title: CRISPR RNA-seq from HepG2 (ENCLB428CDP)

description:
https://www.encodeproject.org/experiments/ENCSR603TOC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CENPI. (CENPI-BGHcLV09)
experiment encode accession: ENCSR603TOC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB428CDP
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 CENPI

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c04a756b-84f6-4ff7-bee0-97639e2233f0/@@download/attachment/L-CENPI-BGHcLV09-3.pdf

value: CENPI

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CENPI. (CENPI-BGHcLV09-3)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS056BIT at ENCODE; https://www.encodeproject.org/ENCBS056BIT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB693OVD)

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/ENCSR704VPL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV22)
experiment encode accession: ENCSR704VPL
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB693OVD
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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/f1235c76-ba26-4ec9-9139-de1840cebe3f/@@download/attachment/L-NT-BGHcLV22-1.pdf

tag: line

value: cell line

tag: description

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV22-1)

tag: biosample encode accession

tag: Sex

value: male

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

value: ATCC

tag: link

value: ENCBS004RTO at ENCODE; https://www.encodeproject.org/ENCBS004RTO/


title: BruChase-seq from Panc1 (ENCLB098EKG)

description:
https://www.encodeproject.org/experiments/ENCSR603TYF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR603TYF
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR639ZOU
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB098EKG
size range: 400-500

source_name: Homo sapiens Panc1 cell line, subjected to a 2 hour pulse-chase

value: pancreatic carcinoma

value: adult

value: 56 year

value: Mats Ljungman, UMichigan

value: ENCBS527BEN at ENCODE; https://www.encodeproject.org/ENCBS527BEN/

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


title: eCLIP from K562 (ENCLB827QDN)

description:
https://www.encodeproject.org/experiments/ENCSR038JME/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against WRN
experiment encode accession: ENCSR038JME
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR925ZRV
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB827QDN
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

tag: antibody

value: WRN

value: 53 year

value: female

tag: passage number

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB758JWQ)

description:
https://www.encodeproject.org/experiments/ENCSR702LIH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL11. (RPL11-BGHcLV16)
experiment encode accession: ENCSR702LIH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB758JWQ
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 RPL11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/761fe588-6b2a-4902-b94b-1bcf8b969869/@@download/attachment/L-RPL11-BGHcLV16-47.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL11. (RPL11-BGHcLV16-47)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS252VWD at ENCODE; https://www.encodeproject.org/ENCBS252VWD/

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


title: CRISPR RNA-seq from HepG2 (ENCLB563PHN)

description:
https://www.encodeproject.org/experiments/ENCSR704VPL/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV22)
experiment encode accession: ENCSR704VPL
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB563PHN
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/a699b734-e7f5-40d0-a3b1-7937dfd1633a/@@download/attachment/L-NT-BGHcLV22-2.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV22-2)

value: ENCBS723CIZ at ENCODE; https://www.encodeproject.org/ENCBS723CIZ/


title: eCLIP from K562 (ENCLB233CTD)

description:
https://www.encodeproject.org/experiments/ENCSR038JME/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against WRN
experiment encode accession: ENCSR038JME
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR925ZRV
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB233CTD
fragmentation methods: see document
size range: 175-300

value: WRN

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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


title: Control eCLIP from HepG2 (ENCLB311GKF)

description:
https://www.encodeproject.org/experiments/ENCSR130ZDS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against SDAD1
experiment encode accession: ENCSR130ZDS
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB311GKF
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: 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: Control eCLIP from HepG2 (ENCLB265CMC)

description:
https://www.encodeproject.org/experiments/ENCSR042RCU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against UPF1
experiment encode accession: ENCSR042RCU
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB265CMC
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: hepatocellular carcinoma

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 (ENCLB503RRJ)

description:
https://www.encodeproject.org/experiments/ENCSR713OTF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV05-E)
experiment encode accession: ENCSR713OTF
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB503RRJ
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/f4766da0-3e3f-45ba-b418-bd59b3581467/@@download/attachment/L-NT-BGHcLV05-1E.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT_BGHcLV05-1)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS332SEB at ENCODE; https://www.encodeproject.org/ENCBS332SEB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB210KIY)

description:
https://www.encodeproject.org/experiments/ENCSR700FWD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD4. (SMAD4-BGHcLV18)
experiment encode accession: ENCSR700FWD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB210KIY
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 SMAD4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a8c8b579-c7b4-4f26-b2d6-db26c2c5d46b/@@download/attachment/L-SMAD4-BGHcLV18-46.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD4. (SMAD4-BGHcLV18-46)

value: ENCBS949DYY at ENCODE; https://www.encodeproject.org/ENCBS949DYY/


title: CRISPR RNA-seq from K562 (ENCLB640GFH)

description:
https://www.encodeproject.org/experiments/ENCSR712CQC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NT. (NT-BGKcLV13)
experiment encode accession: ENCSR712CQC
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB640GFH
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/88e04529-93c8-4696-9737-b73b340a051d/@@download/attachment/L-NT-BGKcLV13-2.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non-target. (NT-BGKcLV13-2)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS160IFA at ENCODE; https://www.encodeproject.org/ENCBS160IFA/

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


title: Bru-seq from HCT116 (ENCLB670TLB)

description:
https://www.encodeproject.org/experiments/ENCSR603HKQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR603HKQ
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR799MPW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB670TLB
size range: 400-500

source_name: Homo sapiens HCT116 cell line treated with 500 rad irradiation

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Mats Ljungman, UMichigan

tag: treatments

value: ENCBS803BGC at ENCODE; https://www.encodeproject.org/ENCBS803BGC/

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


title: CRISPR RNA-seq from K562 (ENCLB578HXA)

description:
https://www.encodeproject.org/experiments/ENCSR600OWF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DNMT1. (DNMT1-BGKcLV13)
experiment encode accession: ENCSR600OWF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB578HXA
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 DNMT1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/80c6a5e2-0dcf-47e2-a476-381d7a7720db/@@download/attachment/L-DNMT1-BGKcLV13-19.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DNMT1. (DNMT1-BGKcLV13-19)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS404MEW at ENCODE; https://www.encodeproject.org/ENCBS404MEW/


title: Control eCLIP from HepG2 (ENCLB308WGT)

description:
https://www.encodeproject.org/experiments/ENCSR129SCO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against POLR2G
experiment encode accession: ENCSR129SCO
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB308WGT
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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

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

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

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


title: Bru-seq from HCT116 (ENCLB886LQS)

description:
https://www.encodeproject.org/experiments/ENCSR603HKQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR603HKQ
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR799MPW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB886LQS
size range: 400-500

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: ENCBS634RMN at ENCODE; https://www.encodeproject.org/ENCBS634RMN/


title: CRISPR RNA-seq from K562 (ENCLB504ZUM)

description:
https://www.encodeproject.org/experiments/ENCSR600OWF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DNMT1. (DNMT1-BGKcLV13)
experiment encode accession: ENCSR600OWF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB504ZUM
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/18f4b74e-8706-48e4-9f99-da55f12a5295/@@download/attachment/L-DNMT1-BGKcLV13-20.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DNMT1. (DNMT1-BGKcLV13-20)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS476ZSX at ENCODE; https://www.encodeproject.org/ENCBS476ZSX/

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


title: Control eCLIP from HepG2 (ENCLB933ZCT)

description:
https://www.encodeproject.org/experiments/ENCSR128BUO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against BCLAF1
experiment encode accession: ENCSR128BUO
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB933ZCT
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: Gene Yeo, UCSD

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


title: CRISPR RNA-seq from HepG2 (ENCLB145NRG)

description:
https://www.encodeproject.org/experiments/ENCSR592AQT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PPP1R8. (PPP1R8-BGHcLV12)
experiment encode accession: ENCSR592AQT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB145NRG
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 PPP1R8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/de85184a-c902-4c1d-9026-1357a15747c3/@@download/attachment/L-PPP1R8-BGHcLV12-64.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PPP1R8. (PPP1R8-BGHcLV12-64)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS866IEI at ENCODE; https://www.encodeproject.org/ENCBS866IEI/

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


title: CRISPR RNA-seq from HepG2 (ENCLB109GOL)

description:
https://www.encodeproject.org/experiments/ENCSR702LIH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL11. (RPL11-BGHcLV16)
experiment encode accession: ENCSR702LIH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB109GOL
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/0c537e5c-55e0-456f-b23b-7564a1b98372/@@download/attachment/L-RPL11-BGHcLV16-48.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL11. (RPL11-BGHcLV16-48)

value: male

value: ENCBS988KQS at ENCODE; https://www.encodeproject.org/ENCBS988KQS/


title: TF ChIP-seq from K562 (ENCLB201KEZ)

description:
https://www.encodeproject.org/experiments/ENCSR034GHQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-HMG20B ChIP-seq on human K562
experiment encode accession: ENCSR034GHQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR012KTG, ENCSR004LZA
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB201KEZ
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 HMG20B

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS059CBV at ENCODE; https://www.encodeproject.org/ENCBS059CBV/


title: CRISPR RNA-seq from HepG2 (ENCLB193USD)

description:
https://www.encodeproject.org/experiments/ENCSR586YGD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NIP7. (NIP7-BGHcLV09)
experiment encode accession: ENCSR586YGD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB193USD
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 NIP7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e47e11e9-eaf3-401c-884b-dc0ab8e471ba/@@download/attachment/L-NIP7-BGHcLV09-5.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NIP7. (NIP7-BGHcLV09-5)

value: child

value: 15 year

value: ENCBS386GOB at ENCODE; https://www.encodeproject.org/ENCBS386GOB/


title: CRISPR RNA-seq from HepG2 (ENCLB635ROV)

description:
https://www.encodeproject.org/experiments/ENCSR592AQT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PPP1R8. (PPP1R8-BGHcLV12)
experiment encode accession: ENCSR592AQT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB635ROV
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/d4fe4a07-c25a-437f-90ec-cad96407d22a/@@download/attachment/L-PPP1R8-BGHcLV12-63.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PPP1R8. (PPP1R8-BGHcLV12-63)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS888XEO at ENCODE; https://www.encodeproject.org/ENCBS888XEO/


title: CRISPR RNA-seq from HepG2 (ENCLB963FVX)

description:
https://www.encodeproject.org/experiments/ENCSR586YGD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NIP7. (NIP7-BGHcLV09)
experiment encode accession: ENCSR586YGD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB963FVX
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/6e0936b5-761f-4b41-b539-c6fcbdd606ae/@@download/attachment/L-NIP7-BGHcLV09-6.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NIP7. (NIP7-BGHcLV09-6)

value: male

value: ENCBS020ARY at ENCODE; https://www.encodeproject.org/ENCBS020ARY/

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


title: Control eCLIP from K562 (ENCLB412KWF)

description:
https://www.encodeproject.org/experiments/ENCSR033FWT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against WDR3
experiment encode accession: ENCSR033FWT
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB412KWF
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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

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

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


title: CRISPR RNA-seq from K562 (ENCLB648YEQ)

description:
https://www.encodeproject.org/experiments/ENCSR390TOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX43. (DDX43-BGKcLV23)
experiment encode accession: ENCSR390TOZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB648YEQ
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 DDX43

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/935f8997-aa08-4306-9f20-669122d01f43/@@download/attachment/L-DDX43-BGKcLV23-31.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX43. (DDX43-BGKcLV23-31)

value: Brenton Graveley, UConn

value: ENCBS486XNY at ENCODE; https://www.encodeproject.org/ENCBS486XNY/


title: CRISPR RNA-seq from HepG2 (ENCLB633RDN)

description:
https://www.encodeproject.org/experiments/ENCSR580XTY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PDCD4. (PDCD4-BGHcLV18)
experiment encode accession: ENCSR580XTY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB633RDN
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 PDCD4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c3ec9d49-ef7f-465d-84a2-753dfcde6d07/@@download/attachment/L-PDCD4-BGHcLV18-31.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PDCD4. (PDCD4-BGHcLV18-31)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS924PSY at ENCODE; https://www.encodeproject.org/ENCBS924PSY/


title: microRNA-seq from Right ventricle myocardium inferior (ENCLB840LHK)

description:
https://www.encodeproject.org/experiments/ENCSR026WQC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 right ventricle myocardium inferior microRNA-seq from Mortazavi
experiment encode accession: ENCSR026WQC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB840LHK
size range: <30

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

value: Right ventricle myocardium inferior

value: tissue

value: Inferior wall of right ventricle.

value: male

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS705XRW at ENCODE; https://www.encodeproject.org/ENCBS705XRW/

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


title: Bru-seq from K562 (ENCLB228KLW)

description:
https://www.encodeproject.org/experiments/ENCSR492DKJ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR492DKJ
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR729WFH
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB228KLW
size range: 400-500

source_name: Homo sapiens K562 cell line treated with 500 rad irradiation

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Mats Ljungman, UMichigan

value: ENCBS573ACC at ENCODE; https://www.encodeproject.org/ENCBS573ACC/

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


title: CRISPR RNA-seq from HepG2 (ENCLB276DVN)

description:
https://www.encodeproject.org/experiments/ENCSR603TOC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CENPI. (CENPI-BGHcLV09)
experiment encode accession: ENCSR603TOC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB276DVN
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 CENPI

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/00af4bd2-1da2-42e2-a41c-e1c781473249/@@download/attachment/L-CENPI-BGHcLV09-4.pdf

value: CENPI

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CENPI. (CENPI-BGHcLV09-4)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS926GVT at ENCODE; https://www.encodeproject.org/ENCBS926GVT/

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


title: CRISPR RNA-seq from K562 (ENCLB885PFO)

description:
https://www.encodeproject.org/experiments/ENCSR490PSG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against TAF9. (TAF9-BGKcLV19)
experiment encode accession: ENCSR490PSG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB885PFO
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 TAF9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/67180d14-41c5-4b18-890e-568ba99678b5/@@download/attachment/L-TAF9-BGKcLV19-53.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against TAF9. (TAF9-BGKcLV19-53)

value: adult

value: ENCBS463TWT at ENCODE; https://www.encodeproject.org/ENCBS463TWT/


title: CRISPR RNA-seq from K562 (ENCLB691ZNK)

description:
https://www.encodeproject.org/experiments/ENCSR490PSG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against TAF9. (TAF9-BGKcLV19)
experiment encode accession: ENCSR490PSG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB691ZNK
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/653771cd-e77e-44a1-bfd9-ce6482b13c5a/@@download/attachment/L-TAF9-BGKcLV19-54.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against TAF9. (TAF9-BGKcLV19-54)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS306DAG at ENCODE; https://www.encodeproject.org/ENCBS306DAG/


title: CRISPR RNA-seq from HepG2 (ENCLB274JXO)

description:
https://www.encodeproject.org/experiments/ENCSR383QYT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD5. (SMAD5-BGHcLV18)
experiment encode accession: ENCSR383QYT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB274JXO
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 SMAD5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8f576592-2e5e-4b76-94c4-29d49591411d/@@download/attachment/L-SMAD5-BGHcLV18-48.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD5. (SMAD5-BGHcLV18-48)

value: male

value: ENCBS919ORJ at ENCODE; https://www.encodeproject.org/ENCBS919ORJ/


title: TF ChIP-seq from K562 (ENCLB635FSL)

description:
https://www.encodeproject.org/experiments/ENCSR214PDW/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF780A ChIP-seq on human K562
experiment encode accession: ENCSR214PDW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR291BKA, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB635FSL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF780A

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS350FGO at ENCODE; https://www.encodeproject.org/ENCBS350FGO/

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


title: CRISPR RNA-seq from K562 (ENCLB525SZD)

description:
https://www.encodeproject.org/experiments/ENCSR499IQB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NIP7. (NIP7-BGKcLV11)
experiment encode accession: ENCSR499IQB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB525SZD
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 PES1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5b3b6693-703f-43dd-b394-9fa9273f19db/@@download/attachment/L-NIP7-BGKcLV11-68.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NIP7. (NIP7-BGKcLV11-68)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS176ZST at ENCODE; https://www.encodeproject.org/ENCBS176ZST/


title: CRISPR RNA-seq from HepG2 (ENCLB654FZM)

description:
https://www.encodeproject.org/experiments/ENCSR580XTY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PDCD4. (PDCD4-BGHcLV18)
experiment encode accession: ENCSR580XTY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB654FZM
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/2f662f89-6d7d-4bdf-9779-6a880754bef5/@@download/attachment/L-PDCD4-BGHcLV18-32.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PDCD4. (PDCD4-BGHcLV18-32)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS432SFH at ENCODE; https://www.encodeproject.org/ENCBS432SFH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB804LQI)

description:
https://www.encodeproject.org/experiments/ENCSR383QYT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD5. (SMAD5-BGHcLV18)
experiment encode accession: ENCSR383QYT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB804LQI
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/9aa88ce0-7949-4db7-8d93-ccdd200b881e/@@download/attachment/L-SMAD5-BGHcLV18-47.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD5. (SMAD5-BGHcLV18-47)

value: ENCBS010YSJ at ENCODE; https://www.encodeproject.org/ENCBS010YSJ/


title: eCLIP from K562 (ENCLB409ESN)

description:
https://www.encodeproject.org/experiments/ENCSR023PKW/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against EIF3G
experiment encode accession: ENCSR023PKW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR761AJD
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB409ESN
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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

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


title: CRISPR RNA-seq from K562 (ENCLB888PSU)

description:
https://www.encodeproject.org/experiments/ENCSR390TOZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX43. (DDX43-BGKcLV23)
experiment encode accession: ENCSR390TOZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB888PSU
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/c4465da5-585d-4b63-b3c2-24a102659807/@@download/attachment/L-DDX43-BGKcLV23-32.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX43. (DDX43-BGKcLV23-32)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS752TGI at ENCODE; https://www.encodeproject.org/ENCBS752TGI/

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


title: CRISPR RNA-seq from HepG2 (ENCLB148DMT)

description:
https://www.encodeproject.org/experiments/ENCSR484QEX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against WBP11. (WBP11-BGHcLV22)
experiment encode accession: ENCSR484QEX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB148DMT
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 WBP11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/429ad231-91fd-4291-a793-941d9ffbb6c0/@@download/attachment/L-WBP11-BGHcLV22-63.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against WBP11. (WBP11-BGHcLV22-63)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS287XWT at ENCODE; https://www.encodeproject.org/ENCBS287XWT/

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


title: TF ChIP-seq from K562 (ENCLB184GFL)

description:
https://www.encodeproject.org/experiments/ENCSR214PDW/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF780A ChIP-seq on human K562
experiment encode accession: ENCSR214PDW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR291BKA, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB184GFL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: female

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS274OWS at ENCODE; https://www.encodeproject.org/ENCBS274OWS/


title: CRISPR RNA-seq from HepG2 (ENCLB472CXH)

description:
https://www.encodeproject.org/experiments/ENCSR380LKB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SUZ12. (SUZ12-BGHcLV18)
experiment encode accession: ENCSR380LKB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB472CXH
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 SUZ12

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c42e98c9-4fe8-442b-a521-740896d3074f/@@download/attachment/L-SUZ12-BGHcLV18-50.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SUZ12. (SUZ12-BGHcLV18-50)

value: Brenton Graveley, UConn

value: ENCBS215AZA at ENCODE; https://www.encodeproject.org/ENCBS215AZA/


title: TF ChIP-seq from K562 (ENCLB916XND)

description:
https://www.encodeproject.org/experiments/ENCSR034GHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-HMG20B ChIP-seq on human K562
experiment encode accession: ENCSR034GHQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR012KTG, ENCSR004LZA
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB916XND
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS115SNC at ENCODE; https://www.encodeproject.org/ENCBS115SNC/

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


title: eCLIP from K562 (ENCLB793VLO)

description:
https://www.encodeproject.org/experiments/ENCSR023PKW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against EIF3G
experiment encode accession: ENCSR023PKW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR761AJD
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB793VLO
fragmentation methods: see document
size range: 175-300

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

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


title: eCLIP from K562 (ENCLB751JDE)

description:
https://www.encodeproject.org/experiments/ENCSR120EAR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RPS3
experiment encode accession: ENCSR120EAR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR494JFR
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB751JDE
fragmentation methods: see document
size range: 175-300

value: cell line

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


title: CRISPR RNA-seq from K562 (ENCLB795LDC)

description:
https://www.encodeproject.org/experiments/ENCSR381NPB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against LARS. (LARS-BGKcLV23)
experiment encode accession: ENCSR381NPB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB795LDC
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 LARS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e3cf23c5-cfd1-484a-900d-801f5a4aa7d3/@@download/attachment/L-LARS-BGKcLV23-45.pdf

value: LARS

value: RNA-seq on K562 cells treated with a CRISPR gRNA against LARS. (LARS-BGKcLV23-45)

value: female

value: adult

value: ENCBS365CHW at ENCODE; https://www.encodeproject.org/ENCBS365CHW/


title: CRISPR RNA-seq from HepG2 (ENCLB914KCH)

description:
https://www.encodeproject.org/experiments/ENCSR380LKB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SUZ12. (SUZ12-BGHcLV18)
experiment encode accession: ENCSR380LKB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB914KCH
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/631dd768-2e55-4e41-8e32-a202bca9f1c3/@@download/attachment/L-SUZ12-BGHcLV18-49.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SUZ12. (SUZ12-BGHcLV18-49)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS180VCE at ENCODE; https://www.encodeproject.org/ENCBS180VCE/

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


title: CRISPR RNA-seq from HepG2 (ENCLB811UZM)

description:
https://www.encodeproject.org/experiments/ENCSR700FWD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD4. (SMAD4-BGHcLV18)
experiment encode accession: ENCSR700FWD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB811UZM
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 SMAD4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/48ba0d0e-8d11-4a5d-91de-739d6f43b4df/@@download/attachment/L-SMAD4-BGHcLV18-45.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD4. (SMAD4-BGHcLV18-45)

value: ATCC

value: ENCBS825NAN at ENCODE; https://www.encodeproject.org/ENCBS825NAN/


title: CRISPR RNA-seq from K562 (ENCLB360HKI)

description:
https://www.encodeproject.org/experiments/ENCSR381NPB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against LARS. (LARS-BGKcLV23)
experiment encode accession: ENCSR381NPB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB360HKI
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/ec790833-1f78-41e5-9637-f2f8e8c418c7/@@download/attachment/L-LARS-BGKcLV23-46.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against LARS. (LARS-BGKcLV23-46)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS504AVE at ENCODE; https://www.encodeproject.org/ENCBS504AVE/

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


title: Bru-seq from K562 (ENCLB024JIZ)

description:
https://www.encodeproject.org/experiments/ENCSR492DKJ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR492DKJ
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR729WFH
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB024JIZ
size range: 400-500

value: female

value: adult

value: Mats Ljungman, UMichigan

value: ENCBS017LVR at ENCODE; https://www.encodeproject.org/ENCBS017LVR/


title: eCLIP from K562 (ENCLB606LJC)

description:
https://www.encodeproject.org/experiments/ENCSR120EAR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RPS3
experiment encode accession: ENCSR120EAR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR494JFR
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB606LJC
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

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

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

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


title: CRISPR RNA-seq from K562 (ENCLB413ZWQ)

description:
https://www.encodeproject.org/experiments/ENCSR499IQB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NIP7. (NIP7-BGKcLV11)
experiment encode accession: ENCSR499IQB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB413ZWQ
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/094f2bc3-8c87-46dc-9aa3-890314f9d1da/@@download/attachment/L-NIP7-BGKcLV11-67.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NIP7. (NIP7-BGKcLV11-67)

value: Brenton Graveley, UConn

value: ENCBS844FIG at ENCODE; https://www.encodeproject.org/ENCBS844FIG/


title: CRISPR RNA-seq from HepG2 (ENCLB402LJS)

description:
https://www.encodeproject.org/experiments/ENCSR481AIB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against TRNAU1AP. (TRNAU1AP-BGHcLV10)
experiment encode accession: ENCSR481AIB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB402LJS
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 TRNAU1AP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2cc79371-b46a-475d-b3bc-1406e7a11a9d/@@download/attachment/L-TRNAU1AP-BGHcLV10-51.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against TRNAU1AP. (TRNAU1AP-BGHcLV10-51)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS210ZHC at ENCODE; https://www.encodeproject.org/ENCBS210ZHC/

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


title: TF ChIP-seq from MCF-7 (ENCLB560RWI)

description:
https://www.encodeproject.org/experiments/ENCSR119OFH/
***************
biological replicate number: 1
technical replicate number: 1
description: BRCA2 ChIP-seq on human MCF-7
experiment encode accession: ENCSR119OFH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR298PFG, ENCSR712GVO
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB560RWI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting BRCA2

value: female

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS787RVT at ENCODE; https://www.encodeproject.org/ENCBS787RVT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB683OOU)

description:
https://www.encodeproject.org/experiments/ENCSR484QEX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against WBP11. (WBP11-BGHcLV22)
experiment encode accession: ENCSR484QEX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB683OOU
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/8df23afe-e1aa-466f-9ddb-58b40057a3ea/@@download/attachment/L-WBP11-BGHcLV22-64.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against WBP11. (WBP11-BGHcLV22-64)

value: Brenton Graveley, UConn

value: ENCBS613BKP at ENCODE; https://www.encodeproject.org/ENCBS613BKP/


title: microRNA-seq from IMR-90 (ENCLB667PFF)

description:
https://www.encodeproject.org/experiments/ENCSR123QKC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation IMR-90 microRNA-seq from Mortazavi
experiment encode accession: ENCSR123QKC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB667PFF
size range: <30

source_name: Homo sapiens IMR-90 cell line

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: unknown

value: ENCBS648NSQ at ENCODE; https://www.encodeproject.org/ENCBS648NSQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB473PDT)

description:
https://www.encodeproject.org/experiments/ENCSR474EJY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GARS. (GARS-BGHcLV18)
experiment encode accession: ENCSR474EJY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB473PDT
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 GARS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b6df5433-fc6e-4a43-a6e1-5ac4658357e7/@@download/attachment/L-GARS-BGHcLV18-24.pdf

value: GARS

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GARS. (GARS-BGHcLV18-24)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS899WLZ at ENCODE; https://www.encodeproject.org/ENCBS899WLZ/

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


title: TF ChIP-seq from MCF-7 (ENCLB036XSN)

description:
https://www.encodeproject.org/experiments/ENCSR119OFH/
***************
biological replicate number: 2
technical replicate number: 1
description: BRCA2 ChIP-seq on human MCF-7
experiment encode accession: ENCSR119OFH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR298PFG, ENCSR712GVO
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB036XSN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: female

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS917MFT at ENCODE; https://www.encodeproject.org/ENCBS917MFT/

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


title: microRNA-seq from left ventricle myocardium inferior (ENCLB071PGB)

description:
https://www.encodeproject.org/experiments/ENCSR122DIB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 left ventricle myocardium inferior microRNA-seq from Mortazavi
experiment encode accession: ENCSR122DIB
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB071PGB
size range: <30

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

value: left ventricle myocardium inferior

value: tissue

value: Inferior wall of left ventricle.

value: 60 year

value: Yiing Lin, MD, PhD

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

value: ENCBS735OAR at ENCODE; https://www.encodeproject.org/ENCBS735OAR/

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


title: TF ChIP-seq from A549 (ENCLB045SSW)

description:
https://www.encodeproject.org/experiments/ENCSR112XUO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TP53 ChIP-seq on human A549
experiment encode accession: ENCSR112XUO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR542LGX, ENCSR636AAQ
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB045SSW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting TP53

value: cell line

value: male

value: 58 year

value: ATCC

value: ENCBS851UOX at ENCODE; https://www.encodeproject.org/ENCBS851UOX/

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


title: CRISPR RNA-seq from HepG2 (ENCLB411SJS)

description:
https://www.encodeproject.org/experiments/ENCSR565ZPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS25. (RPS25-BGHcLV20)
experiment encode accession: ENCSR565ZPZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB411SJS
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 RPS25

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3e774667-5444-42fe-b5c2-5e58ee089f6d/@@download/attachment/L-RPS25-BGHcLV20-30.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS25. (RPS25-BGHcLV20-30)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS679EBD at ENCODE; https://www.encodeproject.org/ENCBS679EBD/

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


title: CRISPR RNA-seq from HepG2 (ENCLB433HDA)

description:
https://www.encodeproject.org/experiments/ENCSR474EJY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GARS. (GARS-BGHcLV18)
experiment encode accession: ENCSR474EJY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB433HDA
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/cf482e79-ecd9-4943-8a56-ef4bdb2ecffa/@@download/attachment/L-GARS-BGHcLV18-23.pdf

value: GARS

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GARS. (GARS-BGHcLV18-23)

value: ENCBS080COY at ENCODE; https://www.encodeproject.org/ENCBS080COY/


title: TF ChIP-seq from A549 (ENCLB462YXY)

description:
https://www.encodeproject.org/experiments/ENCSR112XUO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TP53 ChIP-seq on human A549
experiment encode accession: ENCSR112XUO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR542LGX, ENCSR636AAQ
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB462YXY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: adult

value: Michael Snyder, Stanford

value: ENCBS755BZH at ENCODE; https://www.encodeproject.org/ENCBS755BZH/


title: CRISPR RNA-seq from HepG2 (ENCLB230RJR)

description:
https://www.encodeproject.org/experiments/ENCSR565ZPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS25. (RPS25-BGHcLV20)
experiment encode accession: ENCSR565ZPZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB230RJR
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/27c006a0-37b5-4fba-8918-46b2bc0db7d4/@@download/attachment/L-RPS25-BGHcLV20-29.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS25. (RPS25-BGHcLV20-29)

value: male

value: ENCBS814FUV at ENCODE; https://www.encodeproject.org/ENCBS814FUV/


title: CRISPR RNA-seq from K562 (ENCLB464AKE)

description:
https://www.encodeproject.org/experiments/ENCSR473HXR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC2. (EXOSC2-BGKcLV21)
experiment encode accession: ENCSR473HXR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB464AKE
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 EXOSC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/39d97db5-0d09-416d-ac14-914a80d4b034/@@download/attachment/L-EXOSC2-BGKcLV21-24.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC2. (EXOSC2-BGKcLV21-24)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS301NYY at ENCODE; https://www.encodeproject.org/ENCBS301NYY/

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


title: eCLIP from HepG2 (ENCLB073EHG)

description:
https://www.encodeproject.org/experiments/ENCSR018WPY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against AQR
experiment encode accession: ENCSR018WPY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR716AKC
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB073EHG
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: AQR

value: child

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

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

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

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

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


title: eCLIP from HepG2 (ENCLB738NCR)

description:
https://www.encodeproject.org/experiments/ENCSR018WPY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against AQR
experiment encode accession: ENCSR018WPY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR716AKC
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB738NCR
fragmentation methods: see document
size range: 175-300

value: cell line

value: male

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


title: CRISPR RNA-seq from HepG2 (ENCLB040VNF)

description:
https://www.encodeproject.org/experiments/ENCSR481AIB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against TRNAU1AP. (TRNAU1AP-BGHcLV10)
experiment encode accession: ENCSR481AIB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB040VNF
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/9d0e4c2e-1281-469e-867e-b99678c6755f/@@download/attachment/L-TRNAU1AP-BGHcLV10-52.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against TRNAU1AP. (TRNAU1AP-BGHcLV10-52)

value: Brenton Graveley, UConn

value: ENCBS558FIL at ENCODE; https://www.encodeproject.org/ENCBS558FIL/


title: CRISPR RNA-seq from K562 (ENCLB890GDZ)

description:
https://www.encodeproject.org/experiments/ENCSR564RKL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against TRA2A. (TRA2A-BGKcLV11)
experiment encode accession: ENCSR564RKL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB890GDZ
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 TRA2A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/024a30a0-636d-4481-bd96-429c7a68c98a/@@download/attachment/L-TRA2A-BGKcLV11-106.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against TRA2A. (TRA2A-BGKcLV11-106)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS114SKJ at ENCODE; https://www.encodeproject.org/ENCBS114SKJ/


title: CRISPR RNA-seq from K562 (ENCLB661EMQ)

description:
https://www.encodeproject.org/experiments/ENCSR564RKL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against TRA2A. (TRA2A-BGKcLV11)
experiment encode accession: ENCSR564RKL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB661EMQ
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/3f82039f-2a6d-48b8-a6b3-384c5af42edb/@@download/attachment/L-TRA2A-BGKcLV11-105.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against TRA2A. (TRA2A-BGKcLV11-105)

value: ENCBS953RZD at ENCODE; https://www.encodeproject.org/ENCBS953RZD/

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


title: Control eCLIP from K562 (ENCLB282ZSM)

description:
https://www.encodeproject.org/experiments/ENCSR111USM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SAFB
experiment encode accession: ENCSR111USM
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB282ZSM
fragmentation methods: see document
size range: 175-300

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

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


title: CRISPR RNA-seq from K562 (ENCLB020TZE)

description:
https://www.encodeproject.org/experiments/ENCSR473HXR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC2. (EXOSC2-BGKcLV21)
experiment encode accession: ENCSR473HXR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB020TZE
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/54422f0d-fbde-4a7e-8ef7-5f1c63d9c00f/@@download/attachment/L-EXOSC2-BGKcLV21-23.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC2. (EXOSC2-BGKcLV21-23)

value: ENCBS047UIY at ENCODE; https://www.encodeproject.org/ENCBS047UIY/


title: microRNA-seq from right cardiac atrium (ENCLB720DBC)

description:
https://www.encodeproject.org/experiments/ENCSR121NOY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W72 right cardiac atrium microRNA-seq from Mortazavi
experiment encode accession: ENCSR121NOY
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB720DBC
size range: <30

source_name: Homo sapiens female adult (46 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

value: tissue

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS341KAA at ENCODE; https://www.encodeproject.org/ENCBS341KAA/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: CRISPR RNA-seq from K562 (ENCLB673QGO)

description:
https://www.encodeproject.org/experiments/ENCSR469UOO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PDCD4. (PDCD4-BGKcLV17)
experiment encode accession: ENCSR469UOO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB673QGO
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 PDCD4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7e090c74-5fee-4246-9d31-741975a5b95f/@@download/attachment/L-PDCD4-BGKcLV17-36.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PDCD4. (PDCD4-BGKcLV17-36)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS602WPB at ENCODE; https://www.encodeproject.org/ENCBS602WPB/


title: eCLIP from K562 (ENCLB897LSX)

description:
https://www.encodeproject.org/experiments/ENCSR013CTQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against EXOSC5
experiment encode accession: ENCSR013CTQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR308RMD
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB897LSX
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: cell line

value: Gene Yeo, UCSD

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

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

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

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


title: BruChase-seq from MCF-7 (ENCLB940NCV)

description:
https://www.encodeproject.org/experiments/ENCSR562TNZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR562TNZ
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR727IHV
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB940NCV
size range: 400-500

source_name: Homo sapiens MCF-7 cell line, subjected to a 6 hour pulse-chase

value: breast cancer (adenocarcinoma)

value: 69 year

value: Mats Ljungman, UMichigan

value: ENCBS361HFA at ENCODE; https://www.encodeproject.org/ENCBS361HFA/

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


title: CRISPR RNA-seq from K562 (ENCLB490RGU)

description:
https://www.encodeproject.org/experiments/ENCSR469UOO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PDCD4. (PDCD4-BGKcLV17)
experiment encode accession: ENCSR469UOO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB490RGU
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/dcf7af21-5fb2-432b-bc09-ee3b95d12080/@@download/attachment/L-PDCD4-BGKcLV17-35.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PDCD4. (PDCD4-BGKcLV17-35)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS305PYJ at ENCODE; https://www.encodeproject.org/ENCBS305PYJ/


title: BruChase-seq from MCF-7 (ENCLB889NIM)

description:
https://www.encodeproject.org/experiments/ENCSR562TNZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR562TNZ
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR727IHV
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB889NIM
size range: 400-500

value: adult

value: ATCC

value: ENCBS085TXR at ENCODE; https://www.encodeproject.org/ENCBS085TXR/


title: eCLIP from K562 (ENCLB049IVI)

description:
https://www.encodeproject.org/experiments/ENCSR013CTQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against EXOSC5
experiment encode accession: ENCSR013CTQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR308RMD
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB049IVI
fragmentation methods: see document
size range: 175-300

value: cell line

value: 53 year

value: Gene Yeo, UCSD

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


title: CRISPR RNA-seq from HepG2 (ENCLB955ONZ)

description:
https://www.encodeproject.org/experiments/ENCSR468LEL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL18. (RPL18-BGHcLV22)
experiment encode accession: ENCSR468LEL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB955ONZ
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 RPL18

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/39cfe366-61f6-469d-9b9b-15dcfdc76f73/@@download/attachment/L-RPL18-BGHcLV22-45.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL18. (RPL18-BGHcLV22-45)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS404UWM at ENCODE; https://www.encodeproject.org/ENCBS404UWM/

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


title: Control eCLIP from K562 (ENCLB251JHI)

description:
https://www.encodeproject.org/experiments/ENCSR009CIV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against NOLC1
experiment encode accession: ENCSR009CIV
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB251JHI
fragmentation methods: see document
size range: 175-300

value: female

value: chronic myelogenous leukemia (CML)

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

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB396EJD)

description:
https://www.encodeproject.org/experiments/ENCSR556TJU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SF3A1. (SF3A1-BGHcLV18)
experiment encode accession: ENCSR556TJU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB396EJD
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 SF3A1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a3df8b9e-a3a5-4a17-985b-32e213b50973/@@download/attachment/L-SF3A1-BGHcLV18-43.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SF3A1. (SF3A1-BGHcLV18-43)

value: ATCC

value: ENCBS239SWM at ENCODE; https://www.encodeproject.org/ENCBS239SWM/


title: CRISPR RNA-seq from HepG2 (ENCLB324PXG)

description:
https://www.encodeproject.org/experiments/ENCSR561IMV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ERO1L. (ERO1L-BGHcLV16)
experiment encode accession: ENCSR561IMV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB324PXG
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 ERO1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f2b4d95f-4bb3-4198-b060-b0e9dd923e71/@@download/attachment/L-ERO1L-BGHcLV16-43.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ERO1L. (ERO1L-BGHcLV16-43)

value: ENCBS626UNQ at ENCODE; https://www.encodeproject.org/ENCBS626UNQ/


title: TF ChIP-seq from A549 (ENCLB782GJB)

description:
https://www.encodeproject.org/experiments/ENCSR207WFD/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-HMGA2 ChIP-seq on human A549
experiment encode accession: ENCSR207WFD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR855NLW, ENCSR969KWE
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB782GJB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting HMGA2

value: male

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS989IAQ at ENCODE; https://www.encodeproject.org/ENCBS989IAQ/

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


title: CRISPR RNA-seq from K562 (ENCLB414TDK)

description:
https://www.encodeproject.org/experiments/ENCSR550VEL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NSUN4. (NSUN4-BGKcLV15)
experiment encode accession: ENCSR550VEL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB414TDK
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 NSUN4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/db6c65ff-663a-4910-889d-8517f81ed724/@@download/attachment/L-NPM1-BGKcLV15-41.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NSUN4. (NSUN4-BGKcLV15-43)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS871JRU at ENCODE; https://www.encodeproject.org/ENCBS871JRU/


title: CRISPR RNA-seq from HepG2 (ENCLB138MZJ)

description:
https://www.encodeproject.org/experiments/ENCSR556TJU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SF3A1. (SF3A1-BGHcLV18)
experiment encode accession: ENCSR556TJU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB138MZJ
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/42b6c6d8-e778-4ccd-b9fb-528c63a3a330/@@download/attachment/L-SF3A1-BGHcLV18-44.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SF3A1. (SF3A1-BGHcLV18-44)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS684VDW at ENCODE; https://www.encodeproject.org/ENCBS684VDW/

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


title: CRISPR RNA-seq from K562 (ENCLB691UVD)

description:
https://www.encodeproject.org/experiments/ENCSR550VEL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NSUN4. (NSUN4-BGKcLV15)
experiment encode accession: ENCSR550VEL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB691UVD
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/52a68304-3d58-47e7-a5e8-61ed43e41380/@@download/attachment/L-NPM1-BGKcLV15-42.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NSUN4. (NSUN4-BGKcLV15-44)

value: adult

value: ENCBS864BAC at ENCODE; https://www.encodeproject.org/ENCBS864BAC/

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


title: eCLIP from K562 (ENCLB252MQT)

description:
https://www.encodeproject.org/experiments/ENCSR202HKN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against WDR3
experiment encode accession: ENCSR202HKN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR033FWT
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB252MQT
fragmentation methods: see document
size range: 175-300

value: female

value: Gene Yeo, UCSD

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB616UED)

description:
https://www.encodeproject.org/experiments/ENCSR548OTL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against YBX1. (YBX1-BGHcLV16)
experiment encode accession: ENCSR548OTL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB616UED
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 YBX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/27398705-baaf-4354-a20c-7bca6e846be7/@@download/attachment/L-YBX1-BGHcLV16-61.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against YBX1. (YBX1-BGHcLV16-61)

value: male

value: Brenton Graveley, UConn

value: ENCBS970PIQ at ENCODE; https://www.encodeproject.org/ENCBS970PIQ/


title: TF ChIP-seq from A549 (ENCLB536NDK)

description:
https://www.encodeproject.org/experiments/ENCSR207WFD/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-HMGA2 ChIP-seq on human A549
experiment encode accession: ENCSR207WFD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR855NLW, ENCSR969KWE
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB536NDK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS735CQO at ENCODE; https://www.encodeproject.org/ENCBS735CQO/

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


title: CRISPR RNA-seq from HepG2 (ENCLB032OUE)

description:
https://www.encodeproject.org/experiments/ENCSR561IMV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ERO1L. (ERO1L-BGHcLV16)
experiment encode accession: ENCSR561IMV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB032OUE
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/085f37d7-98f0-4fdc-8abb-70ebc53f37bb/@@download/attachment/L-ERO1L-BGHcLV16-44.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ERO1L. (ERO1L-BGHcLV16-44)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS526OCD at ENCODE; https://www.encodeproject.org/ENCBS526OCD/

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


title: CRISPR RNA-seq from HepG2 (ENCLB132KFH)

description:
https://www.encodeproject.org/experiments/ENCSR468LEL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL18. (RPL18-BGHcLV22)
experiment encode accession: ENCSR468LEL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB132KFH
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/96103b7a-6f1e-4182-8368-22c77eabe479/@@download/attachment/L-RPL18-BGHcLV22-46.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL18. (RPL18-BGHcLV22-46)

value: ENCBS706RQK at ENCODE; https://www.encodeproject.org/ENCBS706RQK/


title: CRISPR RNA-seq from HepG2 (ENCLB903XOL)

description:
https://www.encodeproject.org/experiments/ENCSR548ORV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NFX1. (NFX1-BGHcLV10)
experiment encode accession: ENCSR548ORV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB903XOL
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 NFX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9e5bc5c3-4790-498e-b977-ad2086d11228/@@download/attachment/L-NFX1-BGHcLV10-30.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NFX1. (NFX1-BGHcLV10-30)

value: male

value: Brenton Graveley, UConn

value: ENCBS075ZEK at ENCODE; https://www.encodeproject.org/ENCBS075ZEK/


title: CRISPR RNA-seq from HepG2 (ENCLB138QFF)

description:
https://www.encodeproject.org/experiments/ENCSR548ORV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NFX1. (NFX1-BGHcLV10)
experiment encode accession: ENCSR548ORV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB138QFF
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/fbb40568-ecea-489d-8bc4-1078f4eaa905/@@download/attachment/L-NFX1-BGHcLV10-29.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NFX1. (NFX1-BGHcLV10-29)

value: ENCBS889EOR at ENCODE; https://www.encodeproject.org/ENCBS889EOR/


title: TF ChIP-seq from K562 (ENCLB414LNJ)

description:
https://www.encodeproject.org/experiments/ENCSR003GUC/
***************
biological replicate number: 2
technical replicate number: 1
description: E4F1 ChIP-seq on human K562
experiment encode accession: ENCSR003GUC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR192TOE, ENCSR233HNT
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB414LNJ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting E4F1

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS366EPU at ENCODE; https://www.encodeproject.org/ENCBS366EPU/

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


title: CRISPR RNA-seq from K562 (ENCLB233CXM)

description:
https://www.encodeproject.org/experiments/ENCSR455VFL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GNL3. (GNL3-BGKcLV08)
experiment encode accession: ENCSR455VFL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB233CXM
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 GNL3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/898fe564-73c5-4e09-a2f4-eda5f612a6a0/@@download/attachment/L-GNL3-BGKcLV08-94.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GNL3. (GNL3-BGKcLV08-94)

value: ATCC

value: ENCBS252OKO at ENCODE; https://www.encodeproject.org/ENCBS252OKO/


title: CRISPR RNA-seq from K562 (ENCLB572DMW)

description:
https://www.encodeproject.org/experiments/ENCSR547ICR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3A1. (SF3A1-BGKcLV17)
experiment encode accession: ENCSR547ICR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB572DMW
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 SF3A1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cfb6405a-014a-4075-83ef-6047ce3b437d/@@download/attachment/L-SF3A1-BGKcLV17-46.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3A1. (SF3A1-BGKcLV17-46)

value: ENCBS668GOX at ENCODE; https://www.encodeproject.org/ENCBS668GOX/


title: CRISPR RNA-seq from K562 (ENCLB451MES)

description:
https://www.encodeproject.org/experiments/ENCSR547ICR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3A1. (SF3A1-BGKcLV17)
experiment encode accession: ENCSR547ICR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB451MES
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/5ac6f82e-0c8b-4ae8-a744-c1771adec262/@@download/attachment/L-SF3A1-BGKcLV17-45.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3A1. (SF3A1-BGKcLV17-45)

value: Brenton Graveley, UConn

value: ENCBS534HNG at ENCODE; https://www.encodeproject.org/ENCBS534HNG/