title: total RNA-seq from K562 (ENCLB660ZSN)

description:
https://www.encodeproject.org/experiments/ENCSR866UOA/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Panobinostat for 4 hours
experiment encode accession: ENCSR866UOA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB660ZSN
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 7.5 nM Panobinostat for 4 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

value: treatment_term_name:Panobinostat; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS735PLB at ENCODE; https://www.encodeproject.org/ENCBS735PLB/


title: total RNA-seq from K562 (ENCLB726MZU)

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/ENCSR866UOA/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Panobinostat for 4 hours
experiment encode accession: ENCSR866UOA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB726MZU
size range: 300-600

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

tag: line

value: cell line

tag: description

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

value: ATCC

tag: treatments

tag: link

value: ENCBS047LTL at ENCODE; https://www.encodeproject.org/ENCBS047LTL/

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


title: CRISPR RNA-seq from K562 (ENCLB997NCI)

description:
https://www.encodeproject.org/experiments/ENCSR869YRR/
***************
biological replicate number: 2
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: ENCLB997NCI
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/87836ec7-97ae-4ee0-b5bf-3ea15f9343e0/@@download/attachment/L-SMG8-BGKcLV33-60.pdf

tag: antibody

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG8. (SMG8-BGKcLV33-60)

value: Brenton Graveley, UConn

value: ENCBS572GTT at ENCODE; https://www.encodeproject.org/ENCBS572GTT/


title: CRISPR RNA-seq from K562 (ENCLB417IOK)

description:
https://www.encodeproject.org/experiments/ENCSR447ARO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B2. (SF3B2-BGKcLV33)
experiment encode accession: ENCSR447ARO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB417IOK
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 SMG5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f7113df3-956d-4e53-b730-00f170063231/@@download/attachment/L-SF3B2-BGKcLV33-51.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B2. (SF3B2-BGKcLV33-51)

value: ENCBS533HEV at ENCODE; https://www.encodeproject.org/ENCBS533HEV/


title: CRISPR RNA-seq from K562 (ENCLB461LRD)

description:
https://www.encodeproject.org/experiments/ENCSR447ARO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B2. (SF3B2-BGKcLV33)
experiment encode accession: ENCSR447ARO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB461LRD
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/57dbcaf6-9ed9-4166-93d4-0af6dc63cfe3/@@download/attachment/L-SF3B2-BGKcLV33-52.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B2. (SF3B2-BGKcLV33-52)

value: ENCBS793LRT at ENCODE; https://www.encodeproject.org/ENCBS793LRT/


title: total RNA-seq from K562 (ENCLB544PCL)

description:
https://www.encodeproject.org/experiments/ENCSR860RDT/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with DMSO for 48 hours
experiment encode accession: ENCSR860RDT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB544PCL
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 1% DMSO for 48 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

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

value: ENCBS087MBA at ENCODE; https://www.encodeproject.org/ENCBS087MBA/


title: CRISPR RNA-seq from K562 (ENCLB928WJZ)

description:
https://www.encodeproject.org/experiments/ENCSR870TGO/
***************
biological replicate number: 1
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: ENCLB928WJZ
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/71e0e445-6cae-4b2e-b579-e8387f05fbae/@@download/attachment/L-ACTN4-BGKcLV26-5.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ACTN4. (ACTN4-BGKcLV26-5)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS398SEX at ENCODE; https://www.encodeproject.org/ENCBS398SEX/


title: total RNA-seq from K562 (ENCLB540OLQ)

description:
https://www.encodeproject.org/experiments/ENCSR860RDT/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with DMSO for 48 hours
experiment encode accession: ENCSR860RDT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB540OLQ
size range: 300-600

value: adult

value: 53 year

value: ATCC

value: ENCBS283KBT at ENCODE; https://www.encodeproject.org/ENCBS283KBT/

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


title: Bru-seq from A673 (ENCLB589CDO)

description:
https://www.encodeproject.org/experiments/ENCSR436EAB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR436EAB
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR912SRZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB589CDO
size range: 400-500

source_name: Homo sapiens A673 cell line treated with 500 rad irradiation

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ENCBS921WKD at ENCODE; https://www.encodeproject.org/ENCBS921WKD/

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


title: total RNA-seq from K562 (ENCLB845GYG)

description:
https://www.encodeproject.org/experiments/ENCSR844RSF/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Vorinostat for 24 hours
experiment encode accession: ENCSR844RSF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB845GYG
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 7.5 nM Vorinostat for 24 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

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

value: ENCBS297KSK at ENCODE; https://www.encodeproject.org/ENCBS297KSK/


title: Bru-seq from A673 (ENCLB522ACH)

description:
https://www.encodeproject.org/experiments/ENCSR436EAB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR436EAB
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR912SRZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB522ACH
size range: 400-500

value: cell line

value: Homo sapiens

value: female

value: ENCBS270HKL at ENCODE; https://www.encodeproject.org/ENCBS270HKL/


title: CRISPR RNA-seq from HepG2 (ENCLB758XGZ)

description:
https://www.encodeproject.org/experiments/ENCSR840HSL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT3. (ADAT3-BGHcLV24)
experiment encode accession: ENCSR840HSL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB758XGZ
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 ADAT3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4e974a26-0dea-4abd-ab48-35fc6ab2bf9b/@@download/attachment/L-ADAT3-BGHcLV24-8.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT3. (ADAT3-BGHcLV24-8)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS504GSS at ENCODE; https://www.encodeproject.org/ENCBS504GSS/

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


title: CRISPR RNA-seq from HepG2 (ENCLB166THM)

description:
https://www.encodeproject.org/experiments/ENCSR435YKS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSDE1. (CSDE1-BGHcLV29)
experiment encode accession: ENCSR435YKS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB166THM
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 CSDE1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a4d857f8-9a80-47cb-bf53-14cddb3d60e2/@@download/attachment/L-CSDE1-BGHcLV29-41.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSDE1. (CSDE1-BGHcLV29-41)

value: child

value: 15 year

value: ATCC

value: ENCBS204FBI at ENCODE; https://www.encodeproject.org/ENCBS204FBI/


title: CRISPR RNA-seq from HepG2 (ENCLB078VAM)

description:
https://www.encodeproject.org/experiments/ENCSR435YKS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSDE1. (CSDE1-BGHcLV29)
experiment encode accession: ENCSR435YKS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB078VAM
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/a23dbced-1c46-4889-ac01-a750ae6db237/@@download/attachment/L-CSDE1-BGHcLV29-42.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSDE1. (CSDE1-BGHcLV29-42)

value: ENCBS769ODW at ENCODE; https://www.encodeproject.org/ENCBS769ODW/


title: Bru-seq from HCT116 (ENCLB256QZX)

description:
https://www.encodeproject.org/experiments/ENCSR423WIK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR423WIK
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB256QZX
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 POLR2A

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS705PFV at ENCODE; https://www.encodeproject.org/ENCBS705PFV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB805PEV)

description:
https://www.encodeproject.org/experiments/ENCSR840HSL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT3. (ADAT3-BGHcLV24)
experiment encode accession: ENCSR840HSL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB805PEV
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/081eb9e4-99f7-41de-b474-1a484ec4ae02/@@download/attachment/L-ADAT3-BGHcLV24-7.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT3. (ADAT3-BGHcLV24-7)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS373KON at ENCODE; https://www.encodeproject.org/ENCBS373KON/


title: total RNA-seq from K562 (ENCLB296NKW)

description:
https://www.encodeproject.org/experiments/ENCSR844RSF/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Vorinostat for 24 hours
experiment encode accession: ENCSR844RSF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB296NKW
size range: 300-600

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS196EFF at ENCODE; https://www.encodeproject.org/ENCBS196EFF/

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


title: total RNA-seq from A549 (ENCLB151ANN)

description:
https://www.encodeproject.org/experiments/ENCSR414IGI/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR414IGI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB151ANN
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM DMSO (agonist) for 4 hours

extract_protocol:
extraction protocol: https://www.encodeproject.org/documents/e4e1b09a-8fe8-4212-9e76-a2fd6d0c8b49/@@download/attachment/supplemental%20PolyA%20plus%20RNA-seq%20library%20construction%20protocol.pdf
general protocol: https://www.encodeproject.org/documents/c2499c10-935d-4bc9-b374-5a40f69d4af9/@@download/attachment/Reddy_Lab_RNAseq_ENCODE_protocol.pdf
extraction method: Qiagen RNA extraction

value: cell line

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:28262; treatment_term_name:DMSO; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS242ZXS at ENCODE; https://www.encodeproject.org/ENCBS242ZXS/

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


title: CRISPR RNA-seq from HepG2 (ENCLB965WKM)

description:
https://www.encodeproject.org/experiments/ENCSR828XJV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APEH. (APEH-BGHcLV27)
experiment encode accession: ENCSR828XJV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB965WKM
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 APEH

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/78784177-fe59-4650-8d9b-34f5476865b3/@@download/attachment/L-APEH-BGHcLV27-9.pdf

value: APEH

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APEH. (APEH-BGHcLV27-9)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS904ZTD at ENCODE; https://www.encodeproject.org/ENCBS904ZTD/

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


title: total RNA-seq from K562 (ENCLB605TTS)

description:
https://www.encodeproject.org/experiments/ENCSR810ZKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with JQ1 for 24 hours
experiment encode accession: ENCSR810ZKJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB605TTS
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM JQ1 for 24 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:JQ1; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS667JAR at ENCODE; https://www.encodeproject.org/ENCBS667JAR/

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


title: CRISPR RNA-seq from K562 (ENCLB377VVP)

description:
https://www.encodeproject.org/experiments/ENCSR825RYR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CWC15. (CWC15-BGKcLV28)
experiment encode accession: ENCSR825RYR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB377VVP
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 CWC15

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f2ae84d8-e02c-4842-ae21-c9158412b3c2/@@download/attachment/L-CWC15-BGKcLV28-53.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CWC15. (CWC15-BGKcLV28-53)

value: Homo sapiens

value: adult

value: ENCBS757ZRT at ENCODE; https://www.encodeproject.org/ENCBS757ZRT/


title: total RNA-seq from A549 (ENCLB576GSD)

description:
https://www.encodeproject.org/experiments/ENCSR414IGI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR414IGI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB576GSD
size range: 200-300

value: male

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:28262; treatment_term_name:DMSO; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS380OHA at ENCODE; https://www.encodeproject.org/ENCBS380OHA/

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


title: CRISPR RNA-seq from HepG2 (ENCLB282FCX)

description:
https://www.encodeproject.org/experiments/ENCSR828XJV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APEH. (APEH-BGHcLV27)
experiment encode accession: ENCSR828XJV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB282FCX
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/ecc30269-ec12-4249-b718-fb8e2678662c/@@download/attachment/L-APEH-BGHcLV27-10.pdf

value: APEH

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APEH. (APEH-BGHcLV27-10)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS486BLT at ENCODE; https://www.encodeproject.org/ENCBS486BLT/

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


title: CRISPR RNA-seq from K562 (ENCLB130FIV)

description:
https://www.encodeproject.org/experiments/ENCSR825RYR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CWC15. (CWC15-BGKcLV28)
experiment encode accession: ENCSR825RYR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB130FIV
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/23434e9d-c42b-4be8-bbab-7dadc1f32aec/@@download/attachment/L-CWC15-BGKcLV28-54.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CWC15. (CWC15-BGKcLV28-54)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS922IOX at ENCODE; https://www.encodeproject.org/ENCBS922IOX/

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


title: CRISPR RNA-seq from HepG2 (ENCLB847JIH)

description:
https://www.encodeproject.org/experiments/ENCSR402BZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SF3A2. (SF3A2-BGHcLV24)
experiment encode accession: ENCSR402BZZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB847JIH
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 SF3A2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fcb40b29-e5a5-46db-ade7-20be3122cfbb/@@download/attachment/L-SF3A2-BGHcLV24-47.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SF3A2. (SF3A2-BGHcLV24-47)

value: male

value: ENCBS946OYT at ENCODE; https://www.encodeproject.org/ENCBS946OYT/


title: total RNA-seq from A549 (ENCLB574YBL)

description:
https://www.encodeproject.org/experiments/ENCSR414IGI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR414IGI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB574YBL
size range: 200-300

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:28262; treatment_term_name:DMSO; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS722LHW at ENCODE; https://www.encodeproject.org/ENCBS722LHW/

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


title: CRISPR RNA-seq from HepG2 (ENCLB087QPB)

description:
https://www.encodeproject.org/experiments/ENCSR402BZZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SF3A2. (SF3A2-BGHcLV24)
experiment encode accession: ENCSR402BZZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB087QPB
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/2e33946f-2d80-4bb2-818f-d99b2c4fb8a2/@@download/attachment/L-SF3A2-BGHcLV24-48.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SF3A2. (SF3A2-BGHcLV24-48)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS448YLZ at ENCODE; https://www.encodeproject.org/ENCBS448YLZ/

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


title: total RNA-seq from A549 (ENCLB054LLL)

description:
https://www.encodeproject.org/experiments/ENCSR414IGI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR414IGI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB054LLL
size range: 200-300

value: cell line

value: adult

value: ATCC

value: ENCBS625ZVV at ENCODE; https://www.encodeproject.org/ENCBS625ZVV/


title: total RNA-seq from A549 (ENCLB119YQM)

description:
https://www.encodeproject.org/experiments/ENCSR414IGI/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR414IGI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB119YQM
size range: 200-300

value: male

value: 58 year

value: ENCBS573XPO at ENCODE; https://www.encodeproject.org/ENCBS573XPO/


title: total RNA-seq from K562 (ENCLB945ALP)

description:
https://www.encodeproject.org/experiments/ENCSR810ZKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with JQ1 for 24 hours
experiment encode accession: ENCSR810ZKJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB945ALP
size range: 300-600

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:JQ1; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS216TDZ at ENCODE; https://www.encodeproject.org/ENCBS216TDZ/

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


title: CRISPR RNA-seq from K562 (ENCLB280SXO)

description:
https://www.encodeproject.org/experiments/ENCSR821KIN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM14. (RBM14-BGKcLV30)
experiment encode accession: ENCSR821KIN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB280SXO
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 RBM14

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4251004d-4bed-4779-b777-2ae31ea3f8c4/@@download/attachment/L-RBM14-BGKcLV30-5.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM14. (RBM14-BGKcLV30-5)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ENCBS334DIV at ENCODE; https://www.encodeproject.org/ENCBS334DIV/


title: CRISPR RNA-seq from K562 (ENCLB861EYW)

description:
https://www.encodeproject.org/experiments/ENCSR812JYP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ADK. (ADK-BGKcLV26)
experiment encode accession: ENCSR812JYP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB861EYW
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 ADK

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a9084bee-5a20-4e71-a4b7-3dc639fea04e/@@download/attachment/L-ADK-BGKcLV26-12.pdf

value: ADK

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ADK. (ADK-BGKcLV26-12)

value: adult

value: ATCC

value: ENCBS718XWF at ENCODE; https://www.encodeproject.org/ENCBS718XWF/


title: CRISPR RNA-seq from K562 (ENCLB613FJN)

description:
https://www.encodeproject.org/experiments/ENCSR812JYP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ADK. (ADK-BGKcLV26)
experiment encode accession: ENCSR812JYP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB613FJN
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/698084fe-f079-4ba2-814a-237f67daf621/@@download/attachment/L-ADK-BGKcLV26-11.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ADK. (ADK-BGKcLV26-11)

value: female

value: ENCBS502VJO at ENCODE; https://www.encodeproject.org/ENCBS502VJO/


title: Bru-seq from HCT116 (ENCLB363FYK)

description:
https://www.encodeproject.org/experiments/ENCSR810EZV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR810EZV
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB363FYK
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 BRD4

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS702UDW at ENCODE; https://www.encodeproject.org/ENCBS702UDW/

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


title: Bru-seq from HCT116 (ENCLB746FVF)

description:
https://www.encodeproject.org/experiments/ENCSR810EZV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR810EZV
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB746FVF
size range: 400-500

value: Homo sapiens

value: ENCBS762SPI at ENCODE; https://www.encodeproject.org/ENCBS762SPI/


title: Bru-seq from HCT116 (ENCLB286RSR)

description:
https://www.encodeproject.org/experiments/ENCSR423WIK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR423WIK
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB286RSR
size range: 400-500

value: cell line

value: ENCBS764AQQ at ENCODE; https://www.encodeproject.org/ENCBS764AQQ/


title: Bru-seq from HCT116 (ENCLB486SED)

description:
https://www.encodeproject.org/experiments/ENCSR384BVS/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR384BVS
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB486SED
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 SMARCA5

value: adult

value: ENCBS857ZTZ at ENCODE; https://www.encodeproject.org/ENCBS857ZTZ/


title: Bru-seq from HCT116 (ENCLB952PGF)

description:
https://www.encodeproject.org/experiments/ENCSR384BVS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR384BVS
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB952PGF
size range: 400-500

value: ENCBS383JCE at ENCODE; https://www.encodeproject.org/ENCBS383JCE/


title: Bru-seq from HCT116 (ENCLB284PMA)

description:
https://www.encodeproject.org/experiments/ENCSR808SOG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR808SOG
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR423WIK
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB284PMA
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 POLR2A treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

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

value: ENCBS497SRU at ENCODE; https://www.encodeproject.org/ENCBS497SRU/


title: total RNA-seq from K562 (ENCLB583NQH)

description:
https://www.encodeproject.org/experiments/ENCSR806HCA/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with GSK J4 for 12 hours
experiment encode accession: ENCSR806HCA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB583NQH
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 100 nM GSK J4 for 12 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:GSK J4; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS971GPH at ENCODE; https://www.encodeproject.org/ENCBS971GPH/

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


title: CRISPR RNA-seq from K562 (ENCLB200FHT)

description:
https://www.encodeproject.org/experiments/ENCSR383FCI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CD2BP2. (CD2BP2-BGKcLV33)
experiment encode accession: ENCSR383FCI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB200FHT
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 RPS28

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4629fb9a-0a95-49ec-baea-782a45c52187/@@download/attachment/L-CD2BP2-BGKcLV33-6.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CD2BP2. (CD2BP2-BGKcLV33-6)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ENCBS321ZFD at ENCODE; https://www.encodeproject.org/ENCBS321ZFD/


title: CRISPR RNA-seq from K562 (ENCLB118EXU)

description:
https://www.encodeproject.org/experiments/ENCSR821KIN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM14. (RBM14-BGKcLV30)
experiment encode accession: ENCSR821KIN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB118EXU
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/de9c7fce-fde3-43c4-a6d9-175dec54d1ee/@@download/attachment/L-RBM14-BGKcLV30-6.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM14. (RBM14-BGKcLV30-6)

value: adult

value: ENCBS590JCA at ENCODE; https://www.encodeproject.org/ENCBS590JCA/


title: Bru-seq from HCT116 (ENCLB087ULK)

description:
https://www.encodeproject.org/experiments/ENCSR808SOG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR808SOG
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR423WIK
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB087ULK
size range: 400-500

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: ENCBS497REY at ENCODE; https://www.encodeproject.org/ENCBS497REY/

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


title: total RNA-seq from K562 (ENCLB889OKK)

description:
https://www.encodeproject.org/experiments/ENCSR806HCA/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with GSK J4 for 12 hours
experiment encode accession: ENCSR806HCA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB889OKK
size range: 300-600

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:GSK J4; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS428HIV at ENCODE; https://www.encodeproject.org/ENCBS428HIV/

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


title: CRISPR RNA-seq from K562 (ENCLB212ZTZ)

description:
https://www.encodeproject.org/experiments/ENCSR383FCI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CD2BP2. (CD2BP2-BGKcLV33)
experiment encode accession: ENCSR383FCI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB212ZTZ
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/1f4e1550-7162-46fb-a41b-2e3f6e7c690e/@@download/attachment/L-CD2BP2-BGKcLV33-5.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CD2BP2. (CD2BP2-BGKcLV33-5)

value: Homo sapiens

value: adult

value: Brenton Graveley, UConn

value: ENCBS934KIY at ENCODE; https://www.encodeproject.org/ENCBS934KIY/


title: total RNA-seq from motor neuron (ENCLB010YQI)

description:
https://www.encodeproject.org/experiments/ENCSR373XVN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR373XVN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB010YQI
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: male

value: Donor with Amyotrophic Lateral Sclerosis

value: 47 year

value: Michael Snyder, Stanford

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

value: ENCBS833WEY at ENCODE; https://www.encodeproject.org/ENCBS833WEY/

value: Derived from ENCODE donor ENCDO565NIZ; https://www.encodeproject.org/ENCDO565NIZ/


title: Bru-seq from HCT116 (ENCLB959NPA)

description:
https://www.encodeproject.org/experiments/ENCSR801TQK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR801TQK
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR384BVS
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB959NPA
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 SMARCA5 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

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: ENCBS667CTF at ENCODE; https://www.encodeproject.org/ENCBS667CTF/

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


title: Bru-seq from HCT116 (ENCLB558BXL)

description:
https://www.encodeproject.org/experiments/ENCSR366XGV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR366XGV
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR945UXU
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB558BXL
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 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: Homo sapiens

value: adult

value: ENCBS142IPM at ENCODE; https://www.encodeproject.org/ENCBS142IPM/


title: total RNA-seq from motor neuron (ENCLB636CIV)

description:
https://www.encodeproject.org/experiments/ENCSR373XVN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR373XVN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB636CIV
size range: 300-600

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: male

value: Donor with Amyotrophic Lateral Sclerosis

value: ENCBS643AJQ at ENCODE; https://www.encodeproject.org/ENCBS643AJQ/


title: Bru-seq from HCT116 (ENCLB159KEM)

description:
https://www.encodeproject.org/experiments/ENCSR366XGV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR366XGV
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR945UXU
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB159KEM
size range: 400-500

value: colorectal carcinoma

value: ENCBS485QLG at ENCODE; https://www.encodeproject.org/ENCBS485QLG/


title: CRISPR RNA-seq from HepG2 (ENCLB572CNO)

description:
https://www.encodeproject.org/experiments/ENCSR363NMO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AHCYL2. (AHCYL2-BGHcLV25)
experiment encode accession: ENCSR363NMO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB572CNO
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 AHCYL2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bbc5a110-59b3-46d9-a27a-8e73459badde/@@download/attachment/L-AHCYL2-BGHcLV25-21.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AHCYL2. (AHCYL2-BGHcLV25-21)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS060QNZ at ENCODE; https://www.encodeproject.org/ENCBS060QNZ/

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


title: total RNA-seq from K562 (ENCLB106OAH)

description:
https://www.encodeproject.org/experiments/ENCSR798RDG/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with GSK J4 for 48 hours
experiment encode accession: ENCSR798RDG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB106OAH
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 100 nM GSK J4 for 48 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: adult

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:GSK J4; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS267ADR at ENCODE; https://www.encodeproject.org/ENCBS267ADR/

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


title: BruChase-seq from A673 (ENCLB537JDP)

description:
https://www.encodeproject.org/experiments/ENCSR380EZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR380EZD
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR912SRZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB537JDP
size range: 400-500

source_name: Homo sapiens A673 cell line, subjected to a 6 hour pulse-chase

value: child

value: Mats Ljungman, UMichigan

value: ENCBS615UOZ at ENCODE; https://www.encodeproject.org/ENCBS615UOZ/

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


title: total RNA-seq from K562 (ENCLB006NZI)

description:
https://www.encodeproject.org/experiments/ENCSR363HQX/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with C646 for 48 hours
experiment encode accession: ENCSR363HQX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB006NZI
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 50 uM C646 for 48 hours, preserved by flash-freezing

value: ATCC

value: treatment_term_name:C646; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS338LGZ at ENCODE; https://www.encodeproject.org/ENCBS338LGZ/


title: total RNA-seq from K562 (ENCLB716NLS)

description:
https://www.encodeproject.org/experiments/ENCSR363HQX/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with C646 for 48 hours
experiment encode accession: ENCSR363HQX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB716NLS
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: ENCBS881VLN at ENCODE; https://www.encodeproject.org/ENCBS881VLN/


title: CRISPR RNA-seq from HepG2 (ENCLB200COM)

description:
https://www.encodeproject.org/experiments/ENCSR785SZL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGHcLV31)
experiment encode accession: ENCSR785SZL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB200COM
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 RUVBL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e8b38f2e-52f7-40cf-b12a-d3b9b68fc5e2/@@download/attachment/L-RUVBL1-BGHcLV31-19.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGHcLV31-19)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS332QIZ at ENCODE; https://www.encodeproject.org/ENCBS332QIZ/

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


title: CRISPR RNA-seq from K562 (ENCLB268TQL)

description:
https://www.encodeproject.org/experiments/ENCSR785JUR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against APEH. (APEH-BGKcLV26)
experiment encode accession: ENCSR785JUR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB268TQL
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 APEH

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f5746fda-5829-44aa-abcd-79e267a9c4a8/@@download/attachment/L-APEH-BGKcLV26-25.pdf

value: APEH

value: RNA-seq on K562 cells treated with a CRISPR gRNA against APEH. (APEH-BGKcLV26-25)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS022KRD at ENCODE; https://www.encodeproject.org/ENCBS022KRD/

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


title: total RNA-seq from K562 (ENCLB179UFZ)

description:
https://www.encodeproject.org/experiments/ENCSR798RDG/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with GSK J4 for 48 hours
experiment encode accession: ENCSR798RDG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB179UFZ
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:GSK J4; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS896CZM at ENCODE; https://www.encodeproject.org/ENCBS896CZM/


title: total RNA-seq from K562 (ENCLB950QUX)

description:
https://www.encodeproject.org/experiments/ENCSR379BAF/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with MB-3 for 48 hours
experiment encode accession: ENCSR379BAF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB950QUX
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM MB-3 for 48 hours, preserved by flash-freezing

value: Homo sapiens

value: treatment_term_name:MB-3; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS218CMH at ENCODE; https://www.encodeproject.org/ENCBS218CMH/


title: total RNA-seq from K562 (ENCLB109FSB)

description:
https://www.encodeproject.org/experiments/ENCSR369MDF/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with JQ1 for 4 hours
experiment encode accession: ENCSR369MDF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB109FSB
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM JQ1 for 4 hours, preserved by flash-freezing

value: treatment_term_name:JQ1; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS291NHT at ENCODE; https://www.encodeproject.org/ENCBS291NHT/


title: CRISPR RNA-seq from K562 (ENCLB751ZRF)

description:
https://www.encodeproject.org/experiments/ENCSR785JUR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against APEH. (APEH-BGKcLV26)
experiment encode accession: ENCSR785JUR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB751ZRF
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/6dc01d25-1ba5-487c-8fc0-91ee11470e30/@@download/attachment/L-APEH-BGKcLV26-26.pdf

value: APEH

value: RNA-seq on K562 cells treated with a CRISPR gRNA against APEH. (APEH-BGKcLV26-26)

value: female

value: Brenton Graveley, UConn

value: ENCBS652DFI at ENCODE; https://www.encodeproject.org/ENCBS652DFI/


title: total RNA-seq from K562 (ENCLB406IVC)

description:
https://www.encodeproject.org/experiments/ENCSR379BAF/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with MB-3 for 48 hours
experiment encode accession: ENCSR379BAF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB406IVC
size range: 300-600

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS735KPW at ENCODE; https://www.encodeproject.org/ENCBS735KPW/

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


title: BruChase-seq from MCF 10A (ENCLB284KTG)

description:
https://www.encodeproject.org/experiments/ENCSR780VOL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR780VOL
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR444JTC
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB284KTG
size range: 400-500

source_name: Homo sapiens MCF 10A cell line, subjected to a 2 hour pulse-chase

value: MCF 10A

value: cell line

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS502BBM at ENCODE; https://www.encodeproject.org/ENCBS502BBM/

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


title: PRO-cap from HCT116 (ENCLB302UCX)

description:
https://www.encodeproject.org/experiments/ENCSR360MUR/
***************
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 BRD4_U.
experiment encode accession: ENCSR360MUR
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB302UCX
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 BRD4

value: Homo sapiens

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS214JQO at ENCODE; https://www.encodeproject.org/ENCBS214JQO/

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


title: CRISPR RNA-seq from HepG2 (ENCLB074MTY)

description:
https://www.encodeproject.org/experiments/ENCSR785SZL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGHcLV31)
experiment encode accession: ENCSR785SZL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB074MTY
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/6ec61ca2-f52b-4c4e-97b0-d88b939ac920/@@download/attachment/L-RUVBL1-BGHcLV31-20.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGHcLV31-20)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS092QEJ at ENCODE; https://www.encodeproject.org/ENCBS092QEJ/

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


title: total RNA-seq from motor neuron (ENCLB879SOY)

description:
https://www.encodeproject.org/experiments/ENCSR350OKU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR350OKU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB879SOY
size range: 300-600

source_name: Homo sapiens female adult motor neuron in vitro differentiated cells, preserved by flash-freezing

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: female

value: Healthy donor

value: adult

value: unknown

value: Michael Snyder, Stanford

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

value: ENCBS675YCF at ENCODE; https://www.encodeproject.org/ENCBS675YCF/

value: Derived from ENCODE donor ENCDO689YDN; https://www.encodeproject.org/ENCDO689YDN/


title: CRISPR RNA-seq from HepG2 (ENCLB617BGA)

description:
https://www.encodeproject.org/experiments/ENCSR363NMO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AHCYL2. (AHCYL2-BGHcLV25)
experiment encode accession: ENCSR363NMO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB617BGA
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/504e8b09-e59a-43c3-a965-248c914c332c/@@download/attachment/L-AHCYL2-BGHcLV25-22.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AHCYL2. (AHCYL2-BGHcLV25-22)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: ATCC

value: ENCBS617TDS at ENCODE; https://www.encodeproject.org/ENCBS617TDS/


title: total RNA-seq from motor neuron (ENCLB463GSP)

description:
https://www.encodeproject.org/experiments/ENCSR350OKU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR350OKU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB463GSP
size range: 300-600

value: motor neuron

value: in vitro differentiated cells

value: ENCBS671RRR at ENCODE; https://www.encodeproject.org/ENCBS671RRR/


title: PRO-cap from HCT116 (ENCLB331MAK)

description:
https://www.encodeproject.org/experiments/ENCSR360MUR/
***************
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 BRD4_U.
experiment encode accession: ENCSR360MUR
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB331MAK
spikeins used: The drosophila spike-in reference used for alignment

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS930EMD at ENCODE; https://www.encodeproject.org/ENCBS930EMD/

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


title: Bru-seq from HCT116 (ENCLB266ITY)

description:
https://www.encodeproject.org/experiments/ENCSR801TQK/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR801TQK
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR384BVS
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB266ITY
size range: 400-500

value: adult

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

value: ENCBS918VLM at ENCODE; https://www.encodeproject.org/ENCBS918VLM/


title: CRISPR RNA-seq from HepG2 (ENCLB182GWK)

description:
https://www.encodeproject.org/experiments/ENCSR780UNO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGHcLV31)
experiment encode accession: ENCSR780UNO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB182GWK
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 MTREX

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1aaf287d-89f1-416c-a63f-17a5b183875b/@@download/attachment/L-SKIV2L2-BGHcLV31-4.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGHcLV31-4)

value: Homo sapiens

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS481PFI at ENCODE; https://www.encodeproject.org/ENCBS481PFI/

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


title: total RNA-seq from K562 (ENCLB803LTG)

description:
https://www.encodeproject.org/experiments/ENCSR369MDF/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with JQ1 for 4 hours
experiment encode accession: ENCSR369MDF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB803LTG
size range: 300-600

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:JQ1; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS798JQV at ENCODE; https://www.encodeproject.org/ENCBS798JQV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB019RTY)

description:
https://www.encodeproject.org/experiments/ENCSR780UNO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGHcLV31)
experiment encode accession: ENCSR780UNO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB019RTY
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/aecd0d85-8363-45eb-a9d6-1485fa31c199/@@download/attachment/L-SKIV2L2-BGHcLV31-3.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGHcLV31-3)

value: male

value: hepatocellular carcinoma

value: ENCBS994SIY at ENCODE; https://www.encodeproject.org/ENCBS994SIY/


title: BruChase-seq from A673 (ENCLB147EFC)

description:
https://www.encodeproject.org/experiments/ENCSR380EZD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR380EZD
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR912SRZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB147EFC
size range: 400-500

value: Homo sapiens

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ENCBS155PQE at ENCODE; https://www.encodeproject.org/ENCBS155PQE/

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


title: Bru-seq from Caco-2 (ENCLB239JDX)

description:
https://www.encodeproject.org/experiments/ENCSR346ANR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR346ANR
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR892NYB
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB239JDX
size range: 400-500

source_name: Homo sapiens Caco-2 cell line treated with 500 rad irradiation

value: colorectal adenocarcinoma

value: adult

value: 72 year

value: ENCBS201TJP at ENCODE; https://www.encodeproject.org/ENCBS201TJP/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: CRISPR RNA-seq from K562 (ENCLB605ETO)

description:
https://www.encodeproject.org/experiments/ENCSR347NKX/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV30)
experiment encode accession: ENCSR347NKX
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB605ETO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/765d0b60-fc58-42c2-841c-f3b4dbfc4b10/@@download/attachment/L-NT-BGKcLV30-2.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV30-2)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS529AZE at ENCODE; https://www.encodeproject.org/ENCBS529AZE/

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


title: BruChase-seq from MCF 10A (ENCLB114FXG)

description:
https://www.encodeproject.org/experiments/ENCSR780VOL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR780VOL
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR444JTC
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB114FXG
size range: 400-500

value: MCF 10A

value: cell line

value: Homo sapiens

value: fibrocystic disease

value: 36 year

value: ENCBS168DEU at ENCODE; https://www.encodeproject.org/ENCBS168DEU/

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


title: Bru-seq from Caco-2 (ENCLB755LJJ)

description:
https://www.encodeproject.org/experiments/ENCSR346ANR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR346ANR
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR892NYB
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB755LJJ
size range: 400-500

value: male

value: colorectal adenocarcinoma

value: adult

value: 72 year

value: Mats Ljungman, UMichigan

value: ENCBS735CVU at ENCODE; https://www.encodeproject.org/ENCBS735CVU/


title: CRISPR RNA-seq from K562 (ENCLB622QOQ)

description:
https://www.encodeproject.org/experiments/ENCSR347NKX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV30)
experiment encode accession: ENCSR347NKX
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB622QOQ
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/142dd061-5b53-42cb-a5e5-c08a17ab86f2/@@download/attachment/L-NT-BGKcLV30-1.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV30-1)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS915DVB at ENCODE; https://www.encodeproject.org/ENCBS915DVB/


title: CRISPR RNA-seq from HepG2 (ENCLB203ISS)

description:
https://www.encodeproject.org/experiments/ENCSR340ZLQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATP5A1. (ATP5A1-BGHcLV29)
experiment encode accession: ENCSR340ZLQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB203ISS
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 ATP5F1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e43e48f2-e3fd-4be4-aa49-613753596a1d/@@download/attachment/L-ATP5A1-BGHcLV29-10.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATP5A1. (ATP5A1-BGHcLV29-10)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS266VSE at ENCODE; https://www.encodeproject.org/ENCBS266VSE/

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


title: total RNA-seq from K562 (ENCLB394IGY)

description:
https://www.encodeproject.org/experiments/ENCSR340QZY/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with AR-42 for 12 hours
experiment encode accession: ENCSR340QZY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB394IGY
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 uM AR-42 for 12 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: adult

value: Will Greenleaf, Stanford

value: treatment_term_name:AR-42; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS032OUD at ENCODE; https://www.encodeproject.org/ENCBS032OUD/

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


title: Bru-seq from mammary epithelial cell (ENCLB349NGD)

description:
https://www.encodeproject.org/experiments/ENCSR771GZH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR771GZH
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR419IWZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB349NGD
size range: 400-500

source_name: Homo sapiens female adult (19 years) mammary epithelial primary cell treated with 500 rad irradiation

value: mammary epithelial cell

value: primary cell

value: female

value: 19 year

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS176FEN at ENCODE; https://www.encodeproject.org/ENCBS176FEN/

value: Derived from ENCODE donor ENCDO955XOD; https://www.encodeproject.org/ENCDO955XOD/


title: Bru-seq from mammary epithelial cell (ENCLB389BIO)

description:
https://www.encodeproject.org/experiments/ENCSR771GZH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR771GZH
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR419IWZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB389BIO
size range: 400-500

value: Homo sapiens

value: ENCBS391LZS at ENCODE; https://www.encodeproject.org/ENCBS391LZS/


title: BruChase-seq from PC-9 (ENCLB225CFJ)

description:
https://www.encodeproject.org/experiments/ENCSR340JNN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR340JNN
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR223GHJ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB225CFJ
size range: 400-500

source_name: Homo sapiens PC-9 cell line, subjected to a 2 hour pulse-chase

value: cell line

value: not collected

value: unknown

value: Sigma

value: ENCBS823LFQ at ENCODE; https://www.encodeproject.org/ENCBS823LFQ/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: BruChase-seq from PC-9 (ENCLB026SME)

description:
https://www.encodeproject.org/experiments/ENCSR340JNN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR340JNN
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR223GHJ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB026SME
size range: 400-500

value: ENCBS592HZY at ENCODE; https://www.encodeproject.org/ENCBS592HZY/


title: total RNA-seq from K562 (ENCLB088VJW)

description:
https://www.encodeproject.org/experiments/ENCSR340QZY/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with AR-42 for 12 hours
experiment encode accession: ENCSR340QZY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB088VJW
size range: 300-600

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:AR-42; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS517FMR at ENCODE; https://www.encodeproject.org/ENCBS517FMR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB627DOE)

description:
https://www.encodeproject.org/experiments/ENCSR339XFB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF7. (CPSF7-BGHcLV29)
experiment encode accession: ENCSR339XFB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB627DOE
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 CPSF7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7898132b-56d6-466c-a23f-d242e4d129e9/@@download/attachment/L-CPSF7-BGHcLV29-39.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF7. (CPSF7-BGHcLV29-39)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS315ZKM at ENCODE; https://www.encodeproject.org/ENCBS315ZKM/

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


title: microRNA-seq from heart (ENCLB478EZY)

description:
https://www.encodeproject.org/experiments/ENCSR289DPI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND4 male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR289DPI
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB478EZY
size range: <30

organism: Mus musculus

source_name: Mus musculus strain B6CASTF1/J male (4 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND4 Male 03 heart for Wold biobank

value: unknown

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS148ESM at ENCODE; https://www.encodeproject.org/ENCBS148ESM/

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


title: microRNA-seq from heart (ENCLB331JCH)

description:
https://www.encodeproject.org/experiments/ENCSR289DPI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND4 male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR289DPI
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB331JCH
size range: <30

value: B6Cast F1 PND4 Male 04 heart for Wold biobank

value: ENCBS987ISY at ENCODE; https://www.encodeproject.org/ENCBS987ISY/


title: CRISPR RNA-seq from HepG2 (ENCLB303IHK)

description:
https://www.encodeproject.org/experiments/ENCSR339XFB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF7. (CPSF7-BGHcLV29)
experiment encode accession: ENCSR339XFB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB303IHK
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/f448568f-1ab2-4c1a-b092-640dd8d30da6/@@download/attachment/L-CPSF7-BGHcLV29-40.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF7. (CPSF7-BGHcLV29-40)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: ATCC

value: ENCBS512BUS at ENCODE; https://www.encodeproject.org/ENCBS512BUS/


title: microRNA-seq from heart (ENCLB500MLU)

description:
https://www.encodeproject.org/experiments/ENCSR998JES/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND10 male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR998JES
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB500MLU
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (10 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND10 Male 03 heart for Wold biobank

value: 10 day

value: ENCBS840HGS at ENCODE; https://www.encodeproject.org/ENCBS840HGS/


title: CRISPR RNA-seq from K562 (ENCLB570OVB)

description:
https://www.encodeproject.org/experiments/ENCSR778XFE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BMS1. (BMS1-BGKcLV33)
experiment encode accession: ENCSR778XFE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB570OVB
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 RPS21

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6d090a7b-64f8-4870-a2f9-980429793f14/@@download/attachment/L-BMS1-BGKcLV33-3.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BMS1. (BMS1-BGKcLV33-3)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS045QZE at ENCODE; https://www.encodeproject.org/ENCBS045QZE/

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


title: total RNA-seq from K562 (ENCLB254QIH)

description:
https://www.encodeproject.org/experiments/ENCSR758BAT/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with C646 for 4 hours
experiment encode accession: ENCSR758BAT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB254QIH
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 50 uM C646 for 4 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: Will Greenleaf, Stanford

value: treatment_term_name:C646; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS429CMY at ENCODE; https://www.encodeproject.org/ENCBS429CMY/


title: microRNA-seq from gastrocnemius (ENCLB560MBI)

description:
https://www.encodeproject.org/experiments/ENCSR968IVY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR968IVY
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB560MBI
size range: <30

source_name: Mus musculus strain 5xFAD/CAST female adult (8-10 months) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: Mus musculus

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS105OZV at ENCODE; https://www.encodeproject.org/ENCBS105OZV/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: microRNA-seq from heart (ENCLB187PHU)

description:
https://www.encodeproject.org/experiments/ENCSR998JES/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND10 male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR998JES
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB187PHU
size range: <30

value: heart

value: B6Cast F1 PND10 Male 04 heart for Wold biobank

value: male

value: unknown

value: 10 day

value: ENCBS734HOK at ENCODE; https://www.encodeproject.org/ENCBS734HOK/

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


title: CRISPR RNA-seq from HepG2 (ENCLB533IXC)

description:
https://www.encodeproject.org/experiments/ENCSR333JNM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGHcLV32)
experiment encode accession: ENCSR333JNM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB533IXC
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 RPL29

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/af978095-9be1-4b29-9973-4698460e71cc/@@download/attachment/L-RPL29-BGHcLV32-46.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGHcLV32-46)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS446TXU at ENCODE; https://www.encodeproject.org/ENCBS446TXU/

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


title: CRISPR RNA-seq from HepG2 (ENCLB921JRQ)

description:
https://www.encodeproject.org/experiments/ENCSR333JNM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGHcLV32)
experiment encode accession: ENCSR333JNM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB921JRQ
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/eb9d867c-f808-4af5-8f9f-0048f327f4b8/@@download/attachment/L-RPL29-BGHcLV32-45.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGHcLV32-45)

value: ENCBS455JAT at ENCODE; https://www.encodeproject.org/ENCBS455JAT/


title: CRISPR RNA-seq from K562 (ENCLB522WZE)

description:
https://www.encodeproject.org/experiments/ENCSR778XFE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BMS1. (BMS1-BGKcLV33)
experiment encode accession: ENCSR778XFE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB522WZE
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/75e60020-91c2-41f7-a55a-2661e45db71f/@@download/attachment/L-BMS1-BGKcLV33-4.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BMS1. (BMS1-BGKcLV33-4)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS786TTZ at ENCODE; https://www.encodeproject.org/ENCBS786TTZ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB725HCJ)

description:
https://www.encodeproject.org/experiments/ENCSR755DOV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGHcLV29)
experiment encode accession: ENCSR755DOV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB725HCJ
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 CTTN

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0478d553-bbe3-4b23-91b5-1351c1235c55/@@download/attachment/L-CTTN-BGHcLV29-51.pdf

value: CTTN

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGHcLV29-51)

value: Homo sapiens

value: male

value: ENCBS094EUX at ENCODE; https://www.encodeproject.org/ENCBS094EUX/


title: microRNA-seq from heart (ENCLB589MGX)

description:
https://www.encodeproject.org/experiments/ENCSR911AIY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND10 female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR911AIY
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB589MGX
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (10 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND10 Female 04 heart for Wold biobank

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS726RAM at ENCODE; https://www.encodeproject.org/ENCBS726RAM/

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


title: CRISPR RNA-seq from HepG2 (ENCLB347ELK)

description:
https://www.encodeproject.org/experiments/ENCSR755DOV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGHcLV29)
experiment encode accession: ENCSR755DOV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB347ELK
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/9b62101b-bb6e-4378-9b4e-e9d6f9fef165/@@download/attachment/L-CTTN-BGHcLV29-52.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGHcLV29-52)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS984YEV at ENCODE; https://www.encodeproject.org/ENCBS984YEV/

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


title: CRISPR RNA-seq from K562 (ENCLB778RCO)

description:
https://www.encodeproject.org/experiments/ENCSR331MLG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CLASP2. (CLASP2-BGKcLV28)
experiment encode accession: ENCSR331MLG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB778RCO
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 CLASP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/65406357-0bbc-4592-9a9c-4376ecca472d/@@download/attachment/L-CLASP2-BGKcLV28-20.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CLASP2. (CLASP2-BGKcLV28-20)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS686VHT at ENCODE; https://www.encodeproject.org/ENCBS686VHT/

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


title: microRNA-seq from heart (ENCLB441XLS)

description:
https://www.encodeproject.org/experiments/ENCSR858AUW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND14 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR858AUW
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB441XLS
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (14 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND14 Female 04 heart for Wold biobank

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS807VSF at ENCODE; https://www.encodeproject.org/ENCBS807VSF/

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


title: microRNA-seq from heart (ENCLB315REQ)

description:
https://www.encodeproject.org/experiments/ENCSR858AUW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND14 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR858AUW
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB315REQ
size range: <30

value: B6Cast F1 PND14 3x Females 03 heart for Wold biobank

value: ENCBS976RBP at ENCODE; https://www.encodeproject.org/ENCBS976RBP/


title: CRISPR RNA-seq from K562 (ENCLB094LSK)

description:
https://www.encodeproject.org/experiments/ENCSR331MLG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CLASP2. (CLASP2-BGKcLV28)
experiment encode accession: ENCSR331MLG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB094LSK
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/818d3fd8-4ce7-4a1f-a8c2-30137c897a61/@@download/attachment/L-CLASP2-BGKcLV28-19.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CLASP2. (CLASP2-BGKcLV28-19)

value: Homo sapiens

value: female

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS725YIG at ENCODE; https://www.encodeproject.org/ENCBS725YIG/