title: CRISPR RNA-seq from HepG2 (ENCLB769MQL)

description:
https://www.encodeproject.org/experiments/ENCSR548OTL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against YBX1. (YBX1-BGHcLV16)
experiment encode accession: ENCSR548OTL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB769MQL
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/ab739eaf-a4b4-4e09-87da-e1485a110586/@@download/attachment/L-YBX1-BGHcLV16-62.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against YBX1. (YBX1-BGHcLV16-62)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS856DYN at ENCODE; https://www.encodeproject.org/ENCBS856DYN/

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


title: CRISPR RNA-seq from K562 (ENCLB263GGR)

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/ENCSR455VFL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GNL3. (GNL3-BGKcLV08)
experiment encode accession: ENCSR455VFL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB263GGR
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting GNL3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a6fe40ac-b088-4a45-839c-24cc50ed3c92/@@download/attachment/L-GNL3-BGKcLV08-93.pdf

tag: antibody

tag: line

tag: description

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GNL3. (GNL3-BGKcLV08-93)

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Brenton Graveley, UConn

tag: source

value: ATCC

tag: link

value: ENCBS012JTK at ENCODE; https://www.encodeproject.org/ENCBS012JTK/

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


title: CRISPR RNA-seq from K562 (ENCLB955YSA)

description:
https://www.encodeproject.org/experiments/ENCSR452KAP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGKcLV11)
experiment encode accession: ENCSR452KAP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB955YSA
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 CIRBP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fb3526a5-5644-403e-b835-dc7f1e3e9272/@@download/attachment/L-CIRBP-BGKcLV11-34.pdf

value: CIRBP

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGKcLV11-34)

value: ENCBS720APO at ENCODE; https://www.encodeproject.org/ENCBS720APO/


title: Control eCLIP from K562 (ENCLB235RVW)

description:
https://www.encodeproject.org/experiments/ENCSR103HDM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against PHF6
experiment encode accession: ENCSR103HDM
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB235RVW
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

tag: passage number

value: Gene Yeo, UCSD

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

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB753WQP)

description:
https://www.encodeproject.org/experiments/ENCSR455KXW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC10. (EXOSC10-BGHcLV22)
experiment encode accession: ENCSR455KXW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB753WQP
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 EXOSC10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f7a52bf6-8240-41d3-ad44-4e6717c843e1/@@download/attachment/L-EXOSC10-BGHcLV22-24.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC10. (EXOSC10-BGHcLV22-24)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS802NJT at ENCODE; https://www.encodeproject.org/ENCBS802NJT/

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


title: CRISPR RNA-seq from K562 (ENCLB167UXJ)

description:
https://www.encodeproject.org/experiments/ENCSR452KAP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGKcLV11)
experiment encode accession: ENCSR452KAP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB167UXJ
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/7ee1bfb3-86ee-4902-814a-c2e1adb3b6c9/@@download/attachment/L-CIRBP-BGKcLV11-33.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CIRBP. (CIRBP-BGKcLV11-33)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS593KZI at ENCODE; https://www.encodeproject.org/ENCBS593KZI/


title: CRISPR RNA-seq from K562 (ENCLB072KVW)

description:
https://www.encodeproject.org/experiments/ENCSR544ZCR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B1. (SF3B1-BGKcLV11)
experiment encode accession: ENCSR544ZCR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB072KVW
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 SF3B1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c7bdc4d4-1af9-4f8e-930b-c7ef350bc895/@@download/attachment/L-SF3B1-BGKcLV11-93.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B1. (SF3B1-BGKcLV11-93)

value: ENCBS919IYA at ENCODE; https://www.encodeproject.org/ENCBS919IYA/

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


title: CRISPR RNA-seq from HepG2 (ENCLB516VZB)

description:
https://www.encodeproject.org/experiments/ENCSR544LEZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZC3H11A. (ZC3H11A-BGHcLV10)
experiment encode accession: ENCSR544LEZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB516VZB
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 ZC3H11A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bd019672-3956-4d65-804e-589d8d072ceb/@@download/attachment/L-ZC3H11A-BGHcLV10-53.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZC3H11A. (ZC3H11A-BGHcLV10-53)

value: male

value: hepatocellular carcinoma

value: ENCBS941VTX at ENCODE; https://www.encodeproject.org/ENCBS941VTX/


title: CRISPR RNA-seq from HepG2 (ENCLB510CAE)

description:
https://www.encodeproject.org/experiments/ENCSR455KXW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC10. (EXOSC10-BGHcLV22)
experiment encode accession: ENCSR455KXW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB510CAE
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/69a2093c-0978-45ac-bb07-4892f8df163a/@@download/attachment/L-EXOSC10-BGHcLV22-23.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC10. (EXOSC10-BGHcLV22-23)

value: child

value: 15 year

value: ENCBS673PHM at ENCODE; https://www.encodeproject.org/ENCBS673PHM/

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


title: eCLIP from K562 (ENCLB543AYO)

description:
https://www.encodeproject.org/experiments/ENCSR001VAC/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against NOLC1
experiment encode accession: ENCSR001VAC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR009CIV
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB543AYO
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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

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


title: eCLIP from K562 (ENCLB917HUC)

description:
https://www.encodeproject.org/experiments/ENCSR001VAC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against NOLC1
experiment encode accession: ENCSR001VAC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR009CIV
encode release date: 2017-11-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB917HUC
fragmentation methods: see document
size range: 175-300

value: cell line

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB692GYF)

description:
https://www.encodeproject.org/experiments/ENCSR367BWL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APEX1. (APEX1-BGHcLV14)
experiment encode accession: ENCSR367BWL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB692GYF
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 APEX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/242a2499-c085-4455-a61b-6cef8a65388d/@@download/attachment/L-APEX1-BGHcLV14-5.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APEX1. (APEX1-BGHcLV14-5)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS708MXU at ENCODE; https://www.encodeproject.org/ENCBS708MXU/


title: CRISPR RNA-seq from HepG2 (ENCLB024PIE)

description:
https://www.encodeproject.org/experiments/ENCSR367BWL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APEX1. (APEX1-BGHcLV14)
experiment encode accession: ENCSR367BWL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB024PIE
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/0f44a7ed-0fa3-48b3-b529-3807a6d8ca32/@@download/attachment/L-APEX1-BGHcLV14-6.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APEX1. (APEX1-BGHcLV14-6)

value: child

value: 15 year

value: ENCBS208YNU at ENCODE; https://www.encodeproject.org/ENCBS208YNU/

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


title: eCLIP from K562 (ENCLB248OFU)

description:
https://www.encodeproject.org/experiments/ENCSR001KKZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against PHF6
experiment encode accession: ENCSR001KKZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR103HDM
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB248OFU
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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


title: CRISPR RNA-seq from HepG2 (ENCLB879NOS)

description:
https://www.encodeproject.org/experiments/ENCSR544LEZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZC3H11A. (ZC3H11A-BGHcLV10)
experiment encode accession: ENCSR544LEZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB879NOS
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/2d0479a7-b3bd-4e1b-beca-cc8c15a77a09/@@download/attachment/L-ZC3H11A-BGHcLV10-54.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZC3H11A. (ZC3H11A-BGHcLV10-54)

value: ENCBS343EZL at ENCODE; https://www.encodeproject.org/ENCBS343EZL/


title: CRISPR RNA-seq from K562 (ENCLB682HHA)

description:
https://www.encodeproject.org/experiments/ENCSR544ZCR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B1. (SF3B1-BGKcLV11)
experiment encode accession: ENCSR544ZCR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB682HHA
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/e7acb858-8d81-4bd9-92f5-a13226e4241e/@@download/attachment/L-SF3B1-BGKcLV11-94.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B1. (SF3B1-BGKcLV11-94)

value: Brenton Graveley, UConn

value: ENCBS623CLM at ENCODE; https://www.encodeproject.org/ENCBS623CLM/

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


title: CRISPR RNA-seq from K562 (ENCLB770PJA)

description:
https://www.encodeproject.org/experiments/ENCSR359ICP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DHX57. (DHX57-BGKcLV17)
experiment encode accession: ENCSR359ICP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB770PJA
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 DHX57

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/62ed8101-c12d-42e3-a0a5-bebdc094cbb9/@@download/attachment/L-DHX57-BGKcLV17-12.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DHX57. (DHX57-BGKcLV17-12)

value: ATCC

value: ENCBS317WWB at ENCODE; https://www.encodeproject.org/ENCBS317WWB/


title: eCLIP from K562 (ENCLB665OQP)

description:
https://www.encodeproject.org/experiments/ENCSR202HKN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against WDR3
experiment encode accession: ENCSR202HKN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR033FWT
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB665OQP
fragmentation methods: see document
size range: 175-300

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

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


title: microRNA-seq from osteocyte (ENCLB615SYZ)

description:
https://www.encodeproject.org/experiments/ENCSR009LCI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation H9 derived osteocytes microRNA-seq from Mortazavi
experiment encode accession: ENCSR009LCI
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB615SYZ
size range: <30

source_name: Homo sapiens female embryo (5 days) osteocyte in vitro differentiated cells originated from osteocyte

value: osteocyte

value: in vitro differentiated cells

value: WA09 derived osteocytes

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS572IFJ at ENCODE; https://www.encodeproject.org/ENCBS572IFJ/

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


title: eCLIP from K562 (ENCLB256CGZ)

description:
https://www.encodeproject.org/experiments/ENCSR001KKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against PHF6
experiment encode accession: ENCSR001KKZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR103HDM
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB256CGZ
fragmentation methods: see document
size range: 175-300

value: cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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


title: CRISPR RNA-seq from K562 (ENCLB471ZZN)

description:
https://www.encodeproject.org/experiments/ENCSR356PRP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ELAVL1. (ELAVL1-BGKcLV13)
experiment encode accession: ENCSR356PRP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB471ZZN
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 ELAVL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fea11d00-4e51-4f69-a946-f9c7f3e5d84a/@@download/attachment/L-ELAVL1-BGKcLV13-40.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ELAVL1. (ELAVL1-BGKcLV13-40)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS137LOR at ENCODE; https://www.encodeproject.org/ENCBS137LOR/

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


title: microRNA-seq from neural crest cell (ENCLB178PGI)

description:
https://www.encodeproject.org/experiments/ENCSR008VSP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation H9 derived neural crest cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR008VSP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB178PGI
size range: <30

source_name: Homo sapiens female embryo (5 days) neural crest in vitro differentiated cells originated from neural crest cell

value: neural crest cell

value: in vitro differentiated cells

value: WA09 derived neural crest cells

value: healthy

value: embryonic

value: 5 day

value: ENCBS417JEU at ENCODE; https://www.encodeproject.org/ENCBS417JEU/


title: TF ChIP-seq from K562 (ENCLB155DLV)

description:
https://www.encodeproject.org/experiments/ENCSR003GUC/
***************
biological replicate number: 1
technical replicate number: 1
description: E4F1 ChIP-seq on human K562
experiment encode accession: ENCSR003GUC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR192TOE, ENCSR233HNT
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB155DLV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

library_source: genomic

molecule: genomic DNA

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

value: cell line

value: female

value: adult

value: Michael Snyder, Stanford

value: ENCBS063SBN at ENCODE; https://www.encodeproject.org/ENCBS063SBN/


title: CRISPR RNA-seq from HepG2 (ENCLB971OMN)

description:
https://www.encodeproject.org/experiments/ENCSR444IOJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MORC2. (MORC2-BGHcLV20)
experiment encode accession: ENCSR444IOJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB971OMN
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 MORC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c3647e86-3b7a-48a4-91d2-e97ab6c9d177/@@download/attachment/L-MORC2-BGHcLV20-13.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MORC2. (MORC2-BGHcLV20-13)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS581RKB at ENCODE; https://www.encodeproject.org/ENCBS581RKB/

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


title: CRISPR RNA-seq from K562 (ENCLB384SYD)

description:
https://www.encodeproject.org/experiments/ENCSR354DVY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC40. (CDC40-BGKcLV08)
experiment encode accession: ENCSR354DVY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB384SYD
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 CDC40

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/29838b2e-2564-4a53-a873-baa67fcff9b3/@@download/attachment/L-CDC40-BGKcLV08-3.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC40. (CDC40-BGKcLV08-3)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS050VON at ENCODE; https://www.encodeproject.org/ENCBS050VON/

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


title: CRISPR RNA-seq from K562 (ENCLB798YHX)

description:
https://www.encodeproject.org/experiments/ENCSR354DVY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC40. (CDC40-BGKcLV08)
experiment encode accession: ENCSR354DVY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB798YHX
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/ec07f3b2-ba53-4692-87da-f1ea7dd10000/@@download/attachment/L-CDC40-BGKcLV08-4.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC40. (CDC40-BGKcLV08-4)

value: female

value: adult

value: ENCBS194YRU at ENCODE; https://www.encodeproject.org/ENCBS194YRU/


title: CRISPR RNA-seq from K562 (ENCLB471AIY)

description:
https://www.encodeproject.org/experiments/ENCSR353OQP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ERO1L. (ERO1L-BGKcLV15)
experiment encode accession: ENCSR353OQP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB471AIY
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 ERO1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bff76513-99dd-4788-a5d5-d2a234134b31/@@download/attachment/L-NSUN4-BGKcLV15-44.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ERO1L. (ERO1L-BGKcLV15-48)

value: ENCBS590BHJ at ENCODE; https://www.encodeproject.org/ENCBS590BHJ/


title: total RNA-seq from WTC11 (ENCLB872CWU)

description:
https://www.encodeproject.org/experiments/ENCSR450EXF/
***************
biological replicate number: 2
technical replicate number: 1
description: WTC11
experiment encode accession: ENCSR450EXF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB872CWU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens WTC11 cell line

value: Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal

value: male

value: 30 year

value: Barbara Wold, Caltech

value: Yiing Lin, MD, PhD

value: ENCBS593PKA at ENCODE; https://www.encodeproject.org/ENCBS593PKA/

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


title: CRISPR RNA-seq from HepG2 (ENCLB506KZL)

description:
https://www.encodeproject.org/experiments/ENCSR439TMT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RYBP. (RYBP-BGHcLV20)
experiment encode accession: ENCSR439TMT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB506KZL
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 RYBP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2bea0558-f472-4318-9d4e-7f5c9772c550/@@download/attachment/L-RYBP-BGHcLV20-32.pdf

value: RYBP

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RYBP. (RYBP-BGHcLV20-32)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS164VMA at ENCODE; https://www.encodeproject.org/ENCBS164VMA/

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


title: CRISPR RNA-seq from K562 (ENCLB001GKP)

description:
https://www.encodeproject.org/experiments/ENCSR359ICP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DHX57. (DHX57-BGKcLV17)
experiment encode accession: ENCSR359ICP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB001GKP
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/b4f16fbe-348d-46e6-82f9-d9fce5c3f0c5/@@download/attachment/L-DHX57-BGKcLV17-11.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DHX57. (DHX57-BGKcLV17-11)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS802JLM at ENCODE; https://www.encodeproject.org/ENCBS802JLM/

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


title: CRISPR RNA-seq from K562 (ENCLB661BPM)

description:
https://www.encodeproject.org/experiments/ENCSR439CUH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PPP1R10. (PPP1R10-BGKcLV17)
experiment encode accession: ENCSR439CUH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB661BPM
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 PPP1R10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/99724649-de37-4df0-b01b-b36bfc4cd2e5/@@download/attachment/L-PPP1R10-BGKcLV17-37.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PPP1R10. (PPP1R10-BGKcLV17-37)

value: ENCBS599LWW at ENCODE; https://www.encodeproject.org/ENCBS599LWW/


title: total RNA-seq from WTC11 (ENCLB045XLK)

description:
https://www.encodeproject.org/experiments/ENCSR450EXF/
***************
biological replicate number: 1
technical replicate number: 1
description: WTC11
experiment encode accession: ENCSR450EXF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB045XLK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal

value: male

value: 30 year

value: Barbara Wold, Caltech

value: Yiing Lin, MD, PhD

value: ENCBS944CBA at ENCODE; https://www.encodeproject.org/ENCBS944CBA/

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


title: CRISPR RNA-seq from K562 (ENCLB056BLZ)

description:
https://www.encodeproject.org/experiments/ENCSR539PFV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS6. (RPS6-BGKcLV13)
experiment encode accession: ENCSR539PFV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB056BLZ
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 RPS6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e50e6564-3f60-48dc-bed0-4c0f883a110b/@@download/attachment/L-RPS6-BGKcLV13-67.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS6. (RPS6-BGKcLV13-67)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS804XVO at ENCODE; https://www.encodeproject.org/ENCBS804XVO/


title: microRNA-seq from spleen (ENCLB188SQV)

description:
https://www.encodeproject.org/experiments/ENCSR005GLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 spleen microRNA-seq from Mortazavi
experiment encode accession: ENCSR005GLZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB188SQV
size range: <30

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

value: spleen

value: tissue

value: female

value: adult

value: 59 year

value: Michael Snyder, Stanford

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

value: ENCBS078NTB at ENCODE; https://www.encodeproject.org/ENCBS078NTB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB603JLY)

description:
https://www.encodeproject.org/experiments/ENCSR532IHF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM19. (RBM19-BGHcLV20)
experiment encode accession: ENCSR532IHF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB603JLY
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 RBM19

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/534b6bfb-1ccf-4e03-91f8-f7c29803a8f9/@@download/attachment/L-RBM19-BGHcLV20-26.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM19. (RBM19-BGHcLV20-26)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS637PVZ at ENCODE; https://www.encodeproject.org/ENCBS637PVZ/

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


title: CRISPR RNA-seq from K562 (ENCLB566GTR)

description:
https://www.encodeproject.org/experiments/ENCSR356PRP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ELAVL1. (ELAVL1-BGKcLV13)
experiment encode accession: ENCSR356PRP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB566GTR
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/4e9c7940-fc77-4b60-8179-3382de68f7a9/@@download/attachment/L-ELAVL1-BGKcLV13-39.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ELAVL1. (ELAVL1-BGKcLV13-39)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS929OHW at ENCODE; https://www.encodeproject.org/ENCBS929OHW/

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


title: CRISPR RNA-seq from HepG2 (ENCLB006SFL)

description:
https://www.encodeproject.org/experiments/ENCSR428WVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DICER1. (DICER1-BGHcLV16)
experiment encode accession: ENCSR428WVZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB006SFL
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 DICER1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/239b696b-1014-4cd4-9a14-02cac375e67d/@@download/attachment/L-DICER1-BGHcLV16-14.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DICER1. (DICER1-BGHcLV16-14)

value: ENCBS384YKN at ENCODE; https://www.encodeproject.org/ENCBS384YKN/


title: CRISPR RNA-seq from K562 (ENCLB239NUK)

description:
https://www.encodeproject.org/experiments/ENCSR439CUH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PPP1R10. (PPP1R10-BGKcLV17)
experiment encode accession: ENCSR439CUH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB239NUK
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/3ddaee67-3fca-4cb5-a8f8-d7e16db3edf3/@@download/attachment/L-PPP1R10-BGKcLV17-38.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PPP1R10. (PPP1R10-BGKcLV17-38)

value: female

value: adult

value: ENCBS050HZB at ENCODE; https://www.encodeproject.org/ENCBS050HZB/


title: microRNA-seq from neural crest cell (ENCLB015QZI)

description:
https://www.encodeproject.org/experiments/ENCSR008VSP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation H9 derived neural crest cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR008VSP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB015QZI
size range: <30

value: neural crest cell

value: in vitro differentiated cells

value: WA09 derived neural crest cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS200JOD at ENCODE; https://www.encodeproject.org/ENCBS200JOD/

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


title: CRISPR RNA-seq from HepG2 (ENCLB637DRH)

description:
https://www.encodeproject.org/experiments/ENCSR426JCD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GSK3B. (GSK3B-BGHcLV16)
experiment encode accession: ENCSR426JCD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB637DRH
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 GSK3B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dc149b5a-9e7e-4b1c-9bc9-00fa413cf7d1/@@download/attachment/L-GSK3B-BGHcLV16-32.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GSK3B. (GSK3B-BGHcLV16-32)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS654EHE at ENCODE; https://www.encodeproject.org/ENCBS654EHE/

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


title: total RNA-seq from WTC11 (ENCLB480EGW)

description:
https://www.encodeproject.org/experiments/ENCSR450EXF/
***************
biological replicate number: 3
technical replicate number: 1
description: WTC11
experiment encode accession: ENCSR450EXF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB480EGW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal

value: adult

value: 30 year

value: Barbara Wold, Caltech

value: Yiing Lin, MD, PhD

value: ENCBS474NOC at ENCODE; https://www.encodeproject.org/ENCBS474NOC/

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


title: CRISPR RNA-seq from HepG2 (ENCLB115VAG)

description:
https://www.encodeproject.org/experiments/ENCSR444IOJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MORC2. (MORC2-BGHcLV20)
experiment encode accession: ENCSR444IOJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB115VAG
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/0dd8b28a-d79e-4156-89c4-25c8f3903727/@@download/attachment/L-MORC2-BGHcLV20-14.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MORC2. (MORC2-BGHcLV20-14)

value: ENCBS300KME at ENCODE; https://www.encodeproject.org/ENCBS300KME/


title: CRISPR RNA-seq from K562 (ENCLB870EKW)

description:
https://www.encodeproject.org/experiments/ENCSR353OQP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ERO1L. (ERO1L-BGKcLV15)
experiment encode accession: ENCSR353OQP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB870EKW
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/3a6dc1fc-e26d-4137-9b60-51c7d60b199c/@@download/attachment/L-NSUN4-BGKcLV15-43.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ERO1L. (ERO1L-BGKcLV15-47)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS499VIT at ENCODE; https://www.encodeproject.org/ENCBS499VIT/

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


title: CRISPR RNA-seq from K562 (ENCLB367WDN)

description:
https://www.encodeproject.org/experiments/ENCSR529UYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CSTF1. (CSTF1-BGKcLV21)
experiment encode accession: ENCSR529UYQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB367WDN
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 CSTF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b12ba35b-d9cd-49f8-90d9-35fc9f281e3e/@@download/attachment/L-CSTF1-BGKcLV21-13.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CSTF1. (CSTF1-BGKcLV21-13)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS796QWZ at ENCODE; https://www.encodeproject.org/ENCBS796QWZ/


title: CRISPR RNA-seq from K562 (ENCLB381ZQE)

description:
https://www.encodeproject.org/experiments/ENCSR529UYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CSTF1. (CSTF1-BGKcLV21)
experiment encode accession: ENCSR529UYQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB381ZQE
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/34f11e51-528a-4ef4-bdc0-3316de34e49f/@@download/attachment/L-CSTF1-BGKcLV21-14.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CSTF1. (CSTF1-BGKcLV21-14)

value: adult

value: ENCBS556WES at ENCODE; https://www.encodeproject.org/ENCBS556WES/


title: CRISPR RNA-seq from K562 (ENCLB396RFQ)

description:
https://www.encodeproject.org/experiments/ENCSR528YVC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF5. (SRSF5-BGKcLV11)
experiment encode accession: ENCSR528YVC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB396RFQ
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 SRSF5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/99d2fc17-418b-48a7-9550-44383cf8afd5/@@download/attachment/L-SRSF5-BGKcLV11-95.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF5. (SRSF5-BGKcLV11-95)

value: ENCBS778ZTA at ENCODE; https://www.encodeproject.org/ENCBS778ZTA/


title: CRISPR RNA-seq from K562 (ENCLB409WOH)

description:
https://www.encodeproject.org/experiments/ENCSR443BEF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGKcLV15)
experiment encode accession: ENCSR443BEF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB409WOH
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 CD3EAP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6b3d6e4e-0066-4606-bc49-419a849d3512/@@download/attachment/L-CD3EAP-BGKcLV15-9.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGKcLV15-10)

value: ENCBS227RMN at ENCODE; https://www.encodeproject.org/ENCBS227RMN/


title: CRISPR RNA-seq from K562 (ENCLB171MSR)

description:
https://www.encodeproject.org/experiments/ENCSR528YVC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF5. (SRSF5-BGKcLV11)
experiment encode accession: ENCSR528YVC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB171MSR
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/f57c2720-b73b-4a44-ab95-3dfba959e5fb/@@download/attachment/L-SRSF5-BGKcLV11-96.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF5. (SRSF5-BGKcLV11-96)

value: female

value: ENCBS486UHL at ENCODE; https://www.encodeproject.org/ENCBS486UHL/


title: CRISPR RNA-seq from K562 (ENCLB203IGX)

description:
https://www.encodeproject.org/experiments/ENCSR539PFV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS6. (RPS6-BGKcLV13)
experiment encode accession: ENCSR539PFV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB203IGX
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/0db3f77d-b234-4c38-8b63-923a10605e3c/@@download/attachment/L-RPS6-BGKcLV13-68.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS6. (RPS6-BGKcLV13-68)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS044FWN at ENCODE; https://www.encodeproject.org/ENCBS044FWN/


title: CRISPR RNA-seq from K562 (ENCLB963ZFF)

description:
https://www.encodeproject.org/experiments/ENCSR443BEF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGKcLV15)
experiment encode accession: ENCSR443BEF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB963ZFF
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/a6ddc250-a8a3-4f16-805a-164831712613/@@download/attachment/L-CD3EAP-BGKcLV15-10.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGKcLV15-9)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS291VMZ at ENCODE; https://www.encodeproject.org/ENCBS291VMZ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB697ZVK)

description:
https://www.encodeproject.org/experiments/ENCSR429OUR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX20. (DDX20-BGHcLV10)
experiment encode accession: ENCSR429OUR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB697ZVK
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 DDX20

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ea8bbbb4-2424-4fbe-8d90-f03aab9325b4/@@download/attachment/L-DDX20-BGHcLV10-19.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX20. (DDX20-BGHcLV10-19)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS292SMV at ENCODE; https://www.encodeproject.org/ENCBS292SMV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB366WJG)

description:
https://www.encodeproject.org/experiments/ENCSR528LDT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PTGES3. (PTGES3-BGHcLV16)
experiment encode accession: ENCSR528LDT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB366WJG
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 PTGES3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/eee0c5d5-5809-4bb8-a858-7e4313b5f39b/@@download/attachment/L-PTGES3-BGHcLV16-46.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PTGES3. (PTGES3-BGHcLV16-46)

value: ENCBS515RKO at ENCODE; https://www.encodeproject.org/ENCBS515RKO/


title: CRISPR RNA-seq from HepG2 (ENCLB781HVX)

description:
https://www.encodeproject.org/experiments/ENCSR528LDT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PTGES3. (PTGES3-BGHcLV16)
experiment encode accession: ENCSR528LDT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB781HVX
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/15e75312-3a4c-4148-af38-77f7c38831e4/@@download/attachment/L-PTGES3-BGHcLV16-45.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PTGES3. (PTGES3-BGHcLV16-45)

value: ENCBS686VBD at ENCODE; https://www.encodeproject.org/ENCBS686VBD/


title: CRISPR RNA-seq from K562 (ENCLB049DBT)

description:
https://www.encodeproject.org/experiments/ENCSR427KVG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGKcLV23)
experiment encode accession: ENCSR427KVG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB049DBT
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 BARD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7dc9de69-40f8-4d9c-81b0-8b573a2a1175/@@download/attachment/L-BARD1-BGKcLV23-21.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGKcLV23-21)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS024RMA at ENCODE; https://www.encodeproject.org/ENCBS024RMA/


title: CRISPR RNA-seq from K562 (ENCLB312WPF)

description:
https://www.encodeproject.org/experiments/ENCSR005JBU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV04-C)
experiment encode accession: ENCSR005JBU
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-04-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB312WPF
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/e6251d7d-eefd-4476-8069-28c7839fddd5/@@download/attachment/L-NT-BGKcLV04-1C.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT_BGKcLV04-1)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS981XHM at ENCODE; https://www.encodeproject.org/ENCBS981XHM/

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


title: CRISPR RNA-seq from HepG2 (ENCLB327TAV)

description:
https://www.encodeproject.org/experiments/ENCSR416YFB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAFB. (SAFB-BGHcLV09)
experiment encode accession: ENCSR416YFB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB327TAV
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 SAFB

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ce6ba82e-5739-4e95-bfaa-b9462e26359f/@@download/attachment/L-SAFB-BGHcLV09-17.pdf

value: SAFB

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAFB. (SAFB-BGHcLV09-17)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS640FZR at ENCODE; https://www.encodeproject.org/ENCBS640FZR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB764LBO)

description:
https://www.encodeproject.org/experiments/ENCSR416YFB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAFB. (SAFB-BGHcLV09)
experiment encode accession: ENCSR416YFB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR300EBW
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB764LBO
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/8f967857-fd1b-4c29-b75b-a9ef085c2835/@@download/attachment/L-SAFB-BGHcLV09-18.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAFB. (SAFB-BGHcLV09-18)

value: ENCBS080ZER at ENCODE; https://www.encodeproject.org/ENCBS080ZER/


title: CRISPR RNA-seq from K562 (ENCLB856FIO)

description:
https://www.encodeproject.org/experiments/ENCSR416WTE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CACTIN. (CACTIN-BGKcLV23)
experiment encode accession: ENCSR416WTE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB856FIO
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 CACTIN

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ce7cf015-12a7-485f-bbba-3744ecb5c511/@@download/attachment/L-CACTIN-BGKcLV23-27.pdf

value: CACTIN

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CACTIN. (CACTIN-BGKcLV23-27)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS763TFO at ENCODE; https://www.encodeproject.org/ENCBS763TFO/


title: CRISPR RNA-seq from HepG2 (ENCLB155NFZ)

description:
https://www.encodeproject.org/experiments/ENCSR439TMT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RYBP. (RYBP-BGHcLV20)
experiment encode accession: ENCSR439TMT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB155NFZ
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/327298d7-53c5-41e1-a54a-c07291d51fac/@@download/attachment/L-RYBP-BGHcLV20-31.pdf

value: RYBP

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RYBP. (RYBP-BGHcLV20-31)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS537DVW at ENCODE; https://www.encodeproject.org/ENCBS537DVW/


title: CRISPR RNA-seq from K562 (ENCLB232QWZ)

description:
https://www.encodeproject.org/experiments/ENCSR416NPL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CXXC1. (CXXC1-BGKcLV17)
experiment encode accession: ENCSR416NPL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2021-04-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB232QWZ
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 CXXC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7599e5f7-3eb9-405e-8502-d1b9ac247813/@@download/attachment/L-CXXC1-BGKcLV17-8.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CXXC1. (CXXC1-BGKcLV17-8)

value: ENCBS048SGI at ENCODE; https://www.encodeproject.org/ENCBS048SGI/

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


title: CRISPR RNA-seq from K562 (ENCLB874GJR)

description:
https://www.encodeproject.org/experiments/ENCSR423ERM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DCP2. (DCP2-BGKcLV21)
experiment encode accession: ENCSR423ERM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB874GJR
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 DCP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c13c3cbf-98f0-4046-9334-8e1bb15767f6/@@download/attachment/L-DCP2-BGKcLV21-16.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DCP2. (DCP2-BGKcLV21-16)

value: ENCBS340MGE at ENCODE; https://www.encodeproject.org/ENCBS340MGE/


title: CRISPR RNA-seq from HepG2 (ENCLB615FAR)

description:
https://www.encodeproject.org/experiments/ENCSR333OGA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GEMIN2. (GEMIN2-BGHcLV18)
experiment encode accession: ENCSR333OGA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB615FAR
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 GEMIN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1849e400-4dce-4c30-982b-85f96963cc9f/@@download/attachment/L-GEMIN2-BGHcLV18-25.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GEMIN2. (GEMIN2-BGHcLV18-25)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS940CPB at ENCODE; https://www.encodeproject.org/ENCBS940CPB/

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


title: microRNA-seq from left ventricle myocardium superior (ENCLB620QPX)

description:
https://www.encodeproject.org/experiments/ENCSR200VKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 left ventricle superior microRNA-seq from Mortazavi
experiment encode accession: ENCSR200VKZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB620QPX
size range: <30

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

value: left ventricle myocardium superior

value: tissue

value: Superior wall of left ventricle.

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS165LTN at ENCODE; https://www.encodeproject.org/ENCBS165LTN/

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


title: CRISPR RNA-seq from K562 (ENCLB736ZUT)

description:
https://www.encodeproject.org/experiments/ENCSR416NPL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CXXC1. (CXXC1-BGKcLV17)
experiment encode accession: ENCSR416NPL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2021-04-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB736ZUT
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/e3053f89-900c-4d7a-8a73-88bf01afbd85/@@download/attachment/L-CXXC1-BGKcLV17-7.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CXXC1. (CXXC1-BGKcLV17-7)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS312HQY at ENCODE; https://www.encodeproject.org/ENCBS312HQY/

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


title: CRISPR RNA-seq from K562 (ENCLB931NBC)

description:
https://www.encodeproject.org/experiments/ENCSR521WCW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX42. (DDX42-BGKcLV08)
experiment encode accession: ENCSR521WCW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB931NBC
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 DDX42

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3513742a-13f8-4b4f-b49d-ca45c6c7aecf/@@download/attachment/L-DDX42-BGKcLV08-21.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX42. (DDX42-BGKcLV08-21)

value: ENCBS960ZMX at ENCODE; https://www.encodeproject.org/ENCBS960ZMX/


title: CRISPR RNA-seq from K562 (ENCLB973RYA)

description:
https://www.encodeproject.org/experiments/ENCSR423ERM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DCP2. (DCP2-BGKcLV21)
experiment encode accession: ENCSR423ERM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB973RYA
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/385e92ac-9440-4270-8263-4444abd9733c/@@download/attachment/L-DCP2-BGKcLV21-15.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DCP2. (DCP2-BGKcLV21-15)

value: adult

value: ENCBS273URR at ENCODE; https://www.encodeproject.org/ENCBS273URR/


title: CRISPR RNA-seq from HepG2 (ENCLB201RRL)

description:
https://www.encodeproject.org/experiments/ENCSR532IHF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM19. (RBM19-BGHcLV20)
experiment encode accession: ENCSR532IHF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB201RRL
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 RBM19

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/047c6610-6f98-433e-b995-44c2ed8b50e9/@@download/attachment/L-RBM19-BGHcLV20-25.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM19. (RBM19-BGHcLV20-25)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS965FCH at ENCODE; https://www.encodeproject.org/ENCBS965FCH/

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


title: CRISPR RNA-seq from K562 (ENCLB700QMR)

description:
https://www.encodeproject.org/experiments/ENCSR410USU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NOLC1. (NOLC1-BGKcLV08)
experiment encode accession: ENCSR410USU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB700QMR
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 NOLC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/60fc0112-2585-4fd5-ba80-75055e28872a/@@download/attachment/L-NOLC1-BGKcLV08-47.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NOLC1. (NOLC1-BGKcLV08-47)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS087YBZ at ENCODE; https://www.encodeproject.org/ENCBS087YBZ/


title: CRISPR RNA-seq from K562 (ENCLB314FFD)

description:
https://www.encodeproject.org/experiments/ENCSR516TLX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGKcLV17)
experiment encode accession: ENCSR516TLX
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB314FFD
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/57bc7adb-d055-40ed-b934-628549455740/@@download/attachment/L-NT-BGKcLV17-1.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non-target. (NT-BGKcLV17-1)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS935MDR at ENCODE; https://www.encodeproject.org/ENCBS935MDR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB763AYF)

description:
https://www.encodeproject.org/experiments/ENCSR429OUR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX20. (DDX20-BGHcLV10)
experiment encode accession: ENCSR429OUR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB763AYF
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/5e59787f-c150-4cd8-b564-c8eb9138d1fc/@@download/attachment/L-DDX20-BGHcLV10-20.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX20. (DDX20-BGHcLV10-20)

value: male

value: ENCBS223MPM at ENCODE; https://www.encodeproject.org/ENCBS223MPM/


title: CRISPR RNA-seq from K562 (ENCLB878KZJ)

description:
https://www.encodeproject.org/experiments/ENCSR410USU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NOLC1. (NOLC1-BGKcLV08)
experiment encode accession: ENCSR410USU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB878KZJ
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/57ec43ab-4d0e-47e8-a200-ed0a7e684169/@@download/attachment/L-NOLC1-BGKcLV08-48.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NOLC1. (NOLC1-BGKcLV08-48)

value: adult

value: ENCBS147HGT at ENCODE; https://www.encodeproject.org/ENCBS147HGT/


title: CRISPR RNA-seq from K562 (ENCLB798LSA)

description:
https://www.encodeproject.org/experiments/ENCSR516TLX/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGKcLV17)
experiment encode accession: ENCSR516TLX
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB798LSA
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/80ef2e49-8d02-461e-acb3-84da3ca91afa/@@download/attachment/L-NT-BGKcLV17-2.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non-target. (NT-BGKcLV17-2)

value: ENCBS813SYB at ENCODE; https://www.encodeproject.org/ENCBS813SYB/


title: CRISPR RNA-seq from HepG2 (ENCLB339PUP)

description:
https://www.encodeproject.org/experiments/ENCSR324GSI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NCBP1. (NCBP1-BGHcLV10)
experiment encode accession: ENCSR324GSI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB339PUP
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 NCBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/842f5b70-022e-45fe-8f7e-cdc12e029882/@@download/attachment/L-NCBP1-BGHcLV10-25.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NCBP1. (NCBP1-BGHcLV10-25)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS460XAH at ENCODE; https://www.encodeproject.org/ENCBS460XAH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB085WTZ)

description:
https://www.encodeproject.org/experiments/ENCSR324GSI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NCBP1. (NCBP1-BGHcLV10)
experiment encode accession: ENCSR324GSI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB085WTZ
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/2f27adde-216b-45ca-9a1a-d56709f6301c/@@download/attachment/L-NCBP1-BGHcLV10-26.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NCBP1. (NCBP1-BGHcLV10-26)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS798CLM at ENCODE; https://www.encodeproject.org/ENCBS798CLM/


title: CRISPR RNA-seq from HepG2 (ENCLB648PSZ)

description:
https://www.encodeproject.org/experiments/ENCSR428WVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DICER1. (DICER1-BGHcLV16)
experiment encode accession: ENCSR428WVZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB648PSZ
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 DICER1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5a2f35e7-1d1b-4308-91e8-c900a4a08cc5/@@download/attachment/L-DICER1-BGHcLV16-13.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DICER1. (DICER1-BGHcLV16-13)

value: male

value: ENCBS548VNU at ENCODE; https://www.encodeproject.org/ENCBS548VNU/


title: CRISPR RNA-seq from K562 (ENCLB170WJK)

description:
https://www.encodeproject.org/experiments/ENCSR427KVG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGKcLV23)
experiment encode accession: ENCSR427KVG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB170WJK
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/871ab9f9-ea8b-4198-bd3e-8b2d6ba15763/@@download/attachment/L-BARD1-BGKcLV23-22.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGKcLV23-22)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS476NAR at ENCODE; https://www.encodeproject.org/ENCBS476NAR/

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


title: CRISPR RNA-seq from K562 (ENCLB845JQQ)

description:
https://www.encodeproject.org/experiments/ENCSR516EPT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against XRCC6. (XRCC6-BGKcLV15)
experiment encode accession: ENCSR516EPT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB845JQQ
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 XRCC6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f4220539-a827-497f-9fc4-5b067a166dc8/@@download/attachment/L-XRCC6-BGKcLV15-61.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against XRCC6. (XRCC6-BGKcLV15-61)

value: ENCBS954SAF at ENCODE; https://www.encodeproject.org/ENCBS954SAF/


title: CRISPR RNA-seq from HepG2 (ENCLB253SOU)

description:
https://www.encodeproject.org/experiments/ENCSR426JCD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GSK3B. (GSK3B-BGHcLV16)
experiment encode accession: ENCSR426JCD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB253SOU
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 GSK3B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ba6bfe6b-f64d-466e-93b2-0a00c61bc375/@@download/attachment/L-GSK3B-BGHcLV16-31.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GSK3B. (GSK3B-BGHcLV16-31)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS452ZYX at ENCODE; https://www.encodeproject.org/ENCBS452ZYX/

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


title: CRISPR RNA-seq from K562 (ENCLB464IQH)

description:
https://www.encodeproject.org/experiments/ENCSR320IEK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PRPF8. (PRPF8-BGKcLV08)
experiment encode accession: ENCSR320IEK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB464IQH
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 PRPF8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f6326a55-367d-4280-990a-ec538861c500/@@download/attachment/L-PRPF8-BGKcLV08-52.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PRPF8. (PRPF8-BGKcLV08-52)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS235VRF at ENCODE; https://www.encodeproject.org/ENCBS235VRF/


title: CRISPR RNA-seq from K562 (ENCLB422GFB)

description:
https://www.encodeproject.org/experiments/ENCSR335KFN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against METTL3. (METTL3-BGKcLV23)
experiment encode accession: ENCSR335KFN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB422GFB
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 METTL3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4e497ea2-9c04-4dac-b19f-0f8758afb331/@@download/attachment/L-METTL3-BGKcLV23-53.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against METTL3. (METTL3-BGKcLV23-53)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS082RXU at ENCODE; https://www.encodeproject.org/ENCBS082RXU/


title: CRISPR RNA-seq from K562 (ENCLB066CFQ)

description:
https://www.encodeproject.org/experiments/ENCSR320IEK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PRPF8. (PRPF8-BGKcLV08)
experiment encode accession: ENCSR320IEK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB066CFQ
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/5245d1ad-3e10-46f9-83e0-a3070d7f236b/@@download/attachment/L-PRPF8-BGKcLV08-51.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PRPF8. (PRPF8-BGKcLV08-51)

value: 53 year

value: ENCBS820MRK at ENCODE; https://www.encodeproject.org/ENCBS820MRK/

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


title: microRNA-seq from pancreas (ENCLB442TVP)

description:
https://www.encodeproject.org/experiments/ENCSR001HGI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 pancreas microRNA-seq from Mortazavi
experiment encode accession: ENCSR001HGI
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB442TVP
size range: <30

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

value: pancreas

value: tissue

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS193UJO at ENCODE; https://www.encodeproject.org/ENCBS193UJO/

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


title: CRISPR RNA-seq from HepG2 (ENCLB416PXB)

description:
https://www.encodeproject.org/experiments/ENCSR312UYN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF2B3. (EIF2B3-BGHcLV16)
experiment encode accession: ENCSR312UYN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB416PXB
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 EIF2B3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d9e1c155-8f11-4db1-865a-1f7559caa109/@@download/attachment/L-EIF2B3-BGHcLV16-23.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF2B3. (EIF2B3-BGHcLV16-23)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS691PWT at ENCODE; https://www.encodeproject.org/ENCBS691PWT/

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


title: microRNA-seq from HepG2 (ENCLB418RFI)

description:
https://www.encodeproject.org/experiments/ENCSR201MAS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HepG2 microRNA-seq from Mortazavi
experiment encode accession: ENCSR201MAS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB418RFI
size range: <30

source_name: Homo sapiens HepG2 cell line

value: cell line

value: Mats Ljungman, UMichigan

value: ENCBS365LJQ at ENCODE; https://www.encodeproject.org/ENCBS365LJQ/


title: CRISPR RNA-seq from HepG2 (ENCLB226BJQ)

description:
https://www.encodeproject.org/experiments/ENCSR312VLS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against XRCC6. (XRCC6-BGHcLV16)
experiment encode accession: ENCSR312VLS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB226BJQ
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 XRCC6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/56735030-8f5c-43e9-9360-cfed0fce393a/@@download/attachment/L-XRCC6-BGHcLV16-59.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against XRCC6. (XRCC6-BGHcLV16-59)

value: ENCBS161WQQ at ENCODE; https://www.encodeproject.org/ENCBS161WQQ/


title: CRISPR RNA-seq from HepG2 (ENCLB498HEN)

description:
https://www.encodeproject.org/experiments/ENCSR312UYN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF2B3. (EIF2B3-BGHcLV16)
experiment encode accession: ENCSR312UYN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB498HEN
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/7dd1fb4e-084b-4ee4-8fbb-2b2310dd1d65/@@download/attachment/L-EIF2B3-BGHcLV16-24.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF2B3. (EIF2B3-BGHcLV16-24)

value: ENCBS043TYN at ENCODE; https://www.encodeproject.org/ENCBS043TYN/


title: CRISPR RNA-seq from K562 (ENCLB923TMV)

description:
https://www.encodeproject.org/experiments/ENCSR416WTE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CACTIN. (CACTIN-BGKcLV23)
experiment encode accession: ENCSR416WTE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB923TMV
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 CACTIN

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b1407c02-740f-479f-91d4-c63996ed5cc3/@@download/attachment/L-CACTIN-BGKcLV23-28.pdf

value: CACTIN

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CACTIN. (CACTIN-BGKcLV23-28)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS996KHM at ENCODE; https://www.encodeproject.org/ENCBS996KHM/

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


title: CRISPR RNA-seq from K562 (ENCLB500HRS)

description:
https://www.encodeproject.org/experiments/ENCSR307KLI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against LSM7. (LSM7-BGKcLV21)
experiment encode accession: ENCSR307KLI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB500HRS
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 LSM7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7be0867c-6f4a-486a-a253-7a74e49c61bc/@@download/attachment/L-LSM7-BGKcLV21-28.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against LSM7. (LSM7-BGKcLV21-28)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS643NSH at ENCODE; https://www.encodeproject.org/ENCBS643NSH/


title: CRISPR RNA-seq from K562 (ENCLB259SFH)

description:
https://www.encodeproject.org/experiments/ENCSR307KLI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against LSM7. (LSM7-BGKcLV21)
experiment encode accession: ENCSR307KLI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB259SFH
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/37c1b007-7e75-43dd-8613-b8d8dff4fd4c/@@download/attachment/L-LSM7-BGKcLV21-27.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against LSM7. (LSM7-BGKcLV21-27)

value: ENCBS783NZF at ENCODE; https://www.encodeproject.org/ENCBS783NZF/


title: CRISPR RNA-seq from HepG2 (ENCLB066KIU)

description:
https://www.encodeproject.org/experiments/ENCSR308EYT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against E4F1. (E4F1-BGHcLV18)
experiment encode accession: ENCSR308EYT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB066KIU
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 E4F1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f5e5fd8c-f018-47a9-9bd3-fc442b700143/@@download/attachment/L-E4F1-BGHcLV18-16.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against E4F1. (E4F1-BGHcLV18-16)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS641IRB at ENCODE; https://www.encodeproject.org/ENCBS641IRB/

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