title: CRISPR RNA-seq from HepG2 (ENCLB370NMX)

description:
https://www.encodeproject.org/experiments/ENCSR242DBX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHD3. (CHD3-BGHcLV10)
experiment encode accession: ENCSR242DBX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB370NMX
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 CHD3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e64f5215-9177-4f69-bb11-4c714c81e320/@@download/attachment/L-CHD3-BGHcLV10-9.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHD3. (CHD3-BGHcLV10-9)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS194NHW at ENCODE; https://www.encodeproject.org/ENCBS194NHW/


title: Bru-seq from Panc1 (ENCLB360HAX)

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/ENCSR240RKF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR240RKF
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR639ZOU
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB360HAX
size range: 400-500

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens Panc1 cell line treated with 500 rad irradiation

tag: line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: pancreatic carcinoma

tag: dev stage

value: adult

tag: age

value: 56 year

tag: lab

value: Mats Ljungman, UMichigan

tag: source

tag: treatments

tag: link

value: ENCBS873FAB at ENCODE; https://www.encodeproject.org/ENCBS873FAB/

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


title: BruChase-seq from Panc1 (ENCLB676VZU)

description:
https://www.encodeproject.org/experiments/ENCSR069MAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR069MAW
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR639ZOU
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB676VZU
size range: 400-500

source_name: Homo sapiens Panc1 cell line, subjected to a 6 hour pulse-chase

value: ENCBS871DOU at ENCODE; https://www.encodeproject.org/ENCBS871DOU/


title: CRISPR RNA-seq from K562 (ENCLB151KAX)

description:
https://www.encodeproject.org/experiments/ENCSR162HOU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGKcLV23)
experiment encode accession: ENCSR162HOU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB151KAX
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 BRIX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7dddba6c-0ef7-4f32-9c51-d82c0c73b1b4/@@download/attachment/L-BRIX1-BGKcLV23-23.pdf

tag: antibody

tag: description

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGKcLV23-23)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS883HOT at ENCODE; https://www.encodeproject.org/ENCBS883HOT/

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


title: CRISPR RNA-seq from K562 (ENCLB929OGL)

description:
https://www.encodeproject.org/experiments/ENCSR163PNO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against YWHAG. (YWHAG-BGKcLV08)
experiment encode accession: ENCSR163PNO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB929OGL
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 YWHAG

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/20d91353-5293-41d8-82de-6d880f612a42/@@download/attachment/L-YWHAG-BGKcLV08-80.pdf

value: YWHAG

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against YWHAG. (YWHAG-BGKcLV08-80)

value: Brenton Graveley, UConn

value: ENCBS969ZSB at ENCODE; https://www.encodeproject.org/ENCBS969ZSB/


title: CRISPR RNA-seq from K562 (ENCLB805CGQ)

description:
https://www.encodeproject.org/experiments/ENCSR066ZMF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ETF1. (ETF1-BGKcLV08)
experiment encode accession: ENCSR066ZMF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB805CGQ
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 ETF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d637fb63-235d-4e45-8444-1eb60d404e42/@@download/attachment/L-ETF1-BGKcLV08-33.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ETF1. (ETF1-BGKcLV08-33)

value: adult

value: ATCC

value: ENCBS164XZU at ENCODE; https://www.encodeproject.org/ENCBS164XZU/


title: CRISPR RNA-seq from K562 (ENCLB714ZWO)

description:
https://www.encodeproject.org/experiments/ENCSR237QLO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ACO1. (ACO1-BGKcLV11)
experiment encode accession: ENCSR237QLO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB714ZWO
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 ACO1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b6eef9c8-d685-46db-b953-6c3dd0e745ec/@@download/attachment/L-ACO1-BGKcLV11-4.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ACO1. (ACO1-BGKcLV11-4)

value: ENCBS687AKW at ENCODE; https://www.encodeproject.org/ENCBS687AKW/


title: CRISPR RNA-seq from K562 (ENCLB292IIS)

description:
https://www.encodeproject.org/experiments/ENCSR058MCC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGKcLV13)
experiment encode accession: ENCSR058MCC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB292IIS
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 PSMA1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9444127f-d1f2-41ac-8a5d-b4f439cef35b/@@download/attachment/L-PSMA1-BGKcLV13-61.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGKcLV13-61)

value: ENCBS662MSX at ENCODE; https://www.encodeproject.org/ENCBS662MSX/


title: BruChase-seq from HCT116 (ENCLB311SDX)

description:
https://www.encodeproject.org/experiments/ENCSR149QZB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR149QZB
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR799MPW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB311SDX
size range: 400-500

source_name: Homo sapiens HCT116 cell line, subjected to a 6 hour pulse-chase

value: male

value: colorectal carcinoma

value: 48 year

value: Mats Ljungman, UMichigan

value: ENCBS277NAZ at ENCODE; https://www.encodeproject.org/ENCBS277NAZ/

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


title: CRISPR RNA-seq from K562 (ENCLB814XIO)

description:
https://www.encodeproject.org/experiments/ENCSR050ONB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RNF187. (RNF187-BGKcLV19)
experiment encode accession: ENCSR050ONB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB814XIO
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 RNF187

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/80faec13-f9fa-443e-82db-e97f64641cf3/@@download/attachment/L-RNF187-BGKcLV19-39.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RNF187. (RNF187-BGKcLV19-39)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS823JJH at ENCODE; https://www.encodeproject.org/ENCBS823JJH/

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


title: CRISPR RNA-seq from K562 (ENCLB854QCB)

description:
https://www.encodeproject.org/experiments/ENCSR148XGX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GSPT2. (GSPT2-BGKcLV17)
experiment encode accession: ENCSR148XGX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB854QCB
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 GSPT2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a902d334-d272-4837-aba5-b645ed656401/@@download/attachment/L-GSPT2-BGKcLV17-28.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GSPT2. (GSPT2-BGKcLV17-28)

value: adult

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS475WDP at ENCODE; https://www.encodeproject.org/ENCBS475WDP/


title: CRISPR RNA-seq from K562 (ENCLB345SJG)

description:
https://www.encodeproject.org/experiments/ENCSR148XGX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GSPT2. (GSPT2-BGKcLV17)
experiment encode accession: ENCSR148XGX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB345SJG
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/f540dad7-4459-4d78-8bee-31db755267f6/@@download/attachment/L-GSPT2-BGKcLV17-27.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GSPT2. (GSPT2-BGKcLV17-27)

value: ENCBS609LOC at ENCODE; https://www.encodeproject.org/ENCBS609LOC/


title: BruChase-seq from HCT116 (ENCLB112GHS)

description:
https://www.encodeproject.org/experiments/ENCSR149QZB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR149QZB
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR799MPW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB112GHS
size range: 400-500

value: male

value: colorectal carcinoma

value: 48 year

value: Mats Ljungman, UMichigan

value: ENCBS075DRY at ENCODE; https://www.encodeproject.org/ENCBS075DRY/


title: CRISPR RNA-seq from K562 (ENCLB267XPI)

description:
https://www.encodeproject.org/experiments/ENCSR148HLA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against APTX. (APTX-BGKcLV23)
experiment encode accession: ENCSR148HLA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB267XPI
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 APTX

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/020c7d27-1c55-4f19-a144-380047d53dc9/@@download/attachment/L-APTX-BGKcLV23-16.pdf

value: APTX

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against APTX. (APTX-BGKcLV23-16)

value: female

value: ENCBS346LUN at ENCODE; https://www.encodeproject.org/ENCBS346LUN/


title: CRISPR RNA-seq from HepG2 (ENCLB212SBA)

description:
https://www.encodeproject.org/experiments/ENCSR242DBX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHD3. (CHD3-BGHcLV10)
experiment encode accession: ENCSR242DBX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB212SBA
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/30ee9008-3235-4e79-834b-50d12170821f/@@download/attachment/L-CHD3-BGHcLV10-10.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHD3. (CHD3-BGHcLV10-10)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS406LFP at ENCODE; https://www.encodeproject.org/ENCBS406LFP/

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


title: CRISPR RNA-seq from K562 (ENCLB184VXE)

description:
https://www.encodeproject.org/experiments/ENCSR242VKR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CENPI. (CENPI-BGKcLV08)
experiment encode accession: ENCSR242VKR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB184VXE
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 CENPI

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0d79232b-58fe-43ea-891e-6e764676ae99/@@download/attachment/L-CENPI-BGKcLV08-8.pdf

value: CENPI

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CENPI. (CENPI-BGKcLV08-8)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS105PBU at ENCODE; https://www.encodeproject.org/ENCBS105PBU/

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


title: CRISPR RNA-seq from K562 (ENCLB723ZEQ)

description:
https://www.encodeproject.org/experiments/ENCSR242VKR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CENPI. (CENPI-BGKcLV08)
experiment encode accession: ENCSR242VKR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB723ZEQ
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/4c9e49f1-247e-4cad-9a44-59171766cf4a/@@download/attachment/L-CENPI-BGKcLV08-7.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CENPI. (CENPI-BGKcLV08-7)

value: female

value: ENCBS833MOI at ENCODE; https://www.encodeproject.org/ENCBS833MOI/


title: Mint-ChIP-seq from immature natural killer cell (ENCLB628PPN)

description:
https://www.encodeproject.org/experiments/ENCSR234BAD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR234BAD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR169WAD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB628PPN
fragmentation methods: none

library_source: genomic

molecule: genomic DNA

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

value: immature natural killer cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: CRISPR RNA-seq from K562 (ENCLB079VKI)

description:
https://www.encodeproject.org/experiments/ENCSR058MCC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGKcLV13)
experiment encode accession: ENCSR058MCC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB079VKI
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/455427c7-1fcb-42e6-b509-0ab5415cd971/@@download/attachment/L-PSMA1-BGKcLV13-62.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGKcLV13-62)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS903RNW at ENCODE; https://www.encodeproject.org/ENCBS903RNW/


title: Bru-seq from Panc1 (ENCLB099RIP)

description:
https://www.encodeproject.org/experiments/ENCSR240RKF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR240RKF
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR639ZOU
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB099RIP
size range: 400-500

value: cell line

value: male

value: pancreatic carcinoma

value: 56 year

value: Mats Ljungman, UMichigan

value: ENCBS302QSN at ENCODE; https://www.encodeproject.org/ENCBS302QSN/

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


title: CRISPR RNA-seq from K562 (ENCLB521IAP)

description:
https://www.encodeproject.org/experiments/ENCSR234FWR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL28. (RPL28-BGKcLV15)
experiment encode accession: ENCSR234FWR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2021-04-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB521IAP
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 RPL28

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/207bd7c4-3a36-4854-aafe-c8ca5657a279/@@download/attachment/L-RPL28-BGKcLV15-54.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL28. (RPL28-BGKcLV15-54)

value: female

value: ENCBS591WUS at ENCODE; https://www.encodeproject.org/ENCBS591WUS/

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


title: CRISPR RNA-seq from K562 (ENCLB601LGN)

description:
https://www.encodeproject.org/experiments/ENCSR050ONB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RNF187. (RNF187-BGKcLV19)
experiment encode accession: ENCSR050ONB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB601LGN
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/2de231f9-d35c-48d1-aa6e-c1f945d84c82/@@download/attachment/L-RNF187-BGKcLV19-40.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RNF187. (RNF187-BGKcLV19-40)

value: chronic myelogenous leukemia (CML)

value: ENCBS828OWP at ENCODE; https://www.encodeproject.org/ENCBS828OWP/


title: CRISPR RNA-seq from HepG2 (ENCLB373DJP)

description:
https://www.encodeproject.org/experiments/ENCSR144HCM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against IFIT2. (IFIT2-BGHcLV18)
experiment encode accession: ENCSR144HCM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB373DJP
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 IFIT2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5c309b76-976c-49ef-9812-db77e85c2961/@@download/attachment/L-IFIT2-BGHcLV18-28.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against IFIT2. (IFIT2-BGHcLV18-28)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS518VOZ at ENCODE; https://www.encodeproject.org/ENCBS518VOZ/

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


title: Bru-seq from HepG2 (ENCLB953HRZ)

description:
https://www.encodeproject.org/experiments/ENCSR050CVB/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR050CVB
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR974AQD
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB953HRZ
size range: 400-500

source_name: Homo sapiens HepG2 cell line treated with 500 rad irradiation

value: cell line

value: male

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS306USR at ENCODE; https://www.encodeproject.org/ENCBS306USR/


title: Bru-seq from HepG2 (ENCLB147KPE)

description:
https://www.encodeproject.org/experiments/ENCSR050CVB/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR050CVB
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR974AQD
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB147KPE
size range: 400-500

value: ENCBS102LBY at ENCODE; https://www.encodeproject.org/ENCBS102LBY/


title: BruChase-seq from HepG2 (ENCLB986YLA)

description:
https://www.encodeproject.org/experiments/ENCSR135DZR/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR135DZR
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR974AQD
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB986YLA
size range: 400-500

source_name: Homo sapiens HepG2 cell line, subjected to a 6 hour pulse-chase

value: ENCBS366MVG at ENCODE; https://www.encodeproject.org/ENCBS366MVG/


title: CRISPR RNA-seq from K562 (ENCLB851FRO)

description:
https://www.encodeproject.org/experiments/ENCSR226HQD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PARP1. (PARP1-BGKcLV13)
experiment encode accession: ENCSR226HQD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB851FRO
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 PARP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cc00f6ed-2e2e-4c47-a4d2-1431655b5917/@@download/attachment/L-PARP1-BGKcLV13-50.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PARP1. (PARP1-BGKcLV13-50)

value: female

value: adult

value: 53 year

value: ENCBS022VQF at ENCODE; https://www.encodeproject.org/ENCBS022VQF/

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


title: CRISPR RNA-seq from K562 (ENCLB509YTX)

description:
https://www.encodeproject.org/experiments/ENCSR050ATA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS11. (RPS11-BGKcLV08)
experiment encode accession: ENCSR050ATA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB509YTX
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 RPS11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e2b88869-f115-4cff-b403-08775e5f5582/@@download/attachment/L-RPS11-BGKcLV08-63.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS11. (RPS11-BGKcLV08-63)

value: chronic myelogenous leukemia (CML)

value: ENCBS138GDT at ENCODE; https://www.encodeproject.org/ENCBS138GDT/


title: CRISPR RNA-seq from K562 (ENCLB446XOR)

description:
https://www.encodeproject.org/experiments/ENCSR048AUX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZC3H11A. (ZC3H11A-BGKcLV11)
experiment encode accession: ENCSR048AUX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB446XOR
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 ZC3H11A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c65ac74d-2e83-4497-aaa7-ff104fd72ceb/@@download/attachment/L-ZC3H11A-BGKcLV11-114.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZC3H11A. (ZC3H11A-BGKcLV11-114)

value: Brenton Graveley, UConn

value: ENCBS228QAA at ENCODE; https://www.encodeproject.org/ENCBS228QAA/


title: CRISPR RNA-seq from K562 (ENCLB018GVM)

description:
https://www.encodeproject.org/experiments/ENCSR050ATA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS11. (RPS11-BGKcLV08)
experiment encode accession: ENCSR050ATA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB018GVM
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/b0867a81-6df3-4e19-935f-137a9a84b659/@@download/attachment/L-RPS11-BGKcLV08-64.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS11. (RPS11-BGKcLV08-64)

value: ENCBS897WWG at ENCODE; https://www.encodeproject.org/ENCBS897WWG/


title: CRISPR RNA-seq from K562 (ENCLB540JFY)

description:
https://www.encodeproject.org/experiments/ENCSR237QLO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ACO1. (ACO1-BGKcLV11)
experiment encode accession: ENCSR237QLO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB540JFY
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/ec89f9bb-101c-46bd-bb80-b51c9c61a0ef/@@download/attachment/L-ACO1-BGKcLV11-3.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ACO1. (ACO1-BGKcLV11-3)

value: ATCC

value: ENCBS787BHM at ENCODE; https://www.encodeproject.org/ENCBS787BHM/


title: BruChase-seq from PC-3 (ENCLB584DDV)

description:
https://www.encodeproject.org/experiments/ENCSR042DKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR042DKG
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR622SUM
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB584DDV
size range: 400-500

source_name: Homo sapiens PC-3 cell line, subjected to a 2 hour pulse-chase

value: male

value: grade IV, adenocarcinoma

value: 62 year

value: Mats Ljungman, UMichigan

value: ENCBS438BHD at ENCODE; https://www.encodeproject.org/ENCBS438BHD/

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


title: CRISPR RNA-seq from K562 (ENCLB322SVK)

description:
https://www.encodeproject.org/experiments/ENCSR034NAT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NPM1. (NPM1-BGKcLV15)
experiment encode accession: ENCSR034NAT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB322SVK
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 NPM1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/306b15b7-c742-4b7a-b385-9a5199818acc/@@download/attachment/L-MECP2-BGKcLV15-39.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NPM1. (NPM1-BGKcLV15-41)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS665YAY at ENCODE; https://www.encodeproject.org/ENCBS665YAY/

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


title: CRISPR RNA-seq from HepG2 (ENCLB728OVD)

description:
https://www.encodeproject.org/experiments/ENCSR035LEO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC2. (EXOSC2-BGHcLV22)
experiment encode accession: ENCSR035LEO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB728OVD
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 EXOSC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e6dda574-64ec-4d49-be2a-c5676a7446c6/@@download/attachment/L-EXOSC2-BGHcLV22-25.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC2. (EXOSC2-BGHcLV22-25)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS470ESE at ENCODE; https://www.encodeproject.org/ENCBS470ESE/

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


title: BruChase-seq from HepG2 (ENCLB378PJW)

description:
https://www.encodeproject.org/experiments/ENCSR135DZR/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR135DZR
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR974AQD
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB378PJW
size range: 400-500

value: male

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS524KVF at ENCODE; https://www.encodeproject.org/ENCBS524KVF/


title: CRISPR RNA-seq from K562 (ENCLB655CII)

description:
https://www.encodeproject.org/experiments/ENCSR034NAT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NPM1. (NPM1-BGKcLV15)
experiment encode accession: ENCSR034NAT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB655CII
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/e8740672-7bd4-4964-ba47-9ae05def8d3e/@@download/attachment/L-MECP2-BGKcLV15-40.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NPM1. (NPM1-BGKcLV15-42)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS868KHZ at ENCODE; https://www.encodeproject.org/ENCBS868KHZ/


title: CRISPR RNA-seq from K562 (ENCLB212NDH)

description:
https://www.encodeproject.org/experiments/ENCSR129AAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM19. (RBM19-BGKcLV19)
experiment encode accession: ENCSR129AAZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB212NDH
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 RBM19

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/10222801-21d0-4415-97da-049929f87bde/@@download/attachment/L-RBM19-BGKcLV19-37.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM19. (RBM19-BGKcLV19-37)

value: adult

value: 53 year

value: ENCBS358QBF at ENCODE; https://www.encodeproject.org/ENCBS358QBF/

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


title: CRISPR RNA-seq from K562 (ENCLB346ZVV)

description:
https://www.encodeproject.org/experiments/ENCSR048AUX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZC3H11A. (ZC3H11A-BGKcLV11)
experiment encode accession: ENCSR048AUX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB346ZVV
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/c1e465e3-01b0-4b7b-84c1-9f29f22c2c9a/@@download/attachment/L-ZC3H11A-BGKcLV11-113.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZC3H11A. (ZC3H11A-BGKcLV11-113)

value: ENCBS107VIY at ENCODE; https://www.encodeproject.org/ENCBS107VIY/


title: CRISPR RNA-seq from K562 (ENCLB388JNG)

description:
https://www.encodeproject.org/experiments/ENCSR148HLA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against APTX. (APTX-BGKcLV23)
experiment encode accession: ENCSR148HLA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB388JNG
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/f90f49f3-12ed-4212-8347-7a3e46055cfc/@@download/attachment/L-APTX-BGKcLV23-15.pdf

value: APTX

value: RNA-seq on K562 cells treated with a CRISPR gRNA against APTX. (APTX-BGKcLV23-15)

value: Brenton Graveley, UConn

value: ENCBS932ELT at ENCODE; https://www.encodeproject.org/ENCBS932ELT/


title: CRISPR RNA-seq from K562 (ENCLB430SYI)

description:
https://www.encodeproject.org/experiments/ENCSR039SOI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GEMIN2. (GEMIN2-BGKcLV17)
experiment encode accession: ENCSR039SOI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB430SYI
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 GEMIN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8a9ca722-b9e7-4b5d-b8ab-56245d0bc56a/@@download/attachment/L-GEMIN2-BGKcLV17-25.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GEMIN2. (GEMIN2-BGKcLV17-25)

value: ATCC

value: ENCBS351JNN at ENCODE; https://www.encodeproject.org/ENCBS351JNN/


title: CRISPR RNA-seq from K562 (ENCLB692GKG)

description:
https://www.encodeproject.org/experiments/ENCSR234FWR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL28. (RPL28-BGKcLV15)
experiment encode accession: ENCSR234FWR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2021-04-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB692GKG
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/2564a9b7-ee28-4644-b484-895bbdae260d/@@download/attachment/L-RPL28-BGKcLV15-53.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL28. (RPL28-BGKcLV15-53)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS412RPC at ENCODE; https://www.encodeproject.org/ENCBS412RPC/


title: CRISPR RNA-seq from HepG2 (ENCLB233RED)

description:
https://www.encodeproject.org/experiments/ENCSR036ANR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD2. (SMAD2-BGHcLV16)
experiment encode accession: ENCSR036ANR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB233RED
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 SMAD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/48dbb0f3-4cc2-4641-8eba-21e1748b5894/@@download/attachment/L-SMAD2-BGHcLV16-52.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD2. (SMAD2-BGHcLV16-52)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS142KLP at ENCODE; https://www.encodeproject.org/ENCBS142KLP/

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


title: CRISPR RNA-seq from K562 (ENCLB958LHT)

description:
https://www.encodeproject.org/experiments/ENCSR039SOI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GEMIN2. (GEMIN2-BGKcLV17)
experiment encode accession: ENCSR039SOI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB958LHT
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/13abda2b-9f8b-4e2c-b900-3e6e3cbbcf9c/@@download/attachment/L-GEMIN2-BGKcLV17-26.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GEMIN2. (GEMIN2-BGKcLV17-26)

value: adult

value: 53 year

value: ENCBS821IPB at ENCODE; https://www.encodeproject.org/ENCBS821IPB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB993LDK)

description:
https://www.encodeproject.org/experiments/ENCSR029VGU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DHX57. (DHX57-BGHcLV18)
experiment encode accession: ENCSR029VGU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB993LDK
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 DHX57

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/68babe49-cc41-412d-a527-f26c4cf7e8f2/@@download/attachment/L-DHX57-BGHcLV18-12.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DHX57. (DHX57-BGHcLV18-12)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS350MHP at ENCODE; https://www.encodeproject.org/ENCBS350MHP/


title: BruChase-seq from PC-3 (ENCLB913WDI)

description:
https://www.encodeproject.org/experiments/ENCSR042DKG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR042DKG
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR622SUM
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB913WDI
size range: 400-500

value: grade IV, adenocarcinoma

value: 62 year

value: Mats Ljungman, UMichigan

value: ENCBS388MKT at ENCODE; https://www.encodeproject.org/ENCBS388MKT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB521BHC)

description:
https://www.encodeproject.org/experiments/ENCSR036ANR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD2. (SMAD2-BGHcLV16)
experiment encode accession: ENCSR036ANR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB521BHC
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/7c4e77ce-5f2f-4c44-b8e9-d062d47fc711/@@download/attachment/L-SMAD2-BGHcLV16-51.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SMAD2. (SMAD2-BGHcLV16-51)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS554PNG at ENCODE; https://www.encodeproject.org/ENCBS554PNG/


title: CRISPR RNA-seq from K562 (ENCLB279OZG)

description:
https://www.encodeproject.org/experiments/ENCSR026FEM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ERN1. (ERN1-BGKcLV17)
experiment encode accession: ENCSR026FEM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB279OZG
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 ERN1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c16e2b78-f0b0-446b-b747-9696a975e888/@@download/attachment/L-ERN1-BGKcLV17-18.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ERN1. (ERN1-BGKcLV17-18)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS765QWV at ENCODE; https://www.encodeproject.org/ENCBS765QWV/


title: CRISPR RNA-seq from HepG2 (ENCLB782KSD)

description:
https://www.encodeproject.org/experiments/ENCSR144HCM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against IFIT2. (IFIT2-BGHcLV18)
experiment encode accession: ENCSR144HCM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB782KSD
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/06d8335d-8122-49b1-a671-b73ef3354fec/@@download/attachment/L-IFIT2-BGHcLV18-27.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against IFIT2. (IFIT2-BGHcLV18-27)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS131LVO at ENCODE; https://www.encodeproject.org/ENCBS131LVO/

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


title: CRISPR RNA-seq from K562 (ENCLB093JIJ)

description:
https://www.encodeproject.org/experiments/ENCSR129AAZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM19. (RBM19-BGKcLV19)
experiment encode accession: ENCSR129AAZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB093JIJ
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/bffea618-5917-4a00-9e09-67644e9afe7a/@@download/attachment/L-RBM19-BGKcLV19-38.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM19. (RBM19-BGKcLV19-38)

value: ENCBS175FEQ at ENCODE; https://www.encodeproject.org/ENCBS175FEQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB258RIU)

description:
https://www.encodeproject.org/experiments/ENCSR120WNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against LSM7. (LSM7-BGHcLV22)
experiment encode accession: ENCSR120WNJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB258RIU
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 LSM7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8b0ba319-7114-4b62-9b99-b141bdfeb6c5/@@download/attachment/L-LSM7-BGHcLV22-29.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against LSM7. (LSM7-BGHcLV22-29)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS671YCK at ENCODE; https://www.encodeproject.org/ENCBS671YCK/


title: CRISPR RNA-seq from K562 (ENCLB255NPQ)

description:
https://www.encodeproject.org/experiments/ENCSR033XYV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4E. (EIF4E-BGKcLV15)
experiment encode accession: ENCSR033XYV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB255NPQ
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 EIF4E

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9219afb4-e9a1-4bd3-b72f-1c81b1cf3dbe/@@download/attachment/L-EIF4E-BGKcLV15-34.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4E. (EIF4E-BGKcLV15-34)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS485INP at ENCODE; https://www.encodeproject.org/ENCBS485INP/


title: CRISPR RNA-seq from K562 (ENCLB115XJC)

description:
https://www.encodeproject.org/experiments/ENCSR016WTN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD2. (SMAD2-BGKcLV15)
experiment encode accession: ENCSR016WTN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB115XJC
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 SMAD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8102146c-ba0c-4b38-a4c3-d3b1806d4e1f/@@download/attachment/L-SMAD2-BGKcLV15-55.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD2. (SMAD2-BGKcLV15-55)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS962RKJ at ENCODE; https://www.encodeproject.org/ENCBS962RKJ/


title: CRISPR RNA-seq from K562 (ENCLB617RIS)

description:
https://www.encodeproject.org/experiments/ENCSR016WTN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD2. (SMAD2-BGKcLV15)
experiment encode accession: ENCSR016WTN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB617RIS
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/33b0894f-1693-4b36-9c59-cb48b0134dc7/@@download/attachment/L-SMAD2-BGKcLV15-56.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD2. (SMAD2-BGKcLV15-56)

value: ENCBS837HRP at ENCODE; https://www.encodeproject.org/ENCBS837HRP/

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


title: CRISPR RNA-seq from K562 (ENCLB527EKG)

description:
https://www.encodeproject.org/experiments/ENCSR015KGT/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV08)
experiment encode accession: ENCSR015KGT
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB527EKG
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/6ab84f46-ebc4-42c3-8400-1a9e4e9ffe6f/@@download/attachment/L-NT-BGKcLV08-2.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non -target. (NT-BGKcLV08-2)

value: ENCBS727VBW at ENCODE; https://www.encodeproject.org/ENCBS727VBW/


title: CRISPR RNA-seq from HepG2 (ENCLB881OAU)

description:
https://www.encodeproject.org/experiments/ENCSR013PBS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NCL. (NCL-BGHcLV18)
experiment encode accession: ENCSR013PBS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB881OAU
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 NCL

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f2840601-b6c1-44a0-a4b3-e693b69728ca/@@download/attachment/L-NCL-BGHcLV18-30.pdf

value: NCL

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NCL. (NCL-BGHcLV18-30)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS841WPR at ENCODE; https://www.encodeproject.org/ENCBS841WPR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB027CND)

description:
https://www.encodeproject.org/experiments/ENCSR020EBN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DUS3L. (DUS3L-BGHcLV18)
experiment encode accession: ENCSR020EBN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB027CND
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 DUS3L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6ab50e71-c653-42a9-9cc6-3c78bffd3d1e/@@download/attachment/L-DUS3L-BGHcLV18-14.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DUS3L. (DUS3L-BGHcLV18-14)

value: ENCBS902VWJ at ENCODE; https://www.encodeproject.org/ENCBS902VWJ/


title: CRISPR RNA-seq from K562 (ENCLB067IWK)

description:
https://www.encodeproject.org/experiments/ENCSR226HQD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PARP1. (PARP1-BGKcLV13)
experiment encode accession: ENCSR226HQD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB067IWK
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 PARP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2d53eea3-0ff9-415f-b7d0-948ba3a72cec/@@download/attachment/L-PARP1-BGKcLV13-49.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PARP1. (PARP1-BGKcLV13-49)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS739NVD at ENCODE; https://www.encodeproject.org/ENCBS739NVD/


title: CRISPR RNA-seq from HepG2 (ENCLB497XOZ)

description:
https://www.encodeproject.org/experiments/ENCSR035LEO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC2. (EXOSC2-BGHcLV22)
experiment encode accession: ENCSR035LEO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB497XOZ
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/3484b71b-1f71-417c-ab44-f0b746f8b3b8/@@download/attachment/L-EXOSC2-BGHcLV22-26.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC2. (EXOSC2-BGHcLV22-26)

value: male

value: ENCBS744VDF at ENCODE; https://www.encodeproject.org/ENCBS744VDF/


title: CRISPR RNA-seq from K562 (ENCLB692XMT)

description:
https://www.encodeproject.org/experiments/ENCSR033XYV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4E. (EIF4E-BGKcLV15)
experiment encode accession: ENCSR033XYV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB692XMT
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/fdb6dd1c-2e6d-4f2f-a461-95d848cbb4ab/@@download/attachment/L-EIF4E-BGKcLV15-33.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4E. (EIF4E-BGKcLV15-33)

value: ENCBS104TZP at ENCODE; https://www.encodeproject.org/ENCBS104TZP/

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


title: CRISPR RNA-seq from K562 (ENCLB909ITK)

description:
https://www.encodeproject.org/experiments/ENCSR208AJS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SART1. (SART1-BGKcLV21)
experiment encode accession: ENCSR208AJS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB909ITK
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 SART1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3625a33c-3329-4cd7-97f7-5acda9ee6a81/@@download/attachment/L-SART1-BGKcLV21-39.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SART1. (SART1-BGKcLV21-39)

value: ENCBS257WRR at ENCODE; https://www.encodeproject.org/ENCBS257WRR/


title: CRISPR RNA-seq from K562 (ENCLB581ZUO)

description:
https://www.encodeproject.org/experiments/ENCSR026FEM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ERN1. (ERN1-BGKcLV17)
experiment encode accession: ENCSR026FEM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB581ZUO
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/e1b54092-548f-4d4f-bb4a-2da4a81396b9/@@download/attachment/L-ERN1-BGKcLV17-17.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ERN1. (ERN1-BGKcLV17-17)

value: ENCBS635PSX at ENCODE; https://www.encodeproject.org/ENCBS635PSX/


title: CRISPR RNA-seq from K562 (ENCLB414SMO)

description:
https://www.encodeproject.org/experiments/ENCSR208AJS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SART1. (SART1-BGKcLV21)
experiment encode accession: ENCSR208AJS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB414SMO
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/1af65ace-23df-4b7b-94dd-4bd578b3519b/@@download/attachment/L-SART1-BGKcLV21-40.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SART1. (SART1-BGKcLV21-40)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS845NMN at ENCODE; https://www.encodeproject.org/ENCBS845NMN/


title: CRISPR RNA-seq from HepG2 (ENCLB366GGT)

description:
https://www.encodeproject.org/experiments/ENCSR120WNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against LSM7. (LSM7-BGHcLV22)
experiment encode accession: ENCSR120WNJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB366GGT
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/93d6039d-b502-415d-a2f3-f7cbbd167078/@@download/attachment/L-LSM7-BGHcLV22-30.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against LSM7. (LSM7-BGHcLV22-30)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS240ZAB at ENCODE; https://www.encodeproject.org/ENCBS240ZAB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB144QOE)

description:
https://www.encodeproject.org/experiments/ENCSR010XIH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGHcLV12)
experiment encode accession: ENCSR010XIH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB144QOE
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 CIRBP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/09c9c32f-fc96-4fb3-9ad9-34cb8f6d7a7c/@@download/attachment/L-CIRBP-BGHcLV12-20.pdf

value: CIRBP

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGHcLV12-20)

value: male

value: ENCBS035DAB at ENCODE; https://www.encodeproject.org/ENCBS035DAB/


title: CRISPR RNA-seq from K562 (ENCLB359AWJ)

description:
https://www.encodeproject.org/experiments/ENCSR204OEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PAN2. (PAN2-BGKcLV21)
experiment encode accession: ENCSR204OEJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB359AWJ
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 PAN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0ecbda6b-727e-40bd-84bd-efdb7acbfa5f/@@download/attachment/L-PAN2-BGKcLV21-33.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PAN2. (PAN2-BGKcLV21-33)

value: adult

value: 53 year

value: ENCBS024DGO at ENCODE; https://www.encodeproject.org/ENCBS024DGO/

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


title: CRISPR RNA-seq from K562 (ENCLB051IYR)

description:
https://www.encodeproject.org/experiments/ENCSR126UCL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX59. (DDX59-BGKcLV08)
experiment encode accession: ENCSR126UCL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB051IYR
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 DDX59

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6e287be6-29d1-417e-816a-84f725cfc936/@@download/attachment/L-DDX59-BGKcLV08-24.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX59. (DDX59-BGKcLV08-24)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS040AYW at ENCODE; https://www.encodeproject.org/ENCBS040AYW/


title: CRISPR RNA-seq from K562 (ENCLB427PXA)

description:
https://www.encodeproject.org/experiments/ENCSR025XBH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GSK3B. (GSK3B-BGKcLV15)
experiment encode accession: ENCSR025XBH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB427PXA
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 GSK3B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a93accd7-54f8-4bcd-85a3-2584f1a2ef7e/@@download/attachment/L-ERO1L-BGKcLV15-48.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GSK3B. (GSK3B-BGKcLV15-38)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS451MGO at ENCODE; https://www.encodeproject.org/ENCBS451MGO/


title: CRISPR RNA-seq from K562 (ENCLB127TLR)

description:
https://www.encodeproject.org/experiments/ENCSR126UCL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX59. (DDX59-BGKcLV08)
experiment encode accession: ENCSR126UCL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB127TLR
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/6a18ec5a-2fc0-4928-8b8e-09e909ec1eff/@@download/attachment/L-DDX59-BGKcLV08-23.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX59. (DDX59-BGKcLV08-23)

value: ENCBS625ITQ at ENCODE; https://www.encodeproject.org/ENCBS625ITQ/


title: CRISPR RNA-seq from HepG2 (ENCLB850GUR)

description:
https://www.encodeproject.org/experiments/ENCSR020EBN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DUS3L. (DUS3L-BGHcLV18)
experiment encode accession: ENCSR020EBN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB850GUR
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/03e7283b-5c26-447a-ba20-079a96e258e0/@@download/attachment/L-DUS3L-BGHcLV18-13.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DUS3L. (DUS3L-BGHcLV18-13)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS699NLD at ENCODE; https://www.encodeproject.org/ENCBS699NLD/

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


title: CRISPR RNA-seq from K562 (ENCLB826VFL)

description:
https://www.encodeproject.org/experiments/ENCSR025XBH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GSK3B. (GSK3B-BGKcLV15)
experiment encode accession: ENCSR025XBH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB826VFL
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/375c0948-aad6-4e95-a934-996283767542/@@download/attachment/L-ERO1L-BGKcLV15-47.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GSK3B. (GSK3B-BGKcLV15-37)

value: female

value: adult

value: 53 year

value: ENCBS665SIN at ENCODE; https://www.encodeproject.org/ENCBS665SIN/

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


title: CRISPR RNA-seq from HepG2 (ENCLB487YST)

description:
https://www.encodeproject.org/experiments/ENCSR002NQQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT10. (CNOT10-BGHcLV22)
experiment encode accession: ENCSR002NQQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB487YST
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 CNOT10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e99db2fc-8bce-4c01-833b-e8a62e103e82/@@download/attachment/L-CNOT10-BGHcLV22-10.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT10. (CNOT10-BGHcLV22-10)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS966NDP at ENCODE; https://www.encodeproject.org/ENCBS966NDP/


title: CRISPR RNA-seq from HepG2 (ENCLB229UZX)

description:
https://www.encodeproject.org/experiments/ENCSR013PBS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NCL. (NCL-BGHcLV18)
experiment encode accession: ENCSR013PBS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB229UZX
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/2dedf0f7-0301-45f9-84e9-a1b10d33e91d/@@download/attachment/L-NCL-BGHcLV18-29.pdf

value: NCL

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NCL. (NCL-BGHcLV18-29)

value: ENCBS969RYG at ENCODE; https://www.encodeproject.org/ENCBS969RYG/


title: microRNA-seq from layer of hippocampus (ENCLB844SOJ)

description:
https://www.encodeproject.org/experiments/ENCSR760SKT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation WT male mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR760SKT
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB844SOJ
size range: <30

organism: Mus musculus

source_name: Mus musculus strain B6NCrl adult (6 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: Hippocampus from 6 mo C57BL/6 male

value: not collected

value: 6 month

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS398AWS at ENCODE; https://www.encodeproject.org/ENCBS398AWS/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: CRISPR RNA-seq from HepG2 (ENCLB081HVQ)

description:
https://www.encodeproject.org/experiments/ENCSR005UDT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ERN1. (ERN1-BGHcLV18)
experiment encode accession: ENCSR005UDT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB081HVQ
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 ERN1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c5fa0bb9-d93c-44e8-92ba-ad5622adbf4f/@@download/attachment/L-ERN1-BGHcLV18-18.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ERN1. (ERN1-BGHcLV18-18)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS948BPV at ENCODE; https://www.encodeproject.org/ENCBS948BPV/

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


title: CRISPR RNA-seq from K562 (ENCLB932JEX)

description:
https://www.encodeproject.org/experiments/ENCSR204OEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PAN2. (PAN2-BGKcLV21)
experiment encode accession: ENCSR204OEJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB932JEX
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/c4dc712e-64e1-45a3-8133-fc5b7b800b39/@@download/attachment/L-PAN2-BGKcLV21-34.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PAN2. (PAN2-BGKcLV21-34)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS019RRN at ENCODE; https://www.encodeproject.org/ENCBS019RRN/

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


title: CRISPR RNA-seq from HepG2 (ENCLB278VFA)

description:
https://www.encodeproject.org/experiments/ENCSR010XIH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGHcLV12)
experiment encode accession: ENCSR010XIH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB278VFA
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/ca47e3bd-b24a-471d-955e-77db4fcb5287/@@download/attachment/L-CIRBP-BGHcLV12-19.pdf

value: CIRBP

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGHcLV12-19)

value: ENCBS308BII at ENCODE; https://www.encodeproject.org/ENCBS308BII/


title: microRNA-seq from layer of hippocampus (ENCLB334KOH)

description:
https://www.encodeproject.org/experiments/ENCSR436GZP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation WT female mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR436GZP
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB334KOH
size range: <30

source_name: Mus musculus strain B6NCrl layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: Control hippo Female

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS271YAL at ENCODE; https://www.encodeproject.org/ENCBS271YAL/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA-seq from adrenal gland (ENCLB143MYR)

description:
https://www.encodeproject.org/experiments/ENCSR424VMF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND4 female adrenals microRNA-seq from Mortazavi
experiment encode accession: ENCSR424VMF
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-02-13
lab: Ali Mortazavi, UCI
library encode accession: ENCLB143MYR
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (4 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND4 Female 04 adrenal gland for Wold core

value: female

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS118MVG at ENCODE; https://www.encodeproject.org/ENCBS118MVG/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: CRISPR RNA-seq from HepG2 (ENCLB874EUT)

description:
https://www.encodeproject.org/experiments/ENCSR005RUR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SNRPC. (SNRPC-BGHcLV22)
experiment encode accession: ENCSR005RUR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB874EUT
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 SNRPC

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8e9919de-02f3-47f8-aec8-ae118c0c9edb/@@download/attachment/L-SNRPC-BGHcLV22-54.pdf

value: SNRPC

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SNRPC. (SNRPC-BGHcLV22-54)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS360XRD at ENCODE; https://www.encodeproject.org/ENCBS360XRD/

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


title: CRISPR RNA-seq from HepG2 (ENCLB101YNN)

description:
https://www.encodeproject.org/experiments/ENCSR002NQQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT10. (CNOT10-BGHcLV22)
experiment encode accession: ENCSR002NQQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB101YNN
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/ee326426-fed9-4149-b4e8-3c55879df711/@@download/attachment/L-CNOT10-BGHcLV22-9.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT10. (CNOT10-BGHcLV22-9)

value: ENCBS279OVC at ENCODE; https://www.encodeproject.org/ENCBS279OVC/


title: CRISPR RNA-seq from HepG2 (ENCLB450TMT)

description:
https://www.encodeproject.org/experiments/ENCSR005RUR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SNRPC. (SNRPC-BGHcLV22)
experiment encode accession: ENCSR005RUR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB450TMT
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/a4776ca9-ddce-4b09-9454-e18fe05158a9/@@download/attachment/L-SNRPC-BGHcLV22-53.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SNRPC. (SNRPC-BGHcLV22-53)

value: ENCBS909DXM at ENCODE; https://www.encodeproject.org/ENCBS909DXM/


title: total RNA-seq from neutrophil (ENCLB811QCE)

description:
https://www.encodeproject.org/experiments/ENCSR074WOD/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse neutrophil total RNA scriptseqv2 RNA-seq
experiment encode accession: ENCSR074WOD
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-12-01
lab: Ross Hardison, PennState
library encode accession: ENCLB811QCE
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J adult (5-6 weeks) neutrophil primary cell

value: neutrophil

value: primary cell

value: neutrophils from peripheral blood

value: not collected

value: adult

value: 5-6 week

value: Ross Hardison, PennState

value: David Bodine

value: ENCBS622TZA at ENCODE; https://www.encodeproject.org/ENCBS622TZA/

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


title: total RNA-seq from neutrophil (ENCLB090CXJ)

description:
https://www.encodeproject.org/experiments/ENCSR074WOD/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse neutrophil total RNA scriptseqv2 RNA-seq
experiment encode accession: ENCSR074WOD
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-12-01
lab: Ross Hardison, PennState
library encode accession: ENCLB090CXJ
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: ENCBS562NSP at ENCODE; https://www.encodeproject.org/ENCBS562NSP/


title: microRNA-seq from layer of hippocampus (ENCLB853LQU)

description:
https://www.encodeproject.org/experiments/ENCSR659HKO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD female mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR659HKO
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB853LQU
size range: <30

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: 5xFAD hippo het Female

value: unknown

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS418KFY at ENCODE; https://www.encodeproject.org/ENCBS418KFY/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: CRISPR RNA-seq from HepG2 (ENCLB138IUC)

description:
https://www.encodeproject.org/experiments/ENCSR202SRN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PARP1. (PARP1-BGHcLV14)
experiment encode accession: ENCSR202SRN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB138IUC
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 PARP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c2a4cfe6-6554-46e1-91ff-8b853dc953f0/@@download/attachment/L-PARP1-BGHcLV14-49.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PARP1. (PARP1-BGHcLV14-49)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS065JLX at ENCODE; https://www.encodeproject.org/ENCBS065JLX/

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


title: Bru-seq from IMR-90 (ENCLB678IIT)

description:
https://www.encodeproject.org/experiments/ENCSR103IHW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR103IHW
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB678IIT
size range: 400-500

source_name: Homo sapiens IMR-90 cell line

value: female

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ENCBS874PDI at ENCODE; https://www.encodeproject.org/ENCBS874PDI/

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


title: microRNA-seq from layer of hippocampus (ENCLB294QUX)

description:
https://www.encodeproject.org/experiments/ENCSR751IHR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD male mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR751IHR
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB294QUX
size range: <30

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax adult (8 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: 5xFAD hippo 8 mo Male

value: not collected

value: adult

value: 8 month

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS772JNS at ENCODE; https://www.encodeproject.org/ENCBS772JNS/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: CRISPR RNA-seq from HepG2 (ENCLB589LLZ)

description:
https://www.encodeproject.org/experiments/ENCSR005UDT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ERN1. (ERN1-BGHcLV18)
experiment encode accession: ENCSR005UDT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB589LLZ
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/0dc7f378-bc3d-4c6b-b7b3-52e951466fac/@@download/attachment/L-ERN1-BGHcLV18-17.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ERN1. (ERN1-BGHcLV18-17)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS617GJQ at ENCODE; https://www.encodeproject.org/ENCBS617GJQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB601VXU)

description:
https://www.encodeproject.org/experiments/ENCSR029VGU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DHX57. (DHX57-BGHcLV18)
experiment encode accession: ENCSR029VGU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB601VXU
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 DHX57

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/39d35ecf-6dd5-4e6a-aa63-80ac74f46468/@@download/attachment/L-DHX57-BGHcLV18-11.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DHX57. (DHX57-BGHcLV18-11)

value: ENCBS409OZE at ENCODE; https://www.encodeproject.org/ENCBS409OZE/


title: microRNA-seq from cerebral cortex (ENCLB611HTT)

description:
https://www.encodeproject.org/experiments/ENCSR059NOB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation WT female mouse cerebral cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR059NOB
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB611HTT
size range: <30

source_name: Mus musculus strain B6NCrl cerebral cortex tissue

value: cerebral cortex

value: tissue

value: Control cortex Female

value: not collected

value: unknown

value: ENCBS417IYY at ENCODE; https://www.encodeproject.org/ENCBS417IYY/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: CRISPR RNA-seq from K562 (ENCLB181LLL)

description:
https://www.encodeproject.org/experiments/ENCSR015KGT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV08)
experiment encode accession: ENCSR015KGT
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB181LLL
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/bb60422e-f9c2-4957-9207-4102162b5650/@@download/attachment/L-NT-BGKcLV08-1.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non -target. (NT-BGKcLV08-1)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS671ALY at ENCODE; https://www.encodeproject.org/ENCBS671ALY/

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


title: microRNA-seq from cerebral cortex (ENCLB298NTV)

description:
https://www.encodeproject.org/experiments/ENCSR036UMN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD female mouse cerebral cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR036UMN
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB298NTV
size range: <30

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax cerebral cortex tissue

value: 5xFAD cortex het Female

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS172LSS at ENCODE; https://www.encodeproject.org/ENCBS172LSS/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: CRISPR RNA-seq from HepG2 (ENCLB689GOM)

description:
https://www.encodeproject.org/experiments/ENCSR202SRN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PARP1. (PARP1-BGHcLV14)
experiment encode accession: ENCSR202SRN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB689GOM
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/42e35aa1-ad31-4f8b-9050-bafa7c1d210b/@@download/attachment/L-PARP1-BGHcLV14-50.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PARP1. (PARP1-BGHcLV14-50)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS700LBH at ENCODE; https://www.encodeproject.org/ENCBS700LBH/

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