title: CRISPR RNA-seq from K562 (ENCLB933LVK)

description:
https://www.encodeproject.org/experiments/ENCSR002ODC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX10. (DDX10-BGKcLV28)
experiment encode accession: ENCSR002ODC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB933LVK
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 H. sapiens DDX10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c7b14c3d-6100-48a3-bb3c-ad1f2a6ac486/@@download/attachment/L-DDX10-BGKcLV28-67.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX10. (DDX10-BGKcLV28-67)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS065PAT at ENCODE; https://www.encodeproject.org/ENCBS065PAT/


title: CRISPR RNA-seq from K562 (ENCLB663TZM)

status: Public on Dec 04 2022

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/ENCSR971FJU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG9. (SMG9-BGKcLV33)
experiment encode accession: ENCSR971FJU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB663TZM
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 H. sapiens SNW1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1f65ff7f-fedd-43f4-89db-8b6bde01fb9c/@@download/attachment/L-SMG9-BGKcLV33-61.pdf

tag: antibody

tag: line

value: cell line

tag: description

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG9. (SMG9-BGKcLV33-61)

tag: biosample encode accession

tag: organism

value: Homo sapiens

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

tag: source

tag: link

value: ENCBS924AYQ at ENCODE; https://www.encodeproject.org/ENCBS924AYQ/

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


title: BruChase-seq from A673 (ENCLB890PDI)

description:
https://www.encodeproject.org/experiments/ENCSR971YFG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971YFG
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR912SRZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB890PDI
size range: 400-500

source_name: Homo sapiens A673 cell line, subjected to a 2 hour pulse-chase

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ENCBS739QIE at ENCODE; https://www.encodeproject.org/ENCBS739QIE/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: total RNA-seq from K562 (ENCLB547AOJ)

description:
https://www.encodeproject.org/experiments/ENCSR957GVE/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Panobinostat for 12 hours
experiment encode accession: ENCSR957GVE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB547AOJ
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 7.5 nM Panobinostat for 12 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

tag: treatments

value: treatment_term_name:Panobinostat; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS562WXY at ENCODE; https://www.encodeproject.org/ENCBS562WXY/


title: total RNA-seq from K562 (ENCLB831XGQ)

description:
https://www.encodeproject.org/experiments/ENCSR950YTM/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Vorinostat for 48 hours
experiment encode accession: ENCSR950YTM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB831XGQ
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 7.5 nM Vorinostat for 48 hours, preserved by flash-freezing

value: cell line

value: ATCC

value: treatment_term_name:Vorinostat; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS565EUZ at ENCODE; https://www.encodeproject.org/ENCBS565EUZ/


title: CRISPR RNA-seq from HepG2 (ENCLB140KZJ)

description:
https://www.encodeproject.org/experiments/ENCSR958OFR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF3. (CPSF3-BGHcLV29)
experiment encode accession: ENCSR958OFR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB140KZJ
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 H. sapiens CPSF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/de582c63-917c-412f-ba91-19b2d37279d2/@@download/attachment/L-CPSF3-BGHcLV29-35.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF3. (CPSF3-BGHcLV29-35)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS875FPP at ENCODE; https://www.encodeproject.org/ENCBS875FPP/

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


title: CRISPR RNA-seq from HepG2 (ENCLB448KBD)

description:
https://www.encodeproject.org/experiments/ENCSR958OFR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF3. (CPSF3-BGHcLV29)
experiment encode accession: ENCSR958OFR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB448KBD
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/c2e2f180-c639-4924-b221-a0b0ff599e9c/@@download/attachment/L-CPSF3-BGHcLV29-36.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF3. (CPSF3-BGHcLV29-36)

value: child

value: 15 year

value: ENCBS924UAE at ENCODE; https://www.encodeproject.org/ENCBS924UAE/


title: CRISPR RNA-seq from K562 (ENCLB068EAQ)

description:
https://www.encodeproject.org/experiments/ENCSR970WRV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF3. (CPSF3-BGKcLV28)
experiment encode accession: ENCSR970WRV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB068EAQ
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 H. sapiens CPSF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d5081de3-c0b5-46ee-901a-89cc18018490/@@download/attachment/L-CPSF3-BGKcLV28-36.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF3. (CPSF3-BGKcLV28-36)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS952HTR at ENCODE; https://www.encodeproject.org/ENCBS952HTR/

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


title: total RNA-seq from motor neuron (ENCLB411GGC)

description:
https://www.encodeproject.org/experiments/ENCSR967DSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR967DSJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB411GGC
size range: 300-600

source_name: Homo sapiens male adult (47 years) motor neuron in vitro differentiated cells, preserved by flash-freezing

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: Homo sapiens

value: Donor with Amyotrophic Lateral Sclerosis

value: 47 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS442FVR at ENCODE; https://www.encodeproject.org/ENCBS442FVR/

value: Derived from ENCODE donor ENCDO908CUN; https://www.encodeproject.org/ENCDO908CUN/


title: total RNA-seq from K562 (ENCLB420XXL)

description:
https://www.encodeproject.org/experiments/ENCSR957GVE/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Panobinostat for 12 hours
experiment encode accession: ENCSR957GVE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB420XXL
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:Panobinostat; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS370DEJ at ENCODE; https://www.encodeproject.org/ENCBS370DEJ/


title: total RNA-seq from K562 (ENCLB325CWH)

description:
https://www.encodeproject.org/experiments/ENCSR949BBZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Galeterone for 12 hours
experiment encode accession: ENCSR949BBZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB325CWH
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 25 uM Galeterone for 12 hours, preserved by flash-freezing

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: treatment_term_name:Galeterone; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS825COF at ENCODE; https://www.encodeproject.org/ENCBS825COF/

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


title: CRISPR RNA-seq from K562 (ENCLB562WVR)

description:
https://www.encodeproject.org/experiments/ENCSR950KYU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGKcLV28)
experiment encode accession: ENCSR950KYU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB562WVR
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 H. sapiens CLNS1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/575c9235-2079-4903-b3e7-66d2929a4eee/@@download/attachment/L-CLNS1A-BGKcLV28-21.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGKcLV28-21)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ENCBS126MYE at ENCODE; https://www.encodeproject.org/ENCBS126MYE/


title: CRISPR RNA-seq from K562 (ENCLB290DGA)

description:
https://www.encodeproject.org/experiments/ENCSR947EFJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against API5. (API5-BGKcLV26)
experiment encode accession: ENCSR947EFJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB290DGA
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 H. sapiens API5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e351de51-1fc9-4ff7-8616-f67c34313f49/@@download/attachment/L-API5-BGKcLV26-28.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against API5. (API5-BGKcLV26-28)

value: ENCBS811YQF at ENCODE; https://www.encodeproject.org/ENCBS811YQF/


title: CRISPR RNA-seq from HepG2 (ENCLB429UYO)

description:
https://www.encodeproject.org/experiments/ENCSR954VJD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGHcLV31)
experiment encode accession: ENCSR954VJD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB429UYO
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 H. sapiens SAP30BP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/12af5df8-5b02-40b8-bee8-e585e873cc4d/@@download/attachment/L-SAP30BP-BGHcLV31-25.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGHcLV31-25)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS627QRR at ENCODE; https://www.encodeproject.org/ENCBS627QRR/

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


title: total RNA-seq from K562 (ENCLB956CIS)

description:
https://www.encodeproject.org/experiments/ENCSR950YTM/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Vorinostat for 48 hours
experiment encode accession: ENCSR950YTM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB956CIS
size range: 300-600

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:Vorinostat; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS111LHN at ENCODE; https://www.encodeproject.org/ENCBS111LHN/


title: CRISPR RNA-seq from K562 (ENCLB195ICQ)

description:
https://www.encodeproject.org/experiments/ENCSR970WRV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF3. (CPSF3-BGKcLV28)
experiment encode accession: ENCSR970WRV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB195ICQ
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/e5381358-e79b-470d-aa47-4d1eab16ae36/@@download/attachment/L-CPSF3-BGKcLV28-35.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF3. (CPSF3-BGKcLV28-35)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ENCBS749HME at ENCODE; https://www.encodeproject.org/ENCBS749HME/

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


title: CRISPR RNA-seq from K562 (ENCLB679YSY)

description:
https://www.encodeproject.org/experiments/ENCSR950KYU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGKcLV28)
experiment encode accession: ENCSR950KYU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB679YSY
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/0d930f20-aa74-4aef-b286-b1fa288caf15/@@download/attachment/L-CLNS1A-BGKcLV28-22.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGKcLV28-22)

value: ATCC

value: ENCBS528FQJ at ENCODE; https://www.encodeproject.org/ENCBS528FQJ/


title: CRISPR RNA-seq from K562 (ENCLB860ERZ)

description:
https://www.encodeproject.org/experiments/ENCSR947EFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against API5. (API5-BGKcLV26)
experiment encode accession: ENCSR947EFJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB860ERZ
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/d07841cb-30fb-4df0-8767-183b98534882/@@download/attachment/L-API5-BGKcLV26-27.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against API5. (API5-BGKcLV26-27)

value: ENCBS539IOW at ENCODE; https://www.encodeproject.org/ENCBS539IOW/


title: total RNA-seq from K562 (ENCLB879GYN)

description:
https://www.encodeproject.org/experiments/ENCSR949BBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Galeterone for 12 hours
experiment encode accession: ENCSR949BBZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB879GYN
size range: 300-600

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: treatment_term_name:Galeterone; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS911GLO at ENCODE; https://www.encodeproject.org/ENCBS911GLO/


title: CRISPR RNA-seq from K562 (ENCLB435SIW)

description:
https://www.encodeproject.org/experiments/ENCSR928XFZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS28. (RPS28-BGKcLV33)
experiment encode accession: ENCSR928XFZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB435SIW
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 H. sapiens RRP8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a0cdaa80-9158-4668-9c21-e9e0482b7665/@@download/attachment/L-RPS28-BGKcLV33-13.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS28. (RPS28-BGKcLV33-13)

value: adult

value: 53 year

value: ENCBS387CRZ at ENCODE; https://www.encodeproject.org/ENCBS387CRZ/


title: CRISPR RNA-seq from K562 (ENCLB218ROW)

description:
https://www.encodeproject.org/experiments/ENCSR944PAO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDV3. (CDV3-BGKcLV28)
experiment encode accession: ENCSR944PAO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB218ROW
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 H. sapiens CDV3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/14862d65-1d1d-4621-8551-bb4e114b68fd/@@download/attachment/L-CDV3-BGKcLV28-15.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDV3. (CDV3-BGKcLV28-15)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ENCBS154EVT at ENCODE; https://www.encodeproject.org/ENCBS154EVT/


title: Bru-seq from HCT116 (ENCLB049UVP)

description:
https://www.encodeproject.org/experiments/ENCSR945UXU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR945UXU
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB049UVP
size range: 400-500

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS692ZUT at ENCODE; https://www.encodeproject.org/ENCBS692ZUT/

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


title: CRISPR RNA-seq from K562 (ENCLB307ZVV)

description:
https://www.encodeproject.org/experiments/ENCSR928XFZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS28. (RPS28-BGKcLV33)
experiment encode accession: ENCSR928XFZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB307ZVV
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/c6ce43ba-fe83-4f2e-8ef0-dd09e293125e/@@download/attachment/L-RPS28-BGKcLV33-14.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS28. (RPS28-BGKcLV33-14)

value: female

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS359SKL at ENCODE; https://www.encodeproject.org/ENCBS359SKL/

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


title: Bru-seq from HCT116 (ENCLB577UKY)

description:
https://www.encodeproject.org/experiments/ENCSR945UXU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR945UXU
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB577UKY
size range: 400-500

value: cell line

value: adult

value: ENCBS603YYY at ENCODE; https://www.encodeproject.org/ENCBS603YYY/


title: CRISPR RNA-seq from K562 (ENCLB341XRJ)

description:
https://www.encodeproject.org/experiments/ENCSR929YET/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGKcLV26)
experiment encode accession: ENCSR929YET
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB341XRJ
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 H. sapiens AIMP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8968e22d-d57a-443d-bb4d-0db3026d1334/@@download/attachment/L-AIMP1-BGKcLV26-19.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGKcLV26-19)

value: Homo sapiens

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS629JYA at ENCODE; https://www.encodeproject.org/ENCBS629JYA/


title: CRISPR RNA-seq from K562 (ENCLB494JEG)

description:
https://www.encodeproject.org/experiments/ENCSR944PAO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDV3. (CDV3-BGKcLV28)
experiment encode accession: ENCSR944PAO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB494JEG
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/ed6b4f42-6764-4958-938b-0a8c2312da6f/@@download/attachment/L-CDV3-BGKcLV28-16.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDV3. (CDV3-BGKcLV28-16)

value: ENCBS910GVI at ENCODE; https://www.encodeproject.org/ENCBS910GVI/


title: CRISPR RNA-seq from K562 (ENCLB744ORH)

description:
https://www.encodeproject.org/experiments/ENCSR925SFP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS21. (RPS21-BGKcLV33)
experiment encode accession: ENCSR925SFP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB744ORH
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/1b3d476f-9010-4ca5-8ac1-cac0f5dad2da/@@download/attachment/L-RPS21-BGKcLV33-12.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS21. (RPS21-BGKcLV33-12)

value: ENCBS039UVG at ENCODE; https://www.encodeproject.org/ENCBS039UVG/


title: CRISPR RNA-seq from K562 (ENCLB462CRO)

description:
https://www.encodeproject.org/experiments/ENCSR929YET/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGKcLV26)
experiment encode accession: ENCSR929YET
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB462CRO
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/de44d377-edf6-4a36-849a-9aeebdf4b92d/@@download/attachment/L-AIMP1-BGKcLV26-20.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGKcLV26-20)

value: female

value: ENCBS867AQR at ENCODE; https://www.encodeproject.org/ENCBS867AQR/


title: CRISPR RNA-seq from HepG2 (ENCLB195HWZ)

description:
https://www.encodeproject.org/experiments/ENCSR921IQU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGHcLV27)
experiment encode accession: ENCSR921IQU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB195HWZ
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 H. sapiens BZW2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5cefc191-7b7e-4fce-be66-27221a4c0353/@@download/attachment/L-BZW2-BGHcLV27-29.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGHcLV27-29)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS219MYC at ENCODE; https://www.encodeproject.org/ENCBS219MYC/

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


title: CRISPR RNA-seq from HepG2 (ENCLB144NTT)

description:
https://www.encodeproject.org/experiments/ENCSR944KLG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against C1QBP. (C1QBP-BGHcLV27)
experiment encode accession: ENCSR944KLG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB144NTT
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 H. sapiens C1QBP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/32bcd7c9-25a4-4e70-ad90-e6b9ec7194ee/@@download/attachment/L-C1QBP-BGHcLV27-31.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against C1QBP. (C1QBP-BGHcLV27-31)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ENCBS097DNB at ENCODE; https://www.encodeproject.org/ENCBS097DNB/


title: CRISPR RNA-seq from HepG2 (ENCLB087QKG)

description:
https://www.encodeproject.org/experiments/ENCSR925POR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against METTL1. (METTL1-BGHcLV24)
experiment encode accession: ENCSR925POR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB087QKG
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 H. sapiens METTL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/800e83b2-5500-4892-b5ab-ba7595655ca7/@@download/attachment/L-METTL1-BGHcLV24-37.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against METTL1. (METTL1-BGHcLV24-37)

value: ENCBS203SVC at ENCODE; https://www.encodeproject.org/ENCBS203SVC/


title: CRISPR RNA-seq from HepG2 (ENCLB070RXY)

description:
https://www.encodeproject.org/experiments/ENCSR925POR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against METTL1. (METTL1-BGHcLV24)
experiment encode accession: ENCSR925POR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB070RXY
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/11e7eff1-2e1f-4aa1-aa67-2577b33e7ad1/@@download/attachment/L-METTL1-BGHcLV24-38.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against METTL1. (METTL1-BGHcLV24-38)

value: ENCBS805VQZ at ENCODE; https://www.encodeproject.org/ENCBS805VQZ/


title: CRISPR RNA-seq from HepG2 (ENCLB455OAS)

description:
https://www.encodeproject.org/experiments/ENCSR944KLG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against C1QBP. (C1QBP-BGHcLV27)
experiment encode accession: ENCSR944KLG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB455OAS
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/4dcd71e5-90ce-436a-bb08-170c6b0bc656/@@download/attachment/L-C1QBP-BGHcLV27-32.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against C1QBP. (C1QBP-BGHcLV27-32)

value: ENCBS530FWA at ENCODE; https://www.encodeproject.org/ENCBS530FWA/


title: PRO-cap from HCT116 (ENCLB778WJE)

description:
https://www.encodeproject.org/experiments/ENCSR932TRR/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in SMARCA5_U.
experiment encode accession: ENCSR932TRR
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB778WJE
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS032AKF at ENCODE; https://www.encodeproject.org/ENCBS032AKF/

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


title: CRISPR RNA-seq from HepG2 (ENCLB156YES)

description:
https://www.encodeproject.org/experiments/ENCSR918MUU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT2. (CNOT2-BGHcLV24)
experiment encode accession: ENCSR918MUU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB156YES
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 H. sapiens CNOT2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/91ccc7d5-d14e-4595-87b3-e679d02c8b1f/@@download/attachment/L-CNOT2-BGHcLV24-22.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT2. (CNOT2-BGHcLV24-22)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS068UAP at ENCODE; https://www.encodeproject.org/ENCBS068UAP/

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


title: BruChase-seq from MCF 10A (ENCLB934GMV)

description:
https://www.encodeproject.org/experiments/ENCSR917MFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR917MFV
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR444JTC
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB934GMV
size range: 400-500

source_name: Homo sapiens MCF 10A cell line, subjected to a 6 hour pulse-chase

value: MCF 10A

value: female

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

value: ENCBS339UDB at ENCODE; https://www.encodeproject.org/ENCBS339UDB/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: PRO-cap from HCT116 (ENCLB320OGL)

description:
https://www.encodeproject.org/experiments/ENCSR932TRR/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in SMARCA5_U.
experiment encode accession: ENCSR932TRR
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB320OGL
spikeins used: The drosophila spike-in reference used for alignment

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS141BGY at ENCODE; https://www.encodeproject.org/ENCBS141BGY/

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


title: CRISPR RNA-seq from HepG2 (ENCLB376FDM)

description:
https://www.encodeproject.org/experiments/ENCSR921IQU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGHcLV27)
experiment encode accession: ENCSR921IQU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB376FDM
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/003b8169-9120-424d-bd03-1f3c0a3aa391/@@download/attachment/L-BZW2-BGHcLV27-30.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGHcLV27-30)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS376DUX at ENCODE; https://www.encodeproject.org/ENCBS376DUX/


title: CRISPR RNA-seq from HepG2 (ENCLB230AQZ)

description:
https://www.encodeproject.org/experiments/ENCSR924AVW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADK. (ADK-BGHcLV25)
experiment encode accession: ENCSR924AVW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB230AQZ
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 H. sapiens ADK

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/41679f00-251d-4043-b811-990578753faf/@@download/attachment/L-ADK-BGHcLV25-16.pdf

value: ADK

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADK. (ADK-BGHcLV25-16)

value: male

value: ENCBS373FPT at ENCODE; https://www.encodeproject.org/ENCBS373FPT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB386CSX)

description:
https://www.encodeproject.org/experiments/ENCSR924AVW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADK. (ADK-BGHcLV25)
experiment encode accession: ENCSR924AVW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB386CSX
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/71641c7d-2332-4c4e-84f1-9352471f5f0d/@@download/attachment/L-ADK-BGHcLV25-15.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADK. (ADK-BGHcLV25-15)

value: ENCBS273CKO at ENCODE; https://www.encodeproject.org/ENCBS273CKO/


title: Bru-seq from HCT116 (ENCLB176CSE)

description:
https://www.encodeproject.org/experiments/ENCSR914PUX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR914PUX
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR626FRT
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB176CSE
size range: 400-500

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS797LAW at ENCODE; https://www.encodeproject.org/ENCBS797LAW/

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


title: BruChase-seq from MCF 10A (ENCLB558UYO)

description:
https://www.encodeproject.org/experiments/ENCSR917MFV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR917MFV
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR444JTC
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB558UYO
size range: 400-500

value: MCF 10A

value: cell line

value: Homo sapiens

value: female

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS672NOQ at ENCODE; https://www.encodeproject.org/ENCBS672NOQ/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: CRISPR RNA-seq from HepG2 (ENCLB509YAR)

description:
https://www.encodeproject.org/experiments/ENCSR911CLD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32-B)
experiment encode accession: ENCSR911CLD
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB509YAR
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5a7a6781-cccd-44db-b65b-e7b6c6e3844d/@@download/attachment/L-NT-BGHcLV32-1B.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32-1)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS907MRZ at ENCODE; https://www.encodeproject.org/ENCBS907MRZ/

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


title: CRISPR RNA-seq from K562 (ENCLB346SFO)

description:
https://www.encodeproject.org/experiments/ENCSR911ITT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DCP1A. (DCP1A-BGKcLV28)
experiment encode accession: ENCSR911ITT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB346SFO
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 H. sapiens DCP1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5f79f0ba-7313-4059-a41b-d7b03190fbef/@@download/attachment/L-DCP1A-BGKcLV28-61.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DCP1A. (DCP1A-BGKcLV28-61)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS002VIT at ENCODE; https://www.encodeproject.org/ENCBS002VIT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB427SNF)

description:
https://www.encodeproject.org/experiments/ENCSR911CLD/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32-B)
experiment encode accession: ENCSR911CLD
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB427SNF
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/3f622458-b6b6-4540-9f54-c8ca102a4755/@@download/attachment/L-NT-BGHcLV32-2B.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32-2)

value: Homo sapiens

value: ATCC

value: ENCBS969BWM at ENCODE; https://www.encodeproject.org/ENCBS969BWM/


title: CRISPR RNA-seq from K562 (ENCLB273GZE)

description:
https://www.encodeproject.org/experiments/ENCSR911ITT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DCP1A. (DCP1A-BGKcLV28)
experiment encode accession: ENCSR911ITT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB273GZE
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/52842f36-7460-41a3-883d-077ad09ef1e0/@@download/attachment/L-DCP1A-BGKcLV28-62.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DCP1A. (DCP1A-BGKcLV28-62)

value: female

value: ENCBS844MEQ at ENCODE; https://www.encodeproject.org/ENCBS844MEQ/


title: CRISPR RNA-seq from K562 (ENCLB608IDU)

description:
https://www.encodeproject.org/experiments/ENCSR925SFP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS21. (RPS21-BGKcLV33)
experiment encode accession: ENCSR925SFP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB608IDU
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/62653b72-ec8d-4000-a0e8-8dbce1b74ab3/@@download/attachment/L-RPS21-BGKcLV33-11.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS21. (RPS21-BGKcLV33-11)

value: Brenton Graveley, UConn

value: ENCBS916YIG at ENCODE; https://www.encodeproject.org/ENCBS916YIG/


title: total RNA-seq from K562 (ENCLB975JKJ)

description:
https://www.encodeproject.org/experiments/ENCSR900IJI/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Bortezomib for 24 hours
experiment encode accession: ENCSR900IJI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB975JKJ
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 nM Bortezomib for 24 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

value: treatment_term_id:CHEBI:52717; treatment_term_name:Bortezomib; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS643OTR at ENCODE; https://www.encodeproject.org/ENCBS643OTR/


title: total RNA-seq from K562 (ENCLB567WHB)

description:
https://www.encodeproject.org/experiments/ENCSR900IJI/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Bortezomib for 24 hours
experiment encode accession: ENCSR900IJI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB567WHB
size range: 300-600

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS599HZH at ENCODE; https://www.encodeproject.org/ENCBS599HZH/


title: Bru-seq from HCT116 (ENCLB892FJL)

description:
https://www.encodeproject.org/experiments/ENCSR906UFM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR906UFM
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR664LAL
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB892FJL
size range: 400-500

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: Homo sapiens

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS743GHM at ENCODE; https://www.encodeproject.org/ENCBS743GHM/

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


title: PRO-cap from HCT116 (ENCLB613HZL)

description:
https://www.encodeproject.org/experiments/ENCSR900SLO/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in MED14_U.
experiment encode accession: ENCSR900SLO
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB613HZL
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14

value: cell line

value: ENCBS007ZIG at ENCODE; https://www.encodeproject.org/ENCBS007ZIG/


title: PRO-cap from HCT116 (ENCLB325IVW)

description:
https://www.encodeproject.org/experiments/ENCSR900SLO/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in MED14_U.
experiment encode accession: ENCSR900SLO
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB325IVW
spikeins used: The drosophila spike-in reference used for alignment

value: ENCBS904RVQ at ENCODE; https://www.encodeproject.org/ENCBS904RVQ/


title: Bru-seq from HCT116 (ENCLB570TMW)

description:
https://www.encodeproject.org/experiments/ENCSR906UFM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR906UFM
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR664LAL
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB570TMW
size range: 400-500

value: ENCBS592LWX at ENCODE; https://www.encodeproject.org/ENCBS592LWX/


title: CRISPR RNA-seq from HepG2 (ENCLB610FNQ)

description:
https://www.encodeproject.org/experiments/ENCSR892ZGW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGHcLV25)
experiment encode accession: ENCSR892ZGW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB610FNQ
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 H. sapiens AGFG1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/03955a28-6687-4fd7-b8bd-0fd6179b8fab/@@download/attachment/L-AGFG1-BGHcLV25-19.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGHcLV25-19)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS512NDV at ENCODE; https://www.encodeproject.org/ENCBS512NDV/

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


title: CRISPR RNA-seq from K562 (ENCLB126DIU)

description:
https://www.encodeproject.org/experiments/ENCSR899RVY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGKcLV28)
experiment encode accession: ENCSR899RVY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB126DIU
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 H. sapiens CLTC

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e6efcbb2-43ac-4985-a499-4be744a5fdad/@@download/attachment/L-CLTC-BGKcLV28-23.pdf

value: CLTC

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGKcLV28-23)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS043OMI at ENCODE; https://www.encodeproject.org/ENCBS043OMI/

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


title: total RNA-seq from motor neuron (ENCLB394BSC)

description:
https://www.encodeproject.org/experiments/ENCSR892WHX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR892WHX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB394BSC
size range: 300-600

source_name: Homo sapiens male adult (49 years) motor neuron in vitro differentiated cells, preserved by flash-freezing

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: male

value: Donor with Amyotrophic Lateral Sclerosis

value: 49 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS520OTA at ENCODE; https://www.encodeproject.org/ENCBS520OTA/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: CRISPR RNA-seq from HepG2 (ENCLB351QKE)

description:
https://www.encodeproject.org/experiments/ENCSR918MUU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT2. (CNOT2-BGHcLV24)
experiment encode accession: ENCSR918MUU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB351QKE
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/2600c6ab-61ba-41ab-a028-6cd483da37c9/@@download/attachment/L-CNOT2-BGHcLV24-21.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNOT2. (CNOT2-BGHcLV24-21)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS429YTL at ENCODE; https://www.encodeproject.org/ENCBS429YTL/

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


title: total RNA-seq from motor neuron (ENCLB234DTP)

description:
https://www.encodeproject.org/experiments/ENCSR892WHX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR892WHX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB234DTP
size range: 300-600

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: male

value: adult

value: ENCBS252YBV at ENCODE; https://www.encodeproject.org/ENCBS252YBV/


title: Bru-seq from HCT116 (ENCLB723BFO)

description:
https://www.encodeproject.org/experiments/ENCSR914PUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR914PUX
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR626FRT
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB723BFO
size range: 400-500

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS802NBR at ENCODE; https://www.encodeproject.org/ENCBS802NBR/

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


title: CRISPR RNA-seq from K562 (ENCLB444SVC)

description:
https://www.encodeproject.org/experiments/ENCSR887XCL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGKcLV28)
experiment encode accession: ENCSR887XCL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB444SVC
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 H. sapiens CPSF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7953ca28-4456-4059-adc4-cdd39364ef17/@@download/attachment/L-CPSF2-BGKcLV28-34.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGKcLV28-34)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS692WQE at ENCODE; https://www.encodeproject.org/ENCBS692WQE/

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


title: CRISPR RNA-seq from K562 (ENCLB231RII)

description:
https://www.encodeproject.org/experiments/ENCSR887XCL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGKcLV28)
experiment encode accession: ENCSR887XCL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB231RII
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/453f89b7-a6b4-4a97-af50-6ac9db6af7b9/@@download/attachment/L-CPSF2-BGKcLV28-33.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGKcLV28-33)

value: adult

value: ATCC

value: ENCBS862OGM at ENCODE; https://www.encodeproject.org/ENCBS862OGM/


title: total RNA-seq from K562 (ENCLB977ISC)

description:
https://www.encodeproject.org/experiments/ENCSR882NWV/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with C646 for 24 hours
experiment encode accession: ENCSR882NWV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB977ISC
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 50 uM C646 for 24 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

value: treatment_term_name:C646; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS593LYT at ENCODE; https://www.encodeproject.org/ENCBS593LYT/


title: CRISPR RNA-seq from HepG2 (ENCLB969TMO)

description:
https://www.encodeproject.org/experiments/ENCSR462MFN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV29)
experiment encode accession: ENCSR462MFN
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB969TMO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3ab1dde9-e893-4d35-b74a-310212f0895c/@@download/attachment/L-NT-BGHcLV29-2.pdf

value: cell line

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV29-2)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS692PXQ at ENCODE; https://www.encodeproject.org/ENCBS692PXQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB556RJM)

description:
https://www.encodeproject.org/experiments/ENCSR892ZGW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGHcLV25)
experiment encode accession: ENCSR892ZGW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB556RJM
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/e0a24229-de48-47e6-a0f9-c9d686fae9e9/@@download/attachment/L-AGFG1-BGHcLV25-20.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGHcLV25-20)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ENCBS671GNG at ENCODE; https://www.encodeproject.org/ENCBS671GNG/


title: total RNA-seq from K562 (ENCLB617DJO)

description:
https://www.encodeproject.org/experiments/ENCSR882NWV/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with C646 for 24 hours
experiment encode accession: ENCSR882NWV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB617DJO
size range: 300-600

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS739WYJ at ENCODE; https://www.encodeproject.org/ENCBS739WYJ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB242TCT)

description:
https://www.encodeproject.org/experiments/ENCSR462MFN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV29)
experiment encode accession: ENCSR462MFN
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB242TCT
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/d4c4cf30-167b-46c6-be0a-72bb548ee952/@@download/attachment/L-NT-BGHcLV29-1.pdf

value: cell line

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV29-1)

value: male

value: ENCBS125VHW at ENCODE; https://www.encodeproject.org/ENCBS125VHW/


title: Bru-seq from OCI-LY7 (ENCLB783QJE)

description:
https://www.encodeproject.org/experiments/ENCSR459AVM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR459AVM
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR121MLV
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB783QJE
size range: 400-500

source_name: Homo sapiens OCI-LY7 cell line treated with 500 rad irradiation

value: B cell lymphoma

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS626OCD at ENCODE; https://www.encodeproject.org/ENCBS626OCD/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: CRISPR RNA-seq from HepG2 (ENCLB252AWJ)

description:
https://www.encodeproject.org/experiments/ENCSR878TRK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAMHD1. (SAMHD1-BGHcLV31)
experiment encode accession: ENCSR878TRK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB252AWJ
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 H. sapiens SAMHD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e5124d09-5886-44b1-a79d-822a98b382a5/@@download/attachment/L-SAMHD1-BGHcLV31-23.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAMHD1. (SAMHD1-BGHcLV31-23)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS279YBS at ENCODE; https://www.encodeproject.org/ENCBS279YBS/

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


title: CRISPR RNA-seq from HepG2 (ENCLB338BJP)

description:
https://www.encodeproject.org/experiments/ENCSR878TRK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAMHD1. (SAMHD1-BGHcLV31)
experiment encode accession: ENCSR878TRK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB338BJP
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/20ffdad8-51bf-4eb5-8884-a0068c85a7f6/@@download/attachment/L-SAMHD1-BGHcLV31-24.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAMHD1. (SAMHD1-BGHcLV31-24)

value: ATCC

value: ENCBS011AMX at ENCODE; https://www.encodeproject.org/ENCBS011AMX/


title: Bru-seq from HCT116 (ENCLB373RND)

description:
https://www.encodeproject.org/experiments/ENCSR877LIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR877LIZ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB373RND
size range: 400-500

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS264KRF at ENCODE; https://www.encodeproject.org/ENCBS264KRF/

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


title: Bru-seq from OCI-LY7 (ENCLB555RGL)

description:
https://www.encodeproject.org/experiments/ENCSR459AVM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR459AVM
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR121MLV
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB555RGL
size range: 400-500

value: Homo sapiens

value: B cell lymphoma

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS511MHE at ENCODE; https://www.encodeproject.org/ENCBS511MHE/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: CRISPR RNA-seq from K562 (ENCLB770IBM)

description:
https://www.encodeproject.org/experiments/ENCSR900GQL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV26)
experiment encode accession: ENCSR900GQL
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB770IBM
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/76319124-8b94-4a8c-9ea5-560e0a5861a9/@@download/attachment/L-NT-BGKcLV26-1.pdf

value: cell line

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV26-1)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS369CJT at ENCODE; https://www.encodeproject.org/ENCBS369CJT/

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


title: Bru-seq from HCT116 (ENCLB427RTL)

description:
https://www.encodeproject.org/experiments/ENCSR877LIZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR877LIZ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB427RTL
size range: 400-500

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS048HBZ at ENCODE; https://www.encodeproject.org/ENCBS048HBZ/


title: CRISPR RNA-seq from K562 (ENCLB297ZDL)

description:
https://www.encodeproject.org/experiments/ENCSR900GQL/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV26)
experiment encode accession: ENCSR900GQL
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB297ZDL
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/48b38393-ca6f-46e0-98ed-42967626d6aa/@@download/attachment/L-NT-BGKcLV26-2.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV26-2)

value: Homo sapiens

value: ATCC

value: ENCBS791IIZ at ENCODE; https://www.encodeproject.org/ENCBS791IIZ/


title: CRISPR RNA-seq from K562 (ENCLB244MGT)

description:
https://www.encodeproject.org/experiments/ENCSR458FLK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SNW1. (SNW1-BGKcLV33)
experiment encode accession: ENCSR458FLK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB244MGT
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 H. sapiens SPATS2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/776a57c5-9911-472f-9b61-8ce9513e0f2a/@@download/attachment/L-SNW1-BGKcLV33-65.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SNW1. (SNW1-BGKcLV33-65)

value: female

value: ENCBS949WGL at ENCODE; https://www.encodeproject.org/ENCBS949WGL/


title: CRISPR RNA-seq from K562 (ENCLB077XMO)

description:
https://www.encodeproject.org/experiments/ENCSR458FLK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SNW1. (SNW1-BGKcLV33)
experiment encode accession: ENCSR458FLK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB077XMO
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/87fd35a7-450a-4e14-8d69-4cd02f9c51e4/@@download/attachment/L-SNW1-BGKcLV33-66.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SNW1. (SNW1-BGKcLV33-66)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS283NSB at ENCODE; https://www.encodeproject.org/ENCBS283NSB/


title: CRISPR RNA-seq from K562 (ENCLB316XAN)

description:
https://www.encodeproject.org/experiments/ENCSR899RVY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGKcLV28)
experiment encode accession: ENCSR899RVY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB316XAN
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/2e37630e-b402-4541-860b-86219832a83f/@@download/attachment/L-CLTC-BGKcLV28-24.pdf

value: CLTC

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGKcLV28-24)

value: adult

value: ENCBS645RJM at ENCODE; https://www.encodeproject.org/ENCBS645RJM/

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


title: CRISPR RNA-seq from K562 (ENCLB314LIG)

description:
https://www.encodeproject.org/experiments/ENCSR877CJJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CSE1L. (CSE1L-BGKcLV28)
experiment encode accession: ENCSR877CJJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB314LIG
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 H. sapiens CSE1L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/33d465f0-f3e4-4593-8c30-b8419798c811/@@download/attachment/L-CSE1L-BGKcLV28-43.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CSE1L. (CSE1L-BGKcLV28-43)

value: Homo sapiens

value: ENCBS543AIH at ENCODE; https://www.encodeproject.org/ENCBS543AIH/


title: CRISPR RNA-seq from K562 (ENCLB576CDH)

description:
https://www.encodeproject.org/experiments/ENCSR877CJJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CSE1L. (CSE1L-BGKcLV28)
experiment encode accession: ENCSR877CJJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB576CDH
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/e94a9215-e504-411d-b4c9-ce68a2159583/@@download/attachment/L-CSE1L-BGKcLV28-44.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CSE1L. (CSE1L-BGKcLV28-44)

value: ATCC

value: ENCBS744PRW at ENCODE; https://www.encodeproject.org/ENCBS744PRW/


title: BruChase-seq from Calu3 (ENCLB117RHY)

description:
https://www.encodeproject.org/experiments/ENCSR456HKF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR456HKF
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR692DCF
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB117RHY
size range: 400-500

source_name: Homo sapiens Calu3 cell line, subjected to a 6 hour pulse-chase

value: male

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ENCBS434SCV at ENCODE; https://www.encodeproject.org/ENCBS434SCV/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: CRISPR RNA-seq from K562 (ENCLB305TDC)

description:
https://www.encodeproject.org/experiments/ENCSR876IJP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CARHSP1. (CARHSP1-BGKcLV26)
experiment encode accession: ENCSR876IJP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB305TDC
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 H. sapiens CARHSP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e63a03cf-d0e7-4908-afa4-0736631daef7/@@download/attachment/L-CARHSP1-BGKcLV26-55.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CARHSP1. (CARHSP1-BGKcLV26-55)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS430ULM at ENCODE; https://www.encodeproject.org/ENCBS430ULM/


title: BruChase-seq from Calu3 (ENCLB012GDS)

description:
https://www.encodeproject.org/experiments/ENCSR456HKF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR456HKF
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR692DCF
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB012GDS
size range: 400-500

value: Homo sapiens

value: adult

value: ENCBS955DMS at ENCODE; https://www.encodeproject.org/ENCBS955DMS/


title: CRISPR RNA-seq from K562 (ENCLB111UPD)

description:
https://www.encodeproject.org/experiments/ENCSR876IJP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CARHSP1. (CARHSP1-BGKcLV26)
experiment encode accession: ENCSR876IJP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB111UPD
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/ba15e26c-4add-44d2-86db-238cf2b23d11/@@download/attachment/L-CARHSP1-BGKcLV26-56.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CARHSP1. (CARHSP1-BGKcLV26-56)

value: ATCC

value: ENCBS561VWT at ENCODE; https://www.encodeproject.org/ENCBS561VWT/

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


title: PRO-cap from HCT116 (ENCLB754KYJ)

description:
https://www.encodeproject.org/experiments/ENCSR871CUV/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CDK7_T.
experiment encode accession: ENCSR871CUV
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB754KYJ
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS369YWA at ENCODE; https://www.encodeproject.org/ENCBS369YWA/

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


title: CRISPR RNA-seq from HepG2 (ENCLB526WGG)

description:
https://www.encodeproject.org/experiments/ENCSR875UMY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDV3. (CDV3-BGHcLV29)
experiment encode accession: ENCSR875UMY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB526WGG
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 H. sapiens CDV3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2a900b0b-8cd6-481c-8a31-865552806f66/@@download/attachment/L-CDV3-BGHcLV29-15.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDV3. (CDV3-BGHcLV29-15)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS480AAL at ENCODE; https://www.encodeproject.org/ENCBS480AAL/

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


title: CRISPR RNA-seq from HepG2 (ENCLB698PTQ)

description:
https://www.encodeproject.org/experiments/ENCSR875UMY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDV3. (CDV3-BGHcLV29)
experiment encode accession: ENCSR875UMY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB698PTQ
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/c5e17ccc-9c38-4186-9a2d-46cabe120c29/@@download/attachment/L-CDV3-BGHcLV29-16.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDV3. (CDV3-BGHcLV29-16)

value: Homo sapiens

value: ATCC

value: ENCBS450LGX at ENCODE; https://www.encodeproject.org/ENCBS450LGX/


title: PRO-cap from HCT116 (ENCLB673AJV)

description:
https://www.encodeproject.org/experiments/ENCSR871CUV/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CDK7_T.
experiment encode accession: ENCSR871CUV
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB673AJV
spikeins used: The drosophila spike-in reference used for alignment

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: ENCBS143QQX at ENCODE; https://www.encodeproject.org/ENCBS143QQX/


title: CRISPR RNA-seq from HepG2 (ENCLB439RFX)

description:
https://www.encodeproject.org/experiments/ENCSR452TFV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV31)
experiment encode accession: ENCSR452TFV
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB439RFX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fafd274e-a5ca-4381-9632-f49ce0b147f8/@@download/attachment/L-NT-BGHcLV31-2.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV31-2)

value: hepatocellular carcinoma

value: ENCBS143SBN at ENCODE; https://www.encodeproject.org/ENCBS143SBN/


title: CRISPR RNA-seq from HepG2 (ENCLB518ERQ)

description:
https://www.encodeproject.org/experiments/ENCSR452TFV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV31)
experiment encode accession: ENCSR452TFV
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB518ERQ
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/09ae78df-592f-4a3e-b51b-be8e72634b1c/@@download/attachment/L-NT-BGHcLV31-1.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV31-1)

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS426VMT at ENCODE; https://www.encodeproject.org/ENCBS426VMT/


title: total RNA-seq from K562 (ENCLB371GGK)

description:
https://www.encodeproject.org/experiments/ENCSR451LDB/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with C646 for 12 hours
experiment encode accession: ENCSR451LDB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB371GGK
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 50 uM C646 for 12 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:C646; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS662ZJB at ENCODE; https://www.encodeproject.org/ENCBS662ZJB/

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


title: CRISPR RNA-seq from K562 (ENCLB410UJO)

description:
https://www.encodeproject.org/experiments/ENCSR870TGO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ACTN4. (ACTN4-BGKcLV26)
experiment encode accession: ENCSR870TGO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB410UJO
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 H. sapiens ACTN4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/af65290d-ab8a-4f6c-868b-8ce5265ba6ac/@@download/attachment/L-ACTN4-BGKcLV26-6.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ACTN4. (ACTN4-BGKcLV26-6)

value: adult

value: ATCC

value: ENCBS593HDZ at ENCODE; https://www.encodeproject.org/ENCBS593HDZ/


title: total RNA-seq from K562 (ENCLB212PDW)

description:
https://www.encodeproject.org/experiments/ENCSR451LDB/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with C646 for 12 hours
experiment encode accession: ENCSR451LDB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB212PDW
size range: 300-600

value: ENCBS646XIM at ENCODE; https://www.encodeproject.org/ENCBS646XIM/


title: CRISPR RNA-seq from K562 (ENCLB999WOD)

description:
https://www.encodeproject.org/experiments/ENCSR870EBU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SAMHD1. (SAMHD1-BGKcLV33)
experiment encode accession: ENCSR870EBU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB999WOD
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 H. sapiens SCAF8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/632e01b8-d776-41e8-b275-9cbc389e0fa0/@@download/attachment/L-SAMHD1-BGKcLV33-27.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SAMHD1. (SAMHD1-BGKcLV33-27)

value: Brenton Graveley, UConn

value: ENCBS444BPA at ENCODE; https://www.encodeproject.org/ENCBS444BPA/


title: CRISPR RNA-seq from K562 (ENCLB478CAH)

description:
https://www.encodeproject.org/experiments/ENCSR870EBU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SAMHD1. (SAMHD1-BGKcLV33)
experiment encode accession: ENCSR870EBU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB478CAH
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/9c51d343-e342-4e36-b9bd-086cec599ed2/@@download/attachment/L-SAMHD1-BGKcLV33-28.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SAMHD1. (SAMHD1-BGKcLV33-28)

value: ENCBS617OXH at ENCODE; https://www.encodeproject.org/ENCBS617OXH/


title: PRO-cap from HCT116 (ENCLB445QNP)

description:
https://www.encodeproject.org/experiments/ENCSR867EQV/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in SUPT16H_T.
experiment encode accession: ENCSR867EQV
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB445QNP
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: Homo sapiens

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS093CJI at ENCODE; https://www.encodeproject.org/ENCBS093CJI/

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


title: CRISPR RNA-seq from K562 (ENCLB278DCO)

description:
https://www.encodeproject.org/experiments/ENCSR869YRR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG8. (SMG8-BGKcLV33)
experiment encode accession: ENCSR869YRR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB278DCO
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 H. sapiens SNUPN

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a473b843-ef5c-4fee-b2bc-5644a000d097/@@download/attachment/L-SMG8-BGKcLV33-59.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG8. (SMG8-BGKcLV33-59)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS287UQB at ENCODE; https://www.encodeproject.org/ENCBS287UQB/

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


title: PRO-cap from HCT116 (ENCLB516LEK)

description:
https://www.encodeproject.org/experiments/ENCSR867EQV/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in SUPT16H_T.
experiment encode accession: ENCSR867EQV
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB516LEK
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: Homo sapiens

value: ENCBS081HJW at ENCODE; https://www.encodeproject.org/ENCBS081HJW/