title: total RNA-seq from K562 (ENCLB184IEH)

status: Public on Dec 04 2022

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR015SAT/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Crizotinib for 48 hours
experiment encode accession: ENCSR015SAT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB184IEH
size range: 300-600

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

source_name: Homo sapiens K562 cell line treated with 10 uM Crizotinib for 48 hours, preserved by flash-freezing

tag: line

value: cell line

tag: description

value: RNA-seq on human cell line K562

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

value: 53 year

tag: lab

value: Will Greenleaf, Stanford

tag: source

value: ATCC

tag: treatments

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

tag: link

value: ENCBS620SIZ at ENCODE; https://www.encodeproject.org/ENCBS620SIZ/

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


title: total RNA-seq from K562 (ENCLB214OSX)

type: SRA

country: USA

description:
https://www.encodeproject.org/experiments/ENCSR518BSQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Crizotinib for 4 hours
experiment encode accession: ENCSR518BSQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB214OSX
size range: 300-600

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line treated with 10 uM Crizotinib for 4 hours, preserved by flash-freezing

tag: age

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

value: ENCBS209BLC at ENCODE; https://www.encodeproject.org/ENCBS209BLC/


title: total RNA-seq from K562 (ENCLB323BTM)

description:
https://www.encodeproject.org/experiments/ENCSR518BSQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Crizotinib for 4 hours
experiment encode accession: ENCSR518BSQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB323BTM
size range: 300-600

value: ENCBS084LOL at ENCODE; https://www.encodeproject.org/ENCBS084LOL/


title: WA_PIZZ1MZ (10X)

status: Public on Dec 06 2022

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

data_processing:
The sample was processed using the standard cellranger pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the STARsolo count pipeline:

molecule: polyA RNA

extract_protocol:
10X Chromium system
NextSeq 500

tag: cell type

value: hepatic


title: CRISPR RNA-seq from HepG2 (ENCLB667ZNE)

description:
https://www.encodeproject.org/experiments/ENCSR513CVF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGHcLV29)
experiment encode accession: ENCSR513CVF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB667ZNE
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 CLNS1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/27261188-bf8c-4806-bc41-642d7b9afbd7/@@download/attachment/L-CLNS1A-BGHcLV29-22.pdf

tag: antibody

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGHcLV29-22)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS286JRV at ENCODE; https://www.encodeproject.org/ENCBS286JRV/

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


title: BruChase-seq from OCI-LY7 (ENCLB321HLD)

description:
https://www.encodeproject.org/experiments/ENCSR014FMT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR014FMT
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR121MLV
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB321HLD
size range: 400-500

source_name: Homo sapiens OCI-LY7 cell line, subjected to a 2 hour pulse-chase

value: cell line

value: Homo sapiens

value: B cell lymphoma

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS969SKN at ENCODE; https://www.encodeproject.org/ENCBS969SKN/

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


title: CRISPR RNA-seq from K562 (ENCLB775UIS)

description:
https://www.encodeproject.org/experiments/ENCSR012OCK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BYSL. (BYSL-BGKcLV26)
experiment encode accession: ENCSR012OCK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB775UIS
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 BYSL

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/eaae0e3b-bc23-4b4f-b49a-cab0be81b090/@@download/attachment/L-BYSL-BGKcLV26-44.pdf

value: BYSL

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BYSL. (BYSL-BGKcLV26-44)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS033RQQ at ENCODE; https://www.encodeproject.org/ENCBS033RQQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB885KIA)

description:
https://www.encodeproject.org/experiments/ENCSR512BIT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGHcLV27)
experiment encode accession: ENCSR512BIT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB885KIA
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 AIMP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0b2ac2fc-a245-4d94-94f6-bc0ee156e835/@@download/attachment/L-AIMP1-BGHcLV27-4.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGHcLV27-4)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS317HMK at ENCODE; https://www.encodeproject.org/ENCBS317HMK/

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


title: CRISPR RNA-seq from HepG2 (ENCLB108BSV)

description:
https://www.encodeproject.org/experiments/ENCSR513CVF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGHcLV29)
experiment encode accession: ENCSR513CVF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB108BSV
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/79d4c990-0653-4449-ba6e-b7a5cc63cd3e/@@download/attachment/L-CLNS1A-BGHcLV29-21.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGHcLV29-21)

value: Homo sapiens

value: ENCBS418TNU at ENCODE; https://www.encodeproject.org/ENCBS418TNU/


title: total RNA-seq from motor neuron (ENCLB119YNE)

description:
https://www.encodeproject.org/experiments/ENCSR499AEH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR499AEH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB119YNE
size range: 300-600

source_name: Homo sapiens male adult (55 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: Healthy donor

value: adult

value: 55 year

value: Michael Snyder, Stanford

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

value: ENCBS433QBR at ENCODE; https://www.encodeproject.org/ENCBS433QBR/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: CRISPR RNA-seq from K562 (ENCLB420UVY)

description:
https://www.encodeproject.org/experiments/ENCSR507WAD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX23. (DDX23-BGKcLV28)
experiment encode accession: ENCSR507WAD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB420UVY
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 DDX23

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/78ed52ae-7533-4153-a1f3-6b050cf67de1/@@download/attachment/L-DDX23-BGKcLV28-74.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX23. (DDX23-BGKcLV28-74)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS852NWS at ENCODE; https://www.encodeproject.org/ENCBS852NWS/

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


title: CRISPR RNA-seq from HepG2 (ENCLB765QLM)

description:
https://www.encodeproject.org/experiments/ENCSR512BIT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGHcLV27)
experiment encode accession: ENCSR512BIT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB765QLM
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/1a100198-0697-4aec-a32e-06fc3b1d7090/@@download/attachment/L-AIMP1-BGHcLV27-3.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGHcLV27-3)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS854FIQ at ENCODE; https://www.encodeproject.org/ENCBS854FIQ/

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


title: BruChase-seq from OCI-LY7 (ENCLB579XRI)

description:
https://www.encodeproject.org/experiments/ENCSR014FMT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR014FMT
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR121MLV
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB579XRI
size range: 400-500

value: cell line

value: B cell lymphoma

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS327BWP at ENCODE; https://www.encodeproject.org/ENCBS327BWP/

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


title: CRISPR RNA-seq from HepG2 (ENCLB510VMT)

description:
https://www.encodeproject.org/experiments/ENCSR511EKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGHcLV24)
experiment encode accession: ENCSR511EKJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB510VMT
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 ELAC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/43f1f2f9-c3e2-433d-8bdb-5ba79fb39ae6/@@download/attachment/L-ELAC2-BGHcLV24-31.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGHcLV24-31)

value: ATCC

value: ENCBS167JZF at ENCODE; https://www.encodeproject.org/ENCBS167JZF/


title: BruChase-seq from OCI-LY7 (ENCLB312WOQ)

description:
https://www.encodeproject.org/experiments/ENCSR012JHB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR012JHB
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR121MLV
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB312WOQ
size range: 400-500

source_name: Homo sapiens OCI-LY7 cell line, subjected to a 6 hour pulse-chase

value: Homo sapiens

value: male

value: ENCBS701GNL at ENCODE; https://www.encodeproject.org/ENCBS701GNL/


title: CRISPR RNA-seq from HepG2 (ENCLB034NYK)

description:
https://www.encodeproject.org/experiments/ENCSR511EKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGHcLV24)
experiment encode accession: ENCSR511EKJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB034NYK
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/f2b33294-6c06-4223-9cfc-bd87916337ed/@@download/attachment/L-ELAC2-BGHcLV24-32.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGHcLV24-32)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS626EZN at ENCODE; https://www.encodeproject.org/ENCBS626EZN/


title: BruChase-seq from OCI-LY7 (ENCLB684LWE)

description:
https://www.encodeproject.org/experiments/ENCSR012JHB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR012JHB
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR121MLV
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB684LWE
size range: 400-500

value: cell line

value: B cell lymphoma

value: adult

value: 48 year

value: ENCBS797PYL at ENCODE; https://www.encodeproject.org/ENCBS797PYL/


title: total RNA-seq from motor neuron (ENCLB903BIS)

description:
https://www.encodeproject.org/experiments/ENCSR499AEH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR499AEH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB903BIS
size range: 300-600

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: Healthy donor

value: 55 year

value: Michael Snyder, Stanford

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

value: ENCBS890OMC at ENCODE; https://www.encodeproject.org/ENCBS890OMC/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: Bru-seq from HCT116 (ENCLB602OLK)

description:
https://www.encodeproject.org/experiments/ENCSR008ZZZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR008ZZZ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB602OLK
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 CDK7

value: Homo sapiens

value: male

value: colorectal carcinoma

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS774XNI at ENCODE; https://www.encodeproject.org/ENCBS774XNI/

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


title: CRISPR RNA-seq from K562 (ENCLB435ULD)

description:
https://www.encodeproject.org/experiments/ENCSR012OCK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BYSL. (BYSL-BGKcLV26)
experiment encode accession: ENCSR012OCK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB435ULD
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/06cfb0a8-269a-41b0-8230-66ac65d6c0e2/@@download/attachment/L-BYSL-BGKcLV26-43.pdf

value: BYSL

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BYSL. (BYSL-BGKcLV26-43)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS842HKQ at ENCODE; https://www.encodeproject.org/ENCBS842HKQ/

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


title: CRISPR RNA-seq from K562 (ENCLB445SWB)

description:
https://www.encodeproject.org/experiments/ENCSR008ECN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGKcLV33)
experiment encode accession: ENCSR008ECN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB445SWB
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 SEPT11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f1adc2e8-2d2a-4ba6-a5d4-dd73304cbab3/@@download/attachment/L-SEC62-BGKcLV33-39.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGKcLV33-39)

value: Homo sapiens

value: ENCBS068MOK at ENCODE; https://www.encodeproject.org/ENCBS068MOK/


title: BruChase-seq from mammary epithelial cell (ENCLB872HZO)

description:
https://www.encodeproject.org/experiments/ENCSR497HPX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR497HPX
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR419IWZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB872HZO
size range: 400-500

source_name: Homo sapiens female adult (19 years) mammary epithelial primary cell, subjected to a 6 hour pulse-chase

value: mammary epithelial cell

value: primary cell

value: 19 year

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS538QLS at ENCODE; https://www.encodeproject.org/ENCBS538QLS/

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


title: BruChase-seq from mammary epithelial cell (ENCLB144VIP)

description:
https://www.encodeproject.org/experiments/ENCSR497HPX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR497HPX
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR419IWZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB144VIP
size range: 400-500

value: female

value: ENCBS857TTQ at ENCODE; https://www.encodeproject.org/ENCBS857TTQ/


title: WA_PIZZ1MM (10X)

value: hepatic


title: total RNA-seq from K562 (ENCLB209SSN)

description:
https://www.encodeproject.org/experiments/ENCSR492KRY/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Chaetocin for 4 hours
experiment encode accession: ENCSR492KRY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB209SSN
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 nM Chaetocin for 4 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

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

value: ENCBS068BSV at ENCODE; https://www.encodeproject.org/ENCBS068BSV/


title: CRISPR RNA-seq from K562 (ENCLB458FCR)

description:
https://www.encodeproject.org/experiments/ENCSR008ECN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGKcLV33)
experiment encode accession: ENCSR008ECN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB458FCR
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/fcad352c-e519-4ea3-b150-4e0e1dd87be7/@@download/attachment/L-SEC62-BGKcLV33-40.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGKcLV33-40)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS785JFS at ENCODE; https://www.encodeproject.org/ENCBS785JFS/

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


title: total RNA-seq from K562 (ENCLB539NHE)

description:
https://www.encodeproject.org/experiments/ENCSR492KRY/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Chaetocin for 4 hours
experiment encode accession: ENCSR492KRY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB539NHE
size range: 300-600

value: female

value: ENCBS622OPD at ENCODE; https://www.encodeproject.org/ENCBS622OPD/


title: CRISPR RNA-seq from HepG2 (ENCLB557WOW)

description:
https://www.encodeproject.org/experiments/ENCSR489DNH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APTX. (APTX-BGHcLV24)
experiment encode accession: ENCSR489DNH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB557WOW
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 APTX

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/45fcc553-1a14-4bd5-886f-898c4a3da2ce/@@download/attachment/L-APTX-BGHcLV24-12.pdf

value: APTX

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APTX. (APTX-BGHcLV24-12)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS398SGO at ENCODE; https://www.encodeproject.org/ENCBS398SGO/

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


title: total RNA-seq from K562 (ENCLB173GMM)

description:
https://www.encodeproject.org/experiments/ENCSR006EBD/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with GSK J4 for 4 hours
experiment encode accession: ENCSR006EBD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB173GMM
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 100 nM GSK J4 for 4 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:GSK J4; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS797TJK at ENCODE; https://www.encodeproject.org/ENCBS797TJK/


title: CRISPR RNA-seq from HepG2 (ENCLB377UHH)

description:
https://www.encodeproject.org/experiments/ENCSR489DNH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APTX. (APTX-BGHcLV24)
experiment encode accession: ENCSR489DNH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB377UHH
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/e55dbda6-8de5-406c-9e6f-c2d75c65b281/@@download/attachment/L-APTX-BGHcLV24-11.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against APTX. (APTX-BGHcLV24-11)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS689EVR at ENCODE; https://www.encodeproject.org/ENCBS689EVR/


title: CRISPR RNA-seq from K562 (ENCLB037SNY)

description:
https://www.encodeproject.org/experiments/ENCSR507WAD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX23. (DDX23-BGKcLV28)
experiment encode accession: ENCSR507WAD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB037SNY
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/9a14a5ab-a758-4636-85a1-467f32709897/@@download/attachment/L-DDX23-BGKcLV28-73.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX23. (DDX23-BGKcLV28-73)

value: female

value: ENCBS188SIQ at ENCODE; https://www.encodeproject.org/ENCBS188SIQ/

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


title: Bru-seq from HCT116 (ENCLB123IVH)

description:
https://www.encodeproject.org/experiments/ENCSR008ZZZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR008ZZZ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB123IVH
size range: 400-500

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS278BDZ at ENCODE; https://www.encodeproject.org/ENCBS278BDZ/

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


title: total RNA-seq from K562 (ENCLB754TBI)

description:
https://www.encodeproject.org/experiments/ENCSR006EBD/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with GSK J4 for 4 hours
experiment encode accession: ENCSR006EBD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB754TBI
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: treatment_term_name:GSK J4; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS976MPA at ENCODE; https://www.encodeproject.org/ENCBS976MPA/


title: CRISPR RNA-seq from K562 (ENCLB047SAE)

description:
https://www.encodeproject.org/experiments/ENCSR002ODC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX10. (DDX10-BGKcLV28)
experiment encode accession: ENCSR002ODC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB047SAE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens DDX10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/df6f061d-b457-49e3-b27f-f07b7bb90f92/@@download/attachment/L-DDX10-BGKcLV28-68.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX10. (DDX10-BGKcLV28-68)

value: Homo sapiens

value: female

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS047GNX at ENCODE; https://www.encodeproject.org/ENCBS047GNX/


title: CRISPR RNA-seq from HepG2 (ENCLB241JQK)

description:
https://www.encodeproject.org/experiments/ENCSR485ZHW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RIOK2. (RIOK2-BGHcLV32-B)
experiment encode accession: ENCSR485ZHW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR911CLD
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB241JQK
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 RIOK2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0d2f4ee5-ad47-44e5-adba-30c799f6e034/@@download/attachment/L-RIOK2-BGHcLV32-34B.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RIOK2. (RIOK2-BGHcLV32-34B)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS628VDP at ENCODE; https://www.encodeproject.org/ENCBS628VDP/

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


title: CRISPR RNA-seq from K562 (ENCLB587UUT)

description:
https://www.encodeproject.org/experiments/ENCSR002JOW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGKcLV30)
experiment encode accession: ENCSR002JOW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB587UUT
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 RNASEH2A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7a465731-20ef-4e0d-b9ac-3f2f9562d2fe/@@download/attachment/L-RNASEH2A-BGKcLV30-37.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGKcLV30-37)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS759ZZR at ENCODE; https://www.encodeproject.org/ENCBS759ZZR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB319QXP)

description:
https://www.encodeproject.org/experiments/ENCSR485ZHW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RIOK2. (RIOK2-BGHcLV32-B)
experiment encode accession: ENCSR485ZHW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR911CLD
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB319QXP
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/6e7a9ad0-b399-4376-bf21-337370c39057/@@download/attachment/L-RIOK2-BGHcLV32-33B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RIOK2. (RIOK2-BGHcLV32-33B)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ENCBS188GNU at ENCODE; https://www.encodeproject.org/ENCBS188GNU/


title: total RNA-seq from K562 (ENCLB858UKF)

description:
https://www.encodeproject.org/experiments/ENCSR303IRE/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Panobinostat for 48 hours
experiment encode accession: ENCSR303IRE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB858UKF
size range: 300-600

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

value: cell line

value: RNA-seq on human cell line K562

value: female

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS146JAV at ENCODE; https://www.encodeproject.org/ENCBS146JAV/


title: CRISPR RNA-seq from HepG2 (ENCLB152HHN)

description:
https://www.encodeproject.org/experiments/ENCSR470SBK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGHcLV29)
experiment encode accession: ENCSR470SBK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB152HHN
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 CDK9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e3a94475-7f2c-4d6c-9e68-7980bd20698e/@@download/attachment/L-CDK9-BGHcLV29-13.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGHcLV29-13)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS784CQN at ENCODE; https://www.encodeproject.org/ENCBS784CQN/

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


title: total RNA-seq from K562 (ENCLB648QUS)

description:
https://www.encodeproject.org/experiments/ENCSR303IRE/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Panobinostat for 48 hours
experiment encode accession: ENCSR303IRE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB648QUS
size range: 300-600

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS926HQL at ENCODE; https://www.encodeproject.org/ENCBS926HQL/

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


title: CRISPR RNA-seq from HepG2 (ENCLB700SMY)

description:
https://www.encodeproject.org/experiments/ENCSR470SBK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGHcLV29)
experiment encode accession: ENCSR470SBK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB700SMY
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/1f962db5-85d1-442d-96a5-7f77d26bb8bb/@@download/attachment/L-CDK9-BGHcLV29-14.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGHcLV29-14)

value: Brenton Graveley, UConn

value: ENCBS409RMM at ENCODE; https://www.encodeproject.org/ENCBS409RMM/


title: total RNA-seq from A549 (ENCLB034TZG)

description:
https://www.encodeproject.org/experiments/ENCSR300FPD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR300FPD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB034TZG
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM dexamethasone (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: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS850LSL at ENCODE; https://www.encodeproject.org/ENCBS850LSL/

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


title: CRISPR RNA-seq from K562 (ENCLB230CRI)

description:
https://www.encodeproject.org/experiments/ENCSR300UBK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGKcLV33)
experiment encode accession: ENCSR300UBK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB230CRI
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 RPUSD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/35af20d5-0e82-4f0b-81f5-176ba4ea0952/@@download/attachment/L-SKIV2L2-BGKcLV33-9.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGKcLV33-9)

value: female

value: ENCBS383XHL at ENCODE; https://www.encodeproject.org/ENCBS383XHL/


title: CRISPR RNA-seq from K562 (ENCLB633OCK)

description:
https://www.encodeproject.org/experiments/ENCSR300LXO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGKcLV28)
experiment encode accession: ENCSR300LXO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB633OCK
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 DDX18

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/19a43854-2f20-471f-8977-74f8f5dd8ca2/@@download/attachment/L-DDX18-BGKcLV28-72.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGKcLV28-72)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS515ZUG at ENCODE; https://www.encodeproject.org/ENCBS515ZUG/


title: total RNA-seq from A549 (ENCLB425IXJ)

description:
https://www.encodeproject.org/experiments/ENCSR300FPD/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR300FPD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB425IXJ
size range: 200-300

value: cell line

value: male

value: ENCBS749YQY at ENCODE; https://www.encodeproject.org/ENCBS749YQY/


title: total RNA-seq from A549 (ENCLB615TXE)

description:
https://www.encodeproject.org/experiments/ENCSR300FPD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR300FPD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB615TXE
size range: 200-300

value: 58 year

value: ENCBS739UNB at ENCODE; https://www.encodeproject.org/ENCBS739UNB/


title: CRISPR RNA-seq from K562 (ENCLB560ACR)

description:
https://www.encodeproject.org/experiments/ENCSR002JOW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGKcLV30)
experiment encode accession: ENCSR002JOW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB560ACR
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/dc47ea41-2f8f-4b3f-bbc1-f572bb3a3afc/@@download/attachment/L-RNASEH2A-BGKcLV30-38.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGKcLV30-38)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS963CVP at ENCODE; https://www.encodeproject.org/ENCBS963CVP/

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


title: CRISPR RNA-seq from HepG2 (ENCLB251PON)

description:
https://www.encodeproject.org/experiments/ENCSR297ONN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGHcLV27)
experiment encode accession: ENCSR297ONN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB251PON
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 CAND1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/05ac2426-2f7a-4f13-8ff5-95faf11fe5af/@@download/attachment/L-CAND1-BGHcLV27-33.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGHcLV27-33)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS072RXM at ENCODE; https://www.encodeproject.org/ENCBS072RXM/

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


title: total RNA-seq from A549 (ENCLB652NUK)

description:
https://www.encodeproject.org/experiments/ENCSR300FPD/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR300FPD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB652NUK
size range: 200-300

value: cell line

value: Homo sapiens

value: adult

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS448MDY at ENCODE; https://www.encodeproject.org/ENCBS448MDY/

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


title: CRISPR RNA-seq from HepG2 (ENCLB993ALE)

description:
https://www.encodeproject.org/experiments/ENCSR297ONN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGHcLV27)
experiment encode accession: ENCSR297ONN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB993ALE
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/0c9237d7-f736-48c3-9704-e2d71b894f5c/@@download/attachment/L-CAND1-BGHcLV27-34.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGHcLV27-34)

value: male

value: Brenton Graveley, UConn

value: ENCBS144VMS at ENCODE; https://www.encodeproject.org/ENCBS144VMS/


title: CRISPR RNA-seq from K562 (ENCLB782KHV)

description:
https://www.encodeproject.org/experiments/ENCSR300LXO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGKcLV28)
experiment encode accession: ENCSR300LXO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB782KHV
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/d656259e-c440-4976-8078-0b6669d968b8/@@download/attachment/L-DDX18-BGKcLV28-71.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGKcLV28-71)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS282XIF at ENCODE; https://www.encodeproject.org/ENCBS282XIF/

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


title: total RNA-seq from A549 (ENCLB294GLR)

description:
https://www.encodeproject.org/experiments/ENCSR300FPD/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR300FPD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB294GLR
size range: 200-300

value: cell line

value: Homo sapiens

value: 58 year

value: ENCBS854SIX at ENCODE; https://www.encodeproject.org/ENCBS854SIX/


title: total RNA-seq from A549 (ENCLB281UQL)

description:
https://www.encodeproject.org/experiments/ENCSR719GYP/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR719GYP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB281UQL
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM ZK216348 (agonist) for 4 hours

value: adult

value: Tim Reddy, Duke

value: treatment_term_name:ZK216348; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS248VGN at ENCODE; https://www.encodeproject.org/ENCBS248VGN/


title: total RNA-seq from A549 (ENCLB082LPG)

description:
https://www.encodeproject.org/experiments/ENCSR719GYP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR719GYP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB082LPG
size range: 200-300

value: male

value: ENCBS074AEV at ENCODE; https://www.encodeproject.org/ENCBS074AEV/

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


title: total RNA-seq from A549 (ENCLB012HYW)

description:
https://www.encodeproject.org/experiments/ENCSR719GYP/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR719GYP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB012HYW
size range: 200-300

value: ENCBS372TCT at ENCODE; https://www.encodeproject.org/ENCBS372TCT/


title: CRISPR RNA-seq from HepG2 (ENCLB100TVZ)

description:
https://www.encodeproject.org/experiments/ENCSR293VAR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGHcLV31)
experiment encode accession: ENCSR293VAR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB100TVZ
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 SPAG9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/90e50ebc-2768-488f-8a05-1e7a26559b67/@@download/attachment/L-SPAG9-BGHcLV31-63.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGHcLV31-63)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS657JNU at ENCODE; https://www.encodeproject.org/ENCBS657JNU/

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


title: CRISPR RNA-seq from K562 (ENCLB212FWY)

description:
https://www.encodeproject.org/experiments/ENCSR292NHK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGKcLV30)
experiment encode accession: ENCSR292NHK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB212FWY
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 RPS15A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2f5e1aac-e97e-433e-adff-a2cfe86f69ea/@@download/attachment/L-RPS15A-BGKcLV30-68.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGKcLV30-68)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS425RTI at ENCODE; https://www.encodeproject.org/ENCBS425RTI/

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


title: total RNA-seq from A549 (ENCLB220WPL)

description:
https://www.encodeproject.org/experiments/ENCSR719GYP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR719GYP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB220WPL
size range: 200-300

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_name:ZK216348; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS314GPV at ENCODE; https://www.encodeproject.org/ENCBS314GPV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB570MZZ)

description:
https://www.encodeproject.org/experiments/ENCSR706QGC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNH1. (RNH1-BGHcLV32)
experiment encode accession: ENCSR706QGC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB570MZZ
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 RNH1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b4226ff8-7de5-488e-936d-8e8d9d93ed1c/@@download/attachment/L-RNH1-BGHcLV32-37.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNH1. (RNH1-BGHcLV32-37)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS131BON at ENCODE; https://www.encodeproject.org/ENCBS131BON/

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


title: CRISPR RNA-seq from HepG2 (ENCLB297GIP)

description:
https://www.encodeproject.org/experiments/ENCSR293VAR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGHcLV31)
experiment encode accession: ENCSR293VAR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB297GIP
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/a6e73b13-97a6-4db6-b9d4-cb186e230443/@@download/attachment/L-SPAG9-BGHcLV31-64.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGHcLV31-64)

value: Homo sapiens

value: ATCC

value: ENCBS558TFT at ENCODE; https://www.encodeproject.org/ENCBS558TFT/


title: total RNA-seq from K562 (ENCLB226KXX)

description:
https://www.encodeproject.org/experiments/ENCSR287DHQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Bortezomib for 12 hours
experiment encode accession: ENCSR287DHQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB226KXX
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 nM Bortezomib for 12 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_id:CHEBI:52717; treatment_term_name:Bortezomib; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS114ZTO at ENCODE; https://www.encodeproject.org/ENCBS114ZTO/

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


title: total RNA-seq from motor neuron (ENCLB230NVA)

description:
https://www.encodeproject.org/experiments/ENCSR701YIC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR701YIC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB230NVA
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: Healthy donor

value: unknown

value: Michael Snyder, Stanford

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

value: ENCBS136YMV at ENCODE; https://www.encodeproject.org/ENCBS136YMV/

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


title: CRISPR RNA-seq from K562 (ENCLB840JDC)

description:
https://www.encodeproject.org/experiments/ENCSR292NHK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGKcLV30)
experiment encode accession: ENCSR292NHK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB840JDC
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/7a8f74da-b7ef-49e6-ae58-bb5ffd9c26f8/@@download/attachment/L-RPS15A-BGKcLV30-67.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGKcLV30-67)

value: Homo sapiens

value: female

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS618IFP at ENCODE; https://www.encodeproject.org/ENCBS618IFP/


title: CRISPR RNA-seq from HepG2 (ENCLB994JYJ)

description:
https://www.encodeproject.org/experiments/ENCSR706QGC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNH1. (RNH1-BGHcLV32)
experiment encode accession: ENCSR706QGC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB994JYJ
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/896bbc62-8b7d-4765-93ac-9d2450d25eaf/@@download/attachment/L-RNH1-BGHcLV32-38.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNH1. (RNH1-BGHcLV32-38)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS428TND at ENCODE; https://www.encodeproject.org/ENCBS428TND/

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


title: CRISPR RNA-seq from K562 (ENCLB617OLR)

description:
https://www.encodeproject.org/experiments/ENCSR274ESZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ACO2. (ACO2-BGKcLV26)
experiment encode accession: ENCSR274ESZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB617OLR
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 ACO2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7aadb421-ee99-4dfb-96f4-8eddaf3b4808/@@download/attachment/L-ACO2-BGKcLV26-4.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ACO2. (ACO2-BGKcLV26-4)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS136FWL at ENCODE; https://www.encodeproject.org/ENCBS136FWL/

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


title: CRISPR RNA-seq from K562 (ENCLB096WFW)

description:
https://www.encodeproject.org/experiments/ENCSR300UBK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGKcLV33)
experiment encode accession: ENCSR300UBK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB096WFW
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/c95b3955-5c90-46ab-9c29-fa76705863f8/@@download/attachment/L-SKIV2L2-BGKcLV33-10.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGKcLV33-10)

value: Homo sapiens

value: female

value: ENCBS500BTR at ENCODE; https://www.encodeproject.org/ENCBS500BTR/


title: CRISPR RNA-seq from K562 (ENCLB007DXF)

description:
https://www.encodeproject.org/experiments/ENCSR274ESZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ACO2. (ACO2-BGKcLV26)
experiment encode accession: ENCSR274ESZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB007DXF
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/953fa6ce-af0d-4f20-87fe-dcb64f525565/@@download/attachment/L-ACO2-BGKcLV26-3.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ACO2. (ACO2-BGKcLV26-3)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS367BPG at ENCODE; https://www.encodeproject.org/ENCBS367BPG/


title: total RNA-seq from K562 (ENCLB954FMC)

description:
https://www.encodeproject.org/experiments/ENCSR287DHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Bortezomib for 12 hours
experiment encode accession: ENCSR287DHQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB954FMC
size range: 300-600

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

value: treatment_term_id:CHEBI:52717; treatment_term_name:Bortezomib; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS142BAL at ENCODE; https://www.encodeproject.org/ENCBS142BAL/


title: CRISPR RNA-seq from K562 (ENCLB678YKG)

description:
https://www.encodeproject.org/experiments/ENCSR700JXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against AHCYL2. (AHCYL2-BGKcLV26)
experiment encode accession: ENCSR700JXJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB678YKG
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 AHCYL2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0b4394ab-2ee4-4c8a-bd30-5c71c7febe9b/@@download/attachment/L-AHCYL2-BGKcLV26-18.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against AHCYL2. (AHCYL2-BGKcLV26-18)

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS082OUT at ENCODE; https://www.encodeproject.org/ENCBS082OUT/


title: CRISPR RNA-seq from HepG2 (ENCLB413MRS)

description:
https://www.encodeproject.org/experiments/ENCSR703FPC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGHcLV32)
experiment encode accession: ENCSR703FPC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB413MRS
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 RNASEH2A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a9c00b50-7402-4e7f-a9c5-2ff107e26b28/@@download/attachment/L-RNASEH2A-BGHcLV32-35.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGHcLV32-35)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS559VPJ at ENCODE; https://www.encodeproject.org/ENCBS559VPJ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB648GDT)

description:
https://www.encodeproject.org/experiments/ENCSR703FPC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGHcLV32)
experiment encode accession: ENCSR703FPC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB648GDT
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/4b895928-ecc4-42bc-b1b3-f73f574593fe/@@download/attachment/L-RNASEH2A-BGHcLV32-36.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGHcLV32-36)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS083RVQ at ENCODE; https://www.encodeproject.org/ENCBS083RVQ/


title: BruChase-seq from PC-9 (ENCLB456DUI)

description:
https://www.encodeproject.org/experiments/ENCSR699DUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR699DUJ
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR223GHJ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB456DUI
size range: 400-500

source_name: Homo sapiens PC-9 cell line, subjected to a 6 hour pulse-chase

value: not collected

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS682DUG at ENCODE; https://www.encodeproject.org/ENCBS682DUG/

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


title: total RNA-seq from motor neuron (ENCLB728VZN)

description:
https://www.encodeproject.org/experiments/ENCSR701YIC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR701YIC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB728VZN
size range: 300-600

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: female

value: Healthy donor

value: adult

value: Michael Snyder, Stanford

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

value: ENCBS203UWG at ENCODE; https://www.encodeproject.org/ENCBS203UWG/

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


title: CRISPR RNA-seq from K562 (ENCLB429ENQ)

description:
https://www.encodeproject.org/experiments/ENCSR700JXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against AHCYL2. (AHCYL2-BGKcLV26)
experiment encode accession: ENCSR700JXJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB429ENQ
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/00eadad0-38e2-4552-af4c-00326d1452df/@@download/attachment/L-AHCYL2-BGKcLV26-17.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against AHCYL2. (AHCYL2-BGKcLV26-17)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS898HTY at ENCODE; https://www.encodeproject.org/ENCBS898HTY/

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


title: PRO-cap from HCT116 (ENCLB706DBO)

description:
https://www.encodeproject.org/experiments/ENCSR273ORE/
***************
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_T.
experiment encode accession: ENCSR273ORE
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB706DBO
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 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS191ARH at ENCODE; https://www.encodeproject.org/ENCBS191ARH/

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


title: total RNA-seq from A549 (ENCLB974JOK)

description:
https://www.encodeproject.org/experiments/ENCSR719GYP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR719GYP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB974JOK
size range: 200-300

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_name:ZK216348; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS768OOX at ENCODE; https://www.encodeproject.org/ENCBS768OOX/

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


title: PRO-cap from HCT116 (ENCLB016YNY)

description:
https://www.encodeproject.org/experiments/ENCSR273ORE/
***************
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_T.
experiment encode accession: ENCSR273ORE
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB016YNY
spikeins used: The drosophila spike-in reference used for alignment

value: Homo sapiens

value: ENCBS745VSI at ENCODE; https://www.encodeproject.org/ENCBS745VSI/


title: BruChase-seq from PC-9 (ENCLB978CJK)

description:
https://www.encodeproject.org/experiments/ENCSR699DUJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR699DUJ
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR223GHJ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB978CJK
size range: 400-500

value: not collected

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS040HBG at ENCODE; https://www.encodeproject.org/ENCBS040HBG/

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


title: CRISPR RNA-seq from K562 (ENCLB376QVA)

description:
https://www.encodeproject.org/experiments/ENCSR271ZAB/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV33)
experiment encode accession: ENCSR271ZAB
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB376QVA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/be8b6f23-2201-408f-ba9e-35494ecd4d59/@@download/attachment/L-NT-BGKcLV33-2.pdf

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV33-2)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS950UYY at ENCODE; https://www.encodeproject.org/ENCBS950UYY/

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


title: CRISPR RNA-seq from K562 (ENCLB939ZUQ)

description:
https://www.encodeproject.org/experiments/ENCSR271ZAB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV33)
experiment encode accession: ENCSR271ZAB
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB939ZUQ
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/bda35bea-f7fd-468a-836f-9c1528e50276/@@download/attachment/L-NT-BGKcLV33-1.pdf

value: cell line

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV33-1)

value: adult

value: ENCBS953FSQ at ENCODE; https://www.encodeproject.org/ENCBS953FSQ/


title: CRISPR RNA-seq from HepG2 (ENCLB309PHS)

description:
https://www.encodeproject.org/experiments/ENCSR994NGU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS8. (RPS8-BGHcLV31)
experiment encode accession: ENCSR994NGU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB309PHS
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 RPS8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5aa3f18d-8eea-47cf-9b81-8949f303fe44/@@download/attachment/L-RPS8-BGHcLV31-10.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS8. (RPS8-BGHcLV31-10)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS069KUQ at ENCODE; https://www.encodeproject.org/ENCBS069KUQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB368SBH)

description:
https://www.encodeproject.org/experiments/ENCSR981TQN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGHcLV31)
experiment encode accession: ENCSR981TQN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB368SBH
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 SEC63

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c52acfb0-c329-4c20-934b-7bbd0d3c5143/@@download/attachment/L-SEC63-BGHcLV31-37.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGHcLV31-37)

value: ENCBS920CHH at ENCODE; https://www.encodeproject.org/ENCBS920CHH/


title: CRISPR RNA-seq from K562 (ENCLB981GTZ)

description:
https://www.encodeproject.org/experiments/ENCSR995XEP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT4. (CCT4-BGKcLV28)
experiment encode accession: ENCSR995XEP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB981GTZ
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 CCT4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8db18373-1ba7-4ac2-9b07-b5c5dcfd258f/@@download/attachment/L-CCT4-BGKcLV28-7.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT4. (CCT4-BGKcLV28-7)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS041CQT at ENCODE; https://www.encodeproject.org/ENCBS041CQT/


title: CRISPR RNA-seq from HepG2 (ENCLB281FMF)

description:
https://www.encodeproject.org/experiments/ENCSR992YRL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGHcLV29)
experiment encode accession: ENCSR992YRL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB281FMF
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 DDX18

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e3ab1554-6aa8-487f-801a-ccbca5de223a/@@download/attachment/L-DDX18-BGHcLV29-71.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGHcLV29-71)

value: ENCBS097LDJ at ENCODE; https://www.encodeproject.org/ENCBS097LDJ/


title: CRISPR RNA-seq from HepG2 (ENCLB349MUK)

description:
https://www.encodeproject.org/experiments/ENCSR981TQN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGHcLV31)
experiment encode accession: ENCSR981TQN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB349MUK
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/4070f426-d6f9-448f-b1c0-aa77bfb892c4/@@download/attachment/L-SEC63-BGHcLV31-38.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGHcLV31-38)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: ENCBS451EGX at ENCODE; https://www.encodeproject.org/ENCBS451EGX/


title: CRISPR RNA-seq from HepG2 (ENCLB764GNJ)

description:
https://www.encodeproject.org/experiments/ENCSR974KDR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARHSP1. (CARHSP1-BGHcLV27)
experiment encode accession: ENCSR974KDR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB764GNJ
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 CARHSP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e02af294-de09-4921-9443-4ad4e236e3df/@@download/attachment/L-CARHSP1-BGHcLV27-38.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARHSP1. (CARHSP1-BGHcLV27-38)

value: child

value: 15 year

value: ENCBS639AFY at ENCODE; https://www.encodeproject.org/ENCBS639AFY/

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


title: CRISPR RNA-seq from HepG2 (ENCLB809NST)

description:
https://www.encodeproject.org/experiments/ENCSR994NGU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS8. (RPS8-BGHcLV31)
experiment encode accession: ENCSR994NGU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB809NST
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/94e4b03e-f3fb-4091-8590-8e1657b49763/@@download/attachment/L-RPS8-BGHcLV31-9.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS8. (RPS8-BGHcLV31-9)

value: ENCBS703JUW at ENCODE; https://www.encodeproject.org/ENCBS703JUW/


title: PRO-cap from HCT116 (ENCLB915OEX)

description:
https://www.encodeproject.org/experiments/ENCSR990FJB/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CDK7_U.
experiment encode accession: ENCSR990FJB
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB915OEX
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS286GJK at ENCODE; https://www.encodeproject.org/ENCBS286GJK/

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


title: CRISPR RNA-seq from HepG2 (ENCLB398HSV)

description:
https://www.encodeproject.org/experiments/ENCSR992YRL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGHcLV29)
experiment encode accession: ENCSR992YRL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB398HSV
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/78c1b7e9-fb26-41b2-9369-970297d15a92/@@download/attachment/L-DDX18-BGHcLV29-72.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGHcLV29-72)

value: Homo sapiens

value: male

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS697LCA at ENCODE; https://www.encodeproject.org/ENCBS697LCA/


title: CRISPR RNA-seq from K562 (ENCLB907TJM)

description:
https://www.encodeproject.org/experiments/ENCSR971FJU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG9. (SMG9-BGKcLV33)
experiment encode accession: ENCSR971FJU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB907TJM
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 SNW1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f55f256e-3ab6-4ea7-b742-abaa8eb3cdfc/@@download/attachment/L-SMG9-BGKcLV33-62.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG9. (SMG9-BGKcLV33-62)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS518YBV at ENCODE; https://www.encodeproject.org/ENCBS518YBV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB686EUX)

description:
https://www.encodeproject.org/experiments/ENCSR974KDR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARHSP1. (CARHSP1-BGHcLV27)
experiment encode accession: ENCSR974KDR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB686EUX
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/b72fb625-d2d4-4ce6-86d5-a0aecd25758f/@@download/attachment/L-CARHSP1-BGHcLV27-37.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARHSP1. (CARHSP1-BGHcLV27-37)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS842VIG at ENCODE; https://www.encodeproject.org/ENCBS842VIG/

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


title: PRO-cap from HCT116 (ENCLB891CSG)

description:
https://www.encodeproject.org/experiments/ENCSR990FJB/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CDK7_U.
experiment encode accession: ENCSR990FJB
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB891CSG
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: Homo sapiens

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS876JPT at ENCODE; https://www.encodeproject.org/ENCBS876JPT/

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


title: total RNA-seq from motor neuron (ENCLB115CLV)

description:
https://www.encodeproject.org/experiments/ENCSR967DSJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR967DSJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB115CLV
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: ENCBS101AYX at ENCODE; https://www.encodeproject.org/ENCBS101AYX/

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


title: BruChase-seq from A673 (ENCLB404JLR)

description:
https://www.encodeproject.org/experiments/ENCSR971YFG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR971YFG
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR912SRZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB404JLR
size range: 400-500

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

value: cell line

value: Homo sapiens

value: female

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS404ERD at ENCODE; https://www.encodeproject.org/ENCBS404ERD/

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


title: CRISPR RNA-seq from HepG2 (ENCLB070USO)

description:
https://www.encodeproject.org/experiments/ENCSR953VMB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV25)
experiment encode accession: ENCSR953VMB
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB070USO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7646bcc7-b9aa-401d-a418-60a8ede9a422/@@download/attachment/L-NT-BGHcLV25-1.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV25-1)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS916PZF at ENCODE; https://www.encodeproject.org/ENCBS916PZF/

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


title: CRISPR RNA-seq from HepG2 (ENCLB699NCV)

description:
https://www.encodeproject.org/experiments/ENCSR954VJD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGHcLV31)
experiment encode accession: ENCSR954VJD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB699NCV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens SAP30BP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a137cd7a-4b76-4794-9246-ca5efad9969c/@@download/attachment/L-SAP30BP-BGHcLV31-26.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGHcLV31-26)

value: male

value: ENCBS652UVX at ENCODE; https://www.encodeproject.org/ENCBS652UVX/


title: CRISPR RNA-seq from HepG2 (ENCLB726SJT)

description:
https://www.encodeproject.org/experiments/ENCSR953VMB/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV25)
experiment encode accession: ENCSR953VMB
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB726SJT
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/01a7760b-7f13-457d-a8d2-2c1e52a7a6a8/@@download/attachment/L-NT-BGHcLV25-2.pdf

value: cell line

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV25-2)

value: ENCBS968PYP at ENCODE; https://www.encodeproject.org/ENCBS968PYP/


title: CRISPR RNA-seq from K562 (ENCLB960HUZ)

description:
https://www.encodeproject.org/experiments/ENCSR995XEP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT4. (CCT4-BGKcLV28)
experiment encode accession: ENCSR995XEP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB960HUZ
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/00ac5a3c-8117-412c-9e08-990c605ff579/@@download/attachment/L-CCT4-BGKcLV28-8.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT4. (CCT4-BGKcLV28-8)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS537UUI at ENCODE; https://www.encodeproject.org/ENCBS537UUI/

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