodeproject.org/experiments/ENCSR464OSH/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against FUS
experiment encode accession: ENCSR464OSH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR986HXA
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB100OQN
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: male

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

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


title: TF ChIP-seq from K562 (ENCLB085JGN)

description:
https://www.encodeproject.org/experiments/ENCSR551KXD/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-RHOXF2B ChIP-seq on human K562
experiment encode accession: ENCSR551KXD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR706RMI, ENCSR532WSQ
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB085JGN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS365IOP at ENCODE; https://www.encodeproject.org/ENCBS365IOP/

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


title: microRNA-seq from kidney (ENCLB073WKA)

description:
https://www.encodeproject.org/experiments/ENCSR272WXU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W71 kidney microRNA-seq from Mortazavi
experiment encode accession: ENCSR272WXU
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB073WKA
size range: <30

source_name: Homo sapiens female adult (47 years) kidney tissue, preserved by flash-freezing

value: kidney

value: tissue

value: 47 year

value: Yiing Lin, MD, PhD

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

value: ENCBS305JCM at ENCODE; https://www.encodeproject.org/ENCBS305JCM/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: TF ChIP-seq from A549 (ENCLB522AVW)

description:
https://www.encodeproject.org/experiments/ENCSR461MQX/
***************
biological replicate number: 1
technical replicate number: 1
description: RARB ChIP-seq on human A549
experiment encode accession: ENCSR461MQX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR779AKU, ENCSR676KGV
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB522AVW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: RARB

value: cell line

value: male

value: 58 year

value: ATCC

value: ENCBS064IXC at ENCODE; https://www.encodeproject.org/ENCBS064IXC/

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


title: TF ChIP-seq from A549 (ENCLB668CVQ)

description:
https://www.encodeproject.org/experiments/ENCSR461MQX/
***************
biological replicate number: 2
technical replicate number: 1
description: RARB ChIP-seq on human A549
experiment encode accession: ENCSR461MQX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR779AKU, ENCSR676KGV
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB668CVQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: adult

value: Michael Snyder, Stanford

value: ENCBS787KXO at ENCODE; https://www.encodeproject.org/ENCBS787KXO/


title: CRISPR RNA-seq from K562 (ENCLB123BXC)

description:
https://www.encodeproject.org/experiments/ENCSR975NHV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGKcLV23)
experiment encode accession: ENCSR975NHV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB123BXC
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 EIF6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/db3c3a59-bc89-49cc-b23b-bcd788c638ab/@@download/attachment/L-EIF6-BGKcLV23-38.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGKcLV23-38)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS990ZZB at ENCODE; https://www.encodeproject.org/ENCBS990ZZB/

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


title: Control eCLIP from HepG2 (ENCLB105BKV)

description:
https://www.encodeproject.org/experiments/ENCSR367ACZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against PRPF4
experiment encode accession: ENCSR367ACZ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB105BKV
fragmentation methods: see document
size range: 175-300

value: hepatocellular carcinoma

value: child

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: CRISPR RNA-seq from K562 (ENCLB592NRN)

description:
https://www.encodeproject.org/experiments/ENCSR877JEM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV23)
experiment encode accession: ENCSR877JEM
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB592NRN
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c78b32ca-6ed5-4c40-ba76-113ad713a499/@@download/attachment/L-NT-BGKcLV23-1.pdf

value: cell line

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV23-1)

value: ATCC

value: ENCBS794DDL at ENCODE; https://www.encodeproject.org/ENCBS794DDL/


title: eCLIP from HepG2 (ENCLB620TTV)

description:
https://www.encodeproject.org/experiments/ENCSR366DGX/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against KHSRP
experiment encode accession: ENCSR366DGX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR423QXH
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB620TTV
fragmentation methods: see document
size range: 175-300

value: KHSRP

value: male

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

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


title: Control eCLIP from HepG2 (ENCLB089INP)

description:
https://www.encodeproject.org/experiments/ENCSR451BRX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against SAFB
experiment encode accession: ENCSR451BRX
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB089INP
fragmentation methods: see document
size range: 175-300

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 HepG2 (ENCLB089OMY)

description:
https://www.encodeproject.org/experiments/ENCSR865WQR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CACTIN. (CACTIN-BGHcLV22)
experiment encode accession: ENCSR865WQR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB089OMY
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 CACTIN

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b2df44d8-e820-4f75-a2d2-69095146b960/@@download/attachment/L-CACTIN-BGHcLV22-4.pdf

value: CACTIN

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CACTIN. (CACTIN-BGHcLV22-4)

value: Brenton Graveley, UConn

value: ENCBS314YFX at ENCODE; https://www.encodeproject.org/ENCBS314YFX/


title: Control eCLIP from K562 (ENCLB095WSX)

description:
https://www.encodeproject.org/experiments/ENCSR544UON/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against AKAP1
experiment encode accession: ENCSR544UON
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB095WSX
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: Gene Yeo, UCSD

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

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


title: eCLIP from HepG2 (ENCLB536RID)

description:
https://www.encodeproject.org/experiments/ENCSR361OCV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against NIP7
experiment encode accession: ENCSR361OCV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR138HJN
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB536RID
fragmentation methods: see document
size range: 175-300

value: cell line

value: child

value: 15 year

value: hepatocellular carcinoma

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


title: CRISPR RNA-seq from HepG2 (ENCLB012EEU)

description:
https://www.encodeproject.org/experiments/ENCSR977NJB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against KPNB1. (KPNB1-BGHcLV14)
experiment encode accession: ENCSR977NJB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB012EEU
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 KPNB1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3475114d-f5e2-4d26-9b3d-d854a9a4c210/@@download/attachment/L-KPNB1-BGHcLV14-48.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against KPNB1. (KPNB1-BGHcLV14-48)

value: male

value: ATCC

value: ENCBS796JCM at ENCODE; https://www.encodeproject.org/ENCBS796JCM/


title: CRISPR RNA-seq from HepG2 (ENCLB085GFH)

description:
https://www.encodeproject.org/experiments/ENCSR862BCF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ANXA2. (ANXA2-BGHcLV12)
experiment encode accession: ENCSR862BCF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB085GFH
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 ANXA2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bef7a1b7-949e-4e86-a3b0-6998e905a049/@@download/attachment/L-ANXA2-BGHcLV12-3.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ANXA2. (ANXA2-BGHcLV12-3)

value: Brenton Graveley, UConn

value: ENCBS857FJC at ENCODE; https://www.encodeproject.org/ENCBS857FJC/


title: CRISPR RNA-seq from HepG2 (ENCLB711TMO)

description:
https://www.encodeproject.org/experiments/ENCSR861BRA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against TAF9. (TAF9-BGHcLV20)
experiment encode accession: ENCSR861BRA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB711TMO
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 TAF9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e07b52eb-c7be-4fe0-bdf8-88b72cb1df7e/@@download/attachment/L-TAF9-BGHcLV20-37.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against TAF9. (TAF9-BGHcLV20-37)

value: ENCBS815SDI at ENCODE; https://www.encodeproject.org/ENCBS815SDI/


title: CRISPR RNA-seq from HepG2 (ENCLB771WLV)

description:
https://www.encodeproject.org/experiments/ENCSR977NJB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against KPNB1. (KPNB1-BGHcLV14)
experiment encode accession: ENCSR977NJB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB771WLV
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/c3307e18-3e8c-40d4-bd9e-13b5afbd6b10/@@download/attachment/L-KPNB1-BGHcLV14-47.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against KPNB1. (KPNB1-BGHcLV14-47)

value: ENCBS503VAO at ENCODE; https://www.encodeproject.org/ENCBS503VAO/


title: CRISPR RNA-seq from K562 (ENCLB438WTF)

description:
https://www.encodeproject.org/experiments/ENCSR867XAL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX20. (DDX20-BGKcLV08)
experiment encode accession: ENCSR867XAL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB438WTF
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 DDX20

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3bad35e5-fb11-401a-90dd-4685da0d3ee6/@@download/attachment/L-DDX20-BGKcLV08-17.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX20. (DDX20-BGKcLV08-17)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS903RSI at ENCODE; https://www.encodeproject.org/ENCBS903RSI/

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


title: Bru-seq from HepG2 (ENCLB467HBZ)

description:
https://www.encodeproject.org/experiments/ENCSR974AQD/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR974AQD
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB467HBZ
size range: 400-500

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ENCBS731YOQ at ENCODE; https://www.encodeproject.org/ENCBS731YOQ/

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


title: eCLIP from HepG2 (ENCLB350JCB)

description:
https://www.encodeproject.org/experiments/ENCSR356ZMO/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against AKAP1
experiment encode accession: ENCSR356ZMO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR902XTJ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB350JCB
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

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

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 (ENCLB739AXP)

description:
https://www.encodeproject.org/experiments/ENCSR871XPX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CTCF. (CTCF-BGHcLV18)
experiment encode accession: ENCSR871XPX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB739AXP
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/c60e8996-89cd-4f34-8275-3e4c38f50b3b/@@download/attachment/L-CTCF-BGHcLV18-5.pdf

value: CTCF

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CTCF. (CTCF-BGHcLV18-5)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS061ERM at ENCODE; https://www.encodeproject.org/ENCBS061ERM/


title: Bru-seq from HepG2 (ENCLB142VFE)

description:
https://www.encodeproject.org/experiments/ENCSR974AQD/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR974AQD
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB142VFE
size range: 400-500

value: cell line

value: ENCBS326GVF at ENCODE; https://www.encodeproject.org/ENCBS326GVF/


title: CRISPR RNA-seq from K562 (ENCLB177RXP)

description:
https://www.encodeproject.org/experiments/ENCSR975NHV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGKcLV23)
experiment encode accession: ENCSR975NHV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB177RXP
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/c4239b0d-e81d-49f0-9476-ffbe31ad7a28/@@download/attachment/L-EIF6-BGKcLV23-37.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGKcLV23-37)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS547HAA at ENCODE; https://www.encodeproject.org/ENCBS547HAA/

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


title: eCLIP from HepG2 (ENCLB368JMW)

description:
https://www.encodeproject.org/experiments/ENCSR539BEV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against UPF1
experiment encode accession: ENCSR539BEV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR042RCU
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB368JMW
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB384FAI)

description:
https://www.encodeproject.org/experiments/ENCSR861BRA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against TAF9. (TAF9-BGHcLV20)
experiment encode accession: ENCSR861BRA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB384FAI
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/0989a485-346d-47ff-bb67-edb24547415c/@@download/attachment/L-TAF9-BGHcLV20-38.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against TAF9. (TAF9-BGHcLV20-38)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS996LWJ at ENCODE; https://www.encodeproject.org/ENCBS996LWJ/


title: Bru-seq from IMR-90 (ENCLB669NCX)

description:
https://www.encodeproject.org/experiments/ENCSR873ZUO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR873ZUO
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR103IHW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB669NCX
size range: 400-500

value: cell line

value: female

value: unknown

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ENCBS014SCG at ENCODE; https://www.encodeproject.org/ENCBS014SCG/

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


title: microRNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB001HZR)

description:
https://www.encodeproject.org/experiments/ENCSR071QRH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human CD4+ T cells (activated day 2) microRNA-seq from Mortazavi
experiment encode accession: ENCSR071QRH
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-06-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB001HZR
size range: <30

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS555KPW at ENCODE; https://www.encodeproject.org/ENCBS555KPW/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: eCLIP from HepG2 (ENCLB946GLU)

description:
https://www.encodeproject.org/experiments/ENCSR356ZMO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against AKAP1
experiment encode accession: ENCSR356ZMO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR902XTJ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB946GLU
fragmentation methods: see document
size range: 175-300

value: cell line

value: child

value: 15 year

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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

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

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


title: microRNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB568JRW)

description:
https://www.encodeproject.org/experiments/ENCSR071QRH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human CD4+ T cells (activated day 2) microRNA-seq from Mortazavi
experiment encode accession: ENCSR071QRH
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-06-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB568JRW
size range: <30

value: primary cell

value: ENCBS883EPS at ENCODE; https://www.encodeproject.org/ENCBS883EPS/


title: CRISPR RNA-seq from K562 (ENCLB123NRK)

description:
https://www.encodeproject.org/experiments/ENCSR965MSX/
***************
biological replicate number: 1
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: ENCLB123NRK
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/f30d6094-f87e-49c7-a905-1290c7fc7363/@@download/attachment/L-SMAD4-BGKcLV17-47.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD4. (SMAD4-BGKcLV17-47)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS099TIX at ENCODE; https://www.encodeproject.org/ENCBS099TIX/

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


title: CRISPR RNA-seq from K562 (ENCLB483KAD)

description:
https://www.encodeproject.org/experiments/ENCSR867XAL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX20. (DDX20-BGKcLV08)
experiment encode accession: ENCSR867XAL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB483KAD
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/fb486dc0-7730-4745-a291-93d18236c176/@@download/attachment/L-DDX20-BGKcLV08-18.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX20. (DDX20-BGKcLV08-18)

value: ENCBS314VQF at ENCODE; https://www.encodeproject.org/ENCBS314VQF/


title: eCLIP from HepG2 (ENCLB822FCH)

description:
https://www.encodeproject.org/experiments/ENCSR539BEV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against UPF1
experiment encode accession: ENCSR539BEV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR042RCU
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB822FCH
fragmentation methods: see document
size range: 175-300

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

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

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


title: eCLIP from HepG2 (ENCLB178KDM)

description:
https://www.encodeproject.org/experiments/ENCSR366DGX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against KHSRP
experiment encode accession: ENCSR366DGX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR423QXH
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB178KDM
fragmentation methods: see document
size range: 175-300

value: KHSRP

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: CRISPR RNA-seq from K562 (ENCLB907KRT)

description:
https://www.encodeproject.org/experiments/ENCSR978MMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV19)
experiment encode accession: ENCSR978MMZ
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB907KRT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/51e64f00-d53c-44f1-9ca4-6a5d4a74052f/@@download/attachment/L-NT-BGKcLV19-1.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV19-1)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS878GWR at ENCODE; https://www.encodeproject.org/ENCBS878GWR/


title: CRISPR RNA-seq from HepG2 (ENCLB320XJO)

description:
https://www.encodeproject.org/experiments/ENCSR865WQR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CACTIN. (CACTIN-BGHcLV22)
experiment encode accession: ENCSR865WQR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB320XJO
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/f73d3f3c-c60b-44ab-9751-71f464f6b806/@@download/attachment/L-CACTIN-BGHcLV22-3.pdf

value: CACTIN

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CACTIN. (CACTIN-BGHcLV22-3)

value: child

value: ATCC

value: ENCBS503ZTZ at ENCODE; https://www.encodeproject.org/ENCBS503ZTZ/


title: eCLIP from K562 (ENCLB851KKE)

description:
https://www.encodeproject.org/experiments/ENCSR356MSW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SSB
experiment encode accession: ENCSR356MSW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR680HYD
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB851KKE
fragmentation methods: see document
size range: 175-300

value: SSB

value: Gene Yeo, UCSD

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

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

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


title: microRNA-seq from H9 (ENCLB978NVX)

description:
https://www.encodeproject.org/experiments/ENCSR071LFN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation H9 hESC microRNA-seq from Mortazavi
experiment encode accession: ENCSR071LFN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB978NVX
size range: <30

source_name: Homo sapiens H9 cell line originated from H9

value: WA09 ES cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/

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


title: CRISPR RNA-seq from K562 (ENCLB010SNF)

description:
https://www.encodeproject.org/experiments/ENCSR854MSP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF4. (CPSF4-BGKcLV21)
experiment encode accession: ENCSR854MSP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB010SNF
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 CPSF4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/269dfa66-1b8e-4c6c-95b6-c993175ed299/@@download/attachment/L-CPSF4-BGKcLV21-12.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF4. (CPSF4-BGKcLV21-12)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS672XZR at ENCODE; https://www.encodeproject.org/ENCBS672XZR/


title: CRISPR RNA-seq from K562 (ENCLB220LMM)

description:
https://www.encodeproject.org/experiments/ENCSR854MSP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF4. (CPSF4-BGKcLV21)
experiment encode accession: ENCSR854MSP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB220LMM
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/dc947954-1f45-4ba8-beda-50023e5f17ec/@@download/attachment/L-CPSF4-BGKcLV21-11.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF4. (CPSF4-BGKcLV21-11)

value: ATCC

value: ENCBS689YZE at ENCODE; https://www.encodeproject.org/ENCBS689YZE/

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


title: CRISPR RNA-seq from HepG2 (ENCLB353EKL)

description:
https://www.encodeproject.org/experiments/ENCSR862BCF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ANXA2. (ANXA2-BGHcLV12)
experiment encode accession: ENCSR862BCF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB353EKL
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/1c7afd05-974b-4d0b-9673-cf974924b35d/@@download/attachment/L-ANXA2-BGHcLV12-4.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ANXA2. (ANXA2-BGHcLV12-4)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS951TYV at ENCODE; https://www.encodeproject.org/ENCBS951TYV/

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


title: microRNA-seq from H9 (ENCLB401GDT)

description:
https://www.encodeproject.org/experiments/ENCSR071LFN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation H9 hESC microRNA-seq from Mortazavi
experiment encode accession: ENCSR071LFN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB401GDT
size range: <30

value: cell line

value: WA09 ES cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/

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


title: eCLIP from HepG2 (ENCLB433SRY)

description:
https://www.encodeproject.org/experiments/ENCSR361OCV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against NIP7
experiment encode accession: ENCSR361OCV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR138HJN
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB433SRY
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: Gene Yeo, UCSD

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

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 K562 (ENCLB078TDC)

description:
https://www.encodeproject.org/experiments/ENCSR963JFM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against POLR2A. (POLR2A-BGKcLV13)
experiment encode accession: ENCSR963JFM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB078TDC
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 POLR2A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ccfd6d34-6b8e-4258-aa44-6e4f6df66ee6/@@download/attachment/L-POLR2A-BGKcLV13-57.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against POLR2A. (POLR2A-BGKcLV13-57)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS723ITA at ENCODE; https://www.encodeproject.org/ENCBS723ITA/

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


title: CRISPR RNA-seq from K562 (ENCLB504XBW)

description:
https://www.encodeproject.org/experiments/ENCSR963JFM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against POLR2A. (POLR2A-BGKcLV13)
experiment encode accession: ENCSR963JFM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB504XBW
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/4cd0a0b6-ef1e-4be9-bef1-772bd002d21e/@@download/attachment/L-POLR2A-BGKcLV13-58.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against POLR2A. (POLR2A-BGKcLV13-58)

value: female

value: ENCBS500NBN at ENCODE; https://www.encodeproject.org/ENCBS500NBN/


title: CRISPR RNA-seq from K562 (ENCLB037CPP)

description:
https://www.encodeproject.org/experiments/ENCSR854OFV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV21)
experiment encode accession: ENCSR854OFV
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB037CPP
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/db7480c1-f8ca-40a2-b639-61aca48dece2/@@download/attachment/L-NT-BGKcLV21-2.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV21-2)

value: ENCBS605AWX at ENCODE; https://www.encodeproject.org/ENCBS605AWX/


title: eCLIP from HepG2 (ENCLB415UGD)

description:
https://www.encodeproject.org/experiments/ENCSR352STY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against SSB
experiment encode accession: ENCSR352STY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR145ZKN
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB415UGD
fragmentation methods: see document
size range: 175-300

value: SSB

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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

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


title: CRISPR RNA-seq from K562 (ENCLB607ZFY)

description:
https://www.encodeproject.org/experiments/ENCSR949QWR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DUS3L. (DUS3L-BGKcLV17)
experiment encode accession: ENCSR949QWR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB607ZFY
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 DUS3L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/57f09153-e0b1-4907-875d-06d907e951aa/@@download/attachment/L-DUS3L-BGKcLV17-13.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DUS3L. (DUS3L-BGKcLV17-13)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS692AVF at ENCODE; https://www.encodeproject.org/ENCBS692AVF/


title: eCLIP from HepG2 (ENCLB069JHI)

description:
https://www.encodeproject.org/experiments/ENCSR352STY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against SSB
experiment encode accession: ENCSR352STY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR145ZKN
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB069JHI
fragmentation methods: see document
size range: 175-300

value: cell line

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

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

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


title: CRISPR RNA-seq from K562 (ENCLB718JGF)

description:
https://www.encodeproject.org/experiments/ENCSR949QWR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DUS3L. (DUS3L-BGKcLV17)
experiment encode accession: ENCSR949QWR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB718JGF
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/a02e006d-9103-4f2d-8c2b-094f428c9d8e/@@download/attachment/L-DUS3L-BGKcLV17-14.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DUS3L. (DUS3L-BGKcLV17-14)

value: female

value: ENCBS989ODK at ENCODE; https://www.encodeproject.org/ENCBS989ODK/

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


title: CRISPR RNA-seq from K562 (ENCLB619QEM)

description:
https://www.encodeproject.org/experiments/ENCSR840JRU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SNRPC. (SNRPC-BGKcLV23)
experiment encode accession: ENCSR840JRU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB619QEM
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 SNRPC

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4992a59d-edde-424a-847a-3f5ed218b49f/@@download/attachment/L-SNRPC-BGKcLV23-61.pdf

value: SNRPC

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SNRPC. (SNRPC-BGKcLV23-61)

value: ENCBS368CQY at ENCODE; https://www.encodeproject.org/ENCBS368CQY/


title: CRISPR RNA-seq from K562 (ENCLB965UGR)

description:
https://www.encodeproject.org/experiments/ENCSR840JRU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SNRPC. (SNRPC-BGKcLV23)
experiment encode accession: ENCSR840JRU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB965UGR
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/8bed5f7e-38cf-415f-b09c-d3a8b951dbbe/@@download/attachment/L-SNRPC-BGKcLV23-62.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SNRPC. (SNRPC-BGKcLV23-62)

value: chronic myelogenous leukemia (CML)

value: ENCBS883NPJ at ENCODE; https://www.encodeproject.org/ENCBS883NPJ/


title: CRISPR RNA-seq from K562 (ENCLB476ZSO)

description:
https://www.encodeproject.org/experiments/ENCSR854OFV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV21)
experiment encode accession: ENCSR854OFV
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB476ZSO
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/d155d9c1-0ad2-48ea-a41c-ece5108955fd/@@download/attachment/L-NT-BGKcLV21-1.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV21-1)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS271III at ENCODE; https://www.encodeproject.org/ENCBS271III/


title: CRISPR RNA-seq from HepG2 (ENCLB441OTM)

description:
https://www.encodeproject.org/experiments/ENCSR964HKT/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV16)
experiment encode accession: ENCSR964HKT
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB441OTM
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/6a7f7b26-1333-4e61-819b-24c6ccdba1d6/@@download/attachment/L-NT-BGHcLV16-2.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV16-2)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS804GDX at ENCODE; https://www.encodeproject.org/ENCBS804GDX/

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


title: eCLIP from K562 (ENCLB647IBZ)

description:
https://www.encodeproject.org/experiments/ENCSR356MSW/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SSB
experiment encode accession: ENCSR356MSW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR680HYD
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB647IBZ
fragmentation methods: see document
size range: 175-300

value: SSB

value: female

value: Gene Yeo, UCSD

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

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

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


title: TF ChIP-seq from K562 (ENCLB877RCX)

description:
https://www.encodeproject.org/experiments/ENCSR444MSK/
***************
biological replicate number: 1
technical replicate number: 1
description: RFX7 ChIP-seq on human K562
experiment encode accession: ENCSR444MSK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR532WSQ, ENCSR851OQN
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB877RCX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting RFX7

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS088IZK at ENCODE; https://www.encodeproject.org/ENCBS088IZK/


title: CRISPR RNA-seq from K562 (ENCLB709TXV)

description:
https://www.encodeproject.org/experiments/ENCSR943CXG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against MDM2. (MDM2-BGKcLV19)
experiment encode accession: ENCSR943CXG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB709TXV
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 MDM2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2aafab9c-26be-427c-9616-9aef3b6b76e6/@@download/attachment/L-MDM2-BGKcLV19-19.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against MDM2. (MDM2-BGKcLV19-19)

value: Brenton Graveley, UConn

value: ENCBS899OZI at ENCODE; https://www.encodeproject.org/ENCBS899OZI/


title: CRISPR RNA-seq from HepG2 (ENCLB349IKL)

description:
https://www.encodeproject.org/experiments/ENCSR836XZH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT7. (CNOT7-BGHcLV10)
experiment encode accession: ENCSR836XZH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB349IKL
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 CNOT7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/50eeee25-4b5c-413f-aae6-895cf12e7351/@@download/attachment/L-CNOT7-BGHcLV10-14.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT7. (CNOT7-BGHcLV10-14)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS856QCN at ENCODE; https://www.encodeproject.org/ENCBS856QCN/


title: eCLIP from K562 (ENCLB990EAA)

description:
https://www.encodeproject.org/experiments/ENCSR440SUX/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against MATR3
experiment encode accession: ENCSR440SUX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR183FVK
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB990EAA
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: female

value: Gene Yeo, UCSD

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

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

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


title: Control eCLIP from HepG2 (ENCLB378XHY)

description:
https://www.encodeproject.org/experiments/ENCSR438XYI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against MATR3
experiment encode accession: ENCSR438XYI
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-12-03
lab: Gene Yeo, UCSD
library encode accession: ENCLB378XHY
fragmentation methods: see document
size range: 175-300

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 K562 (ENCLB205BGV)

description:
https://www.encodeproject.org/experiments/ENCSR832XLB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against FYTTD1. (FYTTD1-BGKcLV21)
experiment encode accession: ENCSR832XLB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB205BGV
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 FYTTD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fe813300-e448-4258-9714-8e80982c7c2d/@@download/attachment/L-FYTTD1-BGKcLV21-26.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against FYTTD1. (FYTTD1-BGKcLV21-26)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS496EAG at ENCODE; https://www.encodeproject.org/ENCBS496EAG/


title: eCLIP from K562 (ENCLB216OEV)

description:
https://www.encodeproject.org/experiments/ENCSR349CMI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against WDR43
experiment encode accession: ENCSR349CMI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR404ABA
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB216OEV
fragmentation methods: see document
size range: 175-300

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

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


title: CRISPR RNA-seq from K562 (ENCLB089THP)

description:
https://www.encodeproject.org/experiments/ENCSR832XLB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against FYTTD1. (FYTTD1-BGKcLV21)
experiment encode accession: ENCSR832XLB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB089THP
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/92017085-156a-4540-9c87-11d5d3f3e965/@@download/attachment/L-FYTTD1-BGKcLV21-25.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against FYTTD1. (FYTTD1-BGKcLV21-25)

value: female

value: ATCC

value: ENCBS108QSS at ENCODE; https://www.encodeproject.org/ENCBS108QSS/


title: eCLIP from K562 (ENCLB619RUW)

description:
https://www.encodeproject.org/experiments/ENCSR349CMI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against WDR43
experiment encode accession: ENCSR349CMI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR404ABA
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB619RUW
fragmentation methods: see document
size range: 175-300

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


title: CRISPR RNA-seq from K562 (ENCLB653MCY)

description:
https://www.encodeproject.org/experiments/ENCSR846OQD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against G3BP1. (G3BP1-BGKcLV11)
experiment encode accession: ENCSR846OQD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB653MCY
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 G3BP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/55f6fbc1-f69a-4322-95ee-ab7d7d72aab2/@@download/attachment/L-G3BP1-BGKcLV11-58.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against G3BP1. (G3BP1-BGKcLV11-58)

value: ENCBS381YAF at ENCODE; https://www.encodeproject.org/ENCBS381YAF/


title: eCLIP from K562 (ENCLB921YYK)

description:
https://www.encodeproject.org/experiments/ENCSR440SUX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against MATR3
experiment encode accession: ENCSR440SUX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR183FVK
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB921YYK
fragmentation methods: see document
size range: 175-300

value: adult

value: chronic myelogenous leukemia (CML)

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


title: TF ChIP-seq from K562 (ENCLB078CYN)

description:
https://www.encodeproject.org/experiments/ENCSR444MSK/
***************
biological replicate number: 2
technical replicate number: 1
description: RFX7 ChIP-seq on human K562
experiment encode accession: ENCSR444MSK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR532WSQ, ENCSR851OQN
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB078CYN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS362CRX at ENCODE; https://www.encodeproject.org/ENCBS362CRX/


title: CRISPR RNA-seq from HepG2 (ENCLB163WPF)

description:
https://www.encodeproject.org/experiments/ENCSR932GTJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PAN2. (PAN2-BGHcLV22)
experiment encode accession: ENCSR932GTJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB163WPF
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 PAN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0c7115da-3c1a-4efc-8b00-dd440aac7dac/@@download/attachment/L-PAN2-BGHcLV22-36.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PAN2. (PAN2-BGHcLV22-36)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS600LVU at ENCODE; https://www.encodeproject.org/ENCBS600LVU/

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


title: Control eCLIP from HepG2 (ENCLB348ATY)

description:
https://www.encodeproject.org/experiments/ENCSR423QXH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against KHSRP
experiment encode accession: ENCSR423QXH
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB348ATY
fragmentation methods: see document
size range: 175-300

value: cell line

value: Gene Yeo, UCSD

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

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: microRNA-seq from sciatic nerve (ENCLB995EIO)

description:
https://www.encodeproject.org/experiments/ENCSR070KPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 sciatic nerve microRNA-seq from Mortazavi
experiment encode accession: ENCSR070KPQ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB995EIO
size range: <30

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

value: sciatic nerve

value: tissue

value: female

value: adult

value: 41 year

value: Yiing Lin, MD, PhD

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

value: ENCBS402EUY at ENCODE; https://www.encodeproject.org/ENCBS402EUY/

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


title: CRISPR RNA-seq from HepG2 (ENCLB975ZEY)

description:
https://www.encodeproject.org/experiments/ENCSR827PII/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NT. (NT-BGHcLV12)
experiment encode accession: ENCSR827PII
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB975ZEY
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/1937cd29-647d-4b7e-ba4b-1a7cc3000230/@@download/attachment/L-NT-BGHcLV12-2.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV12-2)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS372ZCC at ENCODE; https://www.encodeproject.org/ENCBS372ZCC/


title: CRISPR RNA-seq from HepG2 (ENCLB908BWG)

description:
https://www.encodeproject.org/experiments/ENCSR929EIP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRPK2. (SRPK2-BGHcLV12)
experiment encode accession: ENCSR929EIP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB908BWG
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 SRPK2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/618e239c-70d8-473d-a4f6-1dcdd4c88d66/@@download/attachment/L-SRPK2-BGHcLV12-69.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRPK2. (SRPK2-BGHcLV12-69)

value: ENCBS575STC at ENCODE; https://www.encodeproject.org/ENCBS575STC/

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


title: CRISPR RNA-seq from K562 (ENCLB760DGX)

description:
https://www.encodeproject.org/experiments/ENCSR846OQD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against G3BP1. (G3BP1-BGKcLV11)
experiment encode accession: ENCSR846OQD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB760DGX
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/96d32bba-cf56-46d4-a600-c664c468bc3f/@@download/attachment/L-G3BP1-BGKcLV11-57.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against G3BP1. (G3BP1-BGKcLV11-57)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS906TKX at ENCODE; https://www.encodeproject.org/ENCBS906TKX/

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


title: CRISPR RNA-seq from K562 (ENCLB187ZYT)

description:
https://www.encodeproject.org/experiments/ENCSR928MEW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPLP0. (RPLP0-BGKcLV11)
experiment encode accession: ENCSR928MEW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB187ZYT
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 SRSF7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1afa99ac-47d2-4db2-ae0a-688b503cae85/@@download/attachment/L-RPLP0-BGKcLV11-89.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPLP0. (RPLP0-BGKcLV11-89)

value: ENCBS143VWQ at ENCODE; https://www.encodeproject.org/ENCBS143VWQ/


title: CRISPR RNA-seq from K562 (ENCLB608SYZ)

description:
https://www.encodeproject.org/experiments/ENCSR943CXG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against MDM2. (MDM2-BGKcLV19)
experiment encode accession: ENCSR943CXG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB608SYZ
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/f8c897e8-732b-421f-abd6-b531360d0278/@@download/attachment/L-MDM2-BGKcLV19-20.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against MDM2. (MDM2-BGKcLV19-20)

value: ENCBS736JGG at ENCODE; https://www.encodeproject.org/ENCBS736JGG/


title: eCLIP from HepG2 (ENCLB583JOA)

description:
https://www.encodeproject.org/experiments/ENCSR337XGI/
***************
biological replicate number: 2
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: ENCLB583JOA
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 cell line

value: SAFB

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Gene Yeo, UCSD

value: ATCC

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


title: CRISPR RNA-seq from K562 (ENCLB977JBP)

description:
https://www.encodeproject.org/experiments/ENCSR928MEW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPLP0. (RPLP0-BGKcLV11)
experiment encode accession: ENCSR928MEW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB977JBP
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/9ebeaafd-3c11-48b3-8551-fd05672a16fa/@@download/attachment/L-RPLP0-BGKcLV11-90.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPLP0. (RPLP0-BGKcLV11-90)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS091DVU at ENCODE; https://www.encodeproject.org/ENCBS091DVU/


title: CRISPR RNA-seq from HepG2 (ENCLB404GTT)

description:
https://www.encodeproject.org/experiments/ENCSR964HKT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV16)
experiment encode accession: ENCSR964HKT
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB404GTT
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/32c9bcdf-dd8f-4b57-a49a-8ca9dd53e012/@@download/attachment/L-NT-BGHcLV16-1.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV16-1)

value: ENCBS306SIA at ENCODE; https://www.encodeproject.org/ENCBS306SIA/

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


title: CRISPR RNA-seq from HepG2 (ENCLB012PTS)

description:
https://www.encodeproject.org/experiments/ENCSR925OFV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL23A. (RPL23A-BGHcLV09)
experiment encode accession: ENCSR925OFV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB012PTS
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 RPL23A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dfde9575-156d-4c2b-acff-bd39ecb68a0c/@@download/attachment/L-RPL23A-BGHcLV09-12.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL23A. (RPL23A-BGHcLV09-12)

value: ENCBS219EXC at ENCODE; https://www.encodeproject.org/ENCBS219EXC/


title: CRISPR RNA-seq from HepG2 (ENCLB243TQF)

description:
https://www.encodeproject.org/experiments/ENCSR836XZH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT7. (CNOT7-BGHcLV10)
experiment encode accession: ENCSR836XZH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB243TQF
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/db3831ff-6d99-4ea4-b473-f1240b87b5f6/@@download/attachment/L-CNOT7-BGHcLV10-13.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT7. (CNOT7-BGHcLV10-13)

value: male

value: hepatocellular carcinoma

value: ENCBS662RXQ at ENCODE; https://www.encodeproject.org/ENCBS662RXQ/


title: Control eCLIP from K562 (ENCLB783FXM)

description:
https://www.encodeproject.org/experiments/ENCSR533BNK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against CPEB4
experiment encode accession: ENCSR533BNK
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB783FXM
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: Gene Yeo, UCSD

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

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB020NCM)

description:
https://www.encodeproject.org/experiments/ENCSR940FIN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GNL3. (GNL3-BGHcLV05-E)
experiment encode accession: ENCSR940FIN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR713OTF
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB020NCM
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 GNL3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/21133ad3-5614-44cf-b314-a7b061cf54ac/@@download/attachment/L-GNL3-BGHcLV05-20E.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GNL3. (GNL3-BGHcLV05-20E)

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS564UDY at ENCODE; https://www.encodeproject.org/ENCBS564UDY/


title: CRISPR RNA-seq from HepG2 (ENCLB879TDQ)

description:
https://www.encodeproject.org/experiments/ENCSR940FIN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GNL3. (GNL3-BGHcLV05-E)
experiment encode accession: ENCSR940FIN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR713OTF
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB879TDQ
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/9b5f9159-8da7-4735-a342-a284dc1d4453/@@download/attachment/L-GNL3-BGHcLV05-19E.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GNL3. (GNL3-BGHcLV05-19E)

value: ENCBS399GKJ at ENCODE; https://www.encodeproject.org/ENCBS399GKJ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB896OQU)

description:
https://www.encodeproject.org/experiments/ENCSR929EIP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRPK2. (SRPK2-BGHcLV12)
experiment encode accession: ENCSR929EIP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB896OQU
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/b78301bf-3225-4194-80b5-fcf4047837e4/@@download/attachment/L-SRPK2-BGHcLV12-70.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRPK2. (SRPK2-BGHcLV12-70)

value: male

value: hepatocellular carcinoma

value: ENCBS139LMU at ENCODE; https://www.encodeproject.org/ENCBS139LMU/


title: CRISPR RNA-seq from HepG2 (ENCLB834JZQ)

description:
https://www.encodeproject.org/experiments/ENCSR821GQN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZNF574. (ZNF574-BGHcLV18)
experiment encode accession: ENCSR821GQN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB834JZQ
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 ZNF574

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b57773a5-9e57-4831-a314-81a35dd2e4fd/@@download/attachment/L-ZNF574-BGHcLV18-54.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZNF574. (ZNF574-BGHcLV18-54)

value: ENCBS511OGB at ENCODE; https://www.encodeproject.org/ENCBS511OGB/


title: microRNA-seq from lower lobe of left lung (ENCLB661ESG)

description:
https://www.encodeproject.org/experiments/ENCSR183WRP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 lower lobe of left lung microRNA-seq from Mortazavi
experiment encode accession: ENCSR183WRP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB661ESG
size range: <30

source_name: Homo sapiens female adult (59 years) lower lobe of left lung tissue, preserved by flash-freezing

value: lower lobe of left lung

value: tissue

value: female

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS231BSF at ENCODE; https://www.encodeproject.org/ENCBS231BSF/

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


title: Control eCLIP from HepG2 (ENCLB002KIQ)

description:
https://www.encodeproject.org/experiments/ENCSR343MKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against FTO
experiment encode accession: ENCSR343MKJ
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB002KIQ
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: cell line

value: child

value: 15 year

value: Gene Yeo, UCSD

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

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

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB715PIE)

description:
https://www.encodeproject.org/experiments/ENCSR925OFV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL23A. (RPL23A-BGHcLV09)
experiment encode accession: ENCSR925OFV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB715PIE
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/e4d665c7-26df-4412-8a11-3c477c2b49c9/@@download/attachment/L-RPL23A-BGHcLV09-11.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL23A. (RPL23A-BGHcLV09-11)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS145YHJ at ENCODE; https://www.encodeproject.org/ENCBS145YHJ/


title: CRISPR RNA-seq from HepG2 (ENCLB117WMX)

description:
https://www.encodeproject.org/experiments/ENCSR821GQN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZNF574. (ZNF574-BGHcLV18)
experiment encode accession: ENCSR821GQN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB117WMX
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/f9c02532-2063-45e1-b283-57fad1d0613a/@@download/attachment/L-ZNF574-BGHcLV18-53.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZNF574. (ZNF574-BGHcLV18-53)

value: ENCBS278VDI at ENCODE; https://www.encodeproject.org/ENCBS278VDI/


title: CRISPR RNA-seq from K562 (ENCLB436EBP)

description:
https://www.encodeproject.org/experiments/ENCSR921RQX/
***************
biological replicate number: 2
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: ENCLB436EBP
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/3399bed2-e0db-4db8-acf4-552e5eea0dcb/@@download/attachment/L-THOC1-BGKcLV15-60.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against THOC1. (THOC1-BGKcLV15-60)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS629HFX at ENCODE; https://www.encodeproject.org/ENCBS629HFX/

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


title: Control eCLIP from K562 (ENCLB989YTO)

description:
https://www.encodeproject.org/experiments/ENCSR322KLN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against PCBP1
experiment encode accession: ENCSR322KLN
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB989YTO
fragmentation methods: see document
size range: 175-300

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 HepG2 (ENCLB117DUL)

description:
https://www.encodeproject.org/experiments/ENCSR827PII/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NT. (NT-BGHcLV12)
experiment encode accession: ENCSR827PII
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB117DUL
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/6c8d9b2c-7302-4289-ab80-4ef5a92d1f62/@@download/attachment/L-NT-BGHcLV12-1.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV12-1)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS421MNK at ENCODE; https://www.encodeproject.org/ENCBS421MNK/

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


title: CRISPR RNA-seq from K562 (ENCLB260ZWH)

description:
https://www.encodeproject.org/experiments/ENCSR916PCG/
***************
biological replicate number: 1
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: ENCLB260ZWH
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/ee669cf5-29d3-4a3b-9892-183a28a2c33c/@@download/attachment/L-E4F1-BGKcLV17-15.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against E4F1. (E4F1-BGKcLV17-15)

value: female

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS605NDI at ENCODE; https://www.encodeproject.org/ENCBS605NDI/


title: CRISPR RNA-seq from HepG2 (ENCLB927SYC)

description:
https://www.encodeproject.org/experiments/ENCSR932GTJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PAN2. (PAN2-BGHcLV22)
experiment encode accession: ENCSR932GTJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB927SYC
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/cb3a75da-4c21-4b42-80e0-82a056c00174/@@download/attachment/L-PAN2-BGHcLV22-35.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PAN2. (PAN2-BGHcLV22-35)

value: ENCBS647PKG at ENCODE; https://www.encodeproject.org/ENCBS647PKG/


title: Bru-seq from PC-3 (ENCLB899JHD)

description:
https://www.encodeproject.org/experiments/ENCSR916VGW/
***************
biological replicate number: 2
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: ENCLB899JHD
size range: 400-500

source_name: Homo sapiens PC-3 cell line treated with 500 rad irradiation

value: cell line

value: grade IV, adenocarcinoma

value: adult

value: 62 year

value: Mats Ljungman, UMichigan

value: ENCBS381QVQ at ENCODE; https://www.encodeproject.org/ENCBS381QVQ/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/