title: CRISPR RNA-seq from HepG2 (ENCLB952MTZ)

description:
https://www.encodeproject.org/experiments/ENCSR306EWE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV20)
experiment encode accession: ENCSR306EWE
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB952MTZ
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/a5561834-345f-4a17-8509-70f95d37a75b/@@download/attachment/L-NT-BGHcLV20-1.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV20-1)

value: ENCBS989SEX at ENCODE; https://www.encodeproject.org/ENCBS989SEX/


title: CRISPR RNA-seq from HepG2 (ENCLB512NMH)

status: Public on Jun 15 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR333OGA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GEMIN2. (GEMIN2-BGHcLV18)
experiment encode accession: ENCSR333OGA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB512NMH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting GEMIN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bf2d774e-c717-4a1f-bb3f-ddaf9e2d2bad/@@download/attachment/L-GEMIN2-BGHcLV18-26.pdf

tag: antibody

tag: line

value: cell line

tag: description

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GEMIN2. (GEMIN2-BGHcLV18-26)

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Brenton Graveley, UConn

tag: source

value: ATCC

tag: link

value: ENCBS574RYJ at ENCODE; https://www.encodeproject.org/ENCBS574RYJ/

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


title: CRISPR RNA-seq from K562 (ENCLB913WIF)

description:
https://www.encodeproject.org/experiments/ENCSR335KFN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against METTL3. (METTL3-BGKcLV23)
experiment encode accession: ENCSR335KFN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB913WIF
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting METTL3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1c61c798-3a82-476a-b6f4-1745bba9e338/@@download/attachment/L-METTL3-BGKcLV23-54.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against METTL3. (METTL3-BGKcLV23-54)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS960LGF at ENCODE; https://www.encodeproject.org/ENCBS960LGF/

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


title: CRISPR RNA-seq from K562 (ENCLB240FPK)

description:
https://www.encodeproject.org/experiments/ENCSR521WCW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX42. (DDX42-BGKcLV08)
experiment encode accession: ENCSR521WCW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB240FPK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting DDX42

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a0713079-f9f8-4115-9998-4510a2b623af/@@download/attachment/L-DDX42-BGKcLV08-22.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX42. (DDX42-BGKcLV08-22)

value: ENCBS826MJI at ENCODE; https://www.encodeproject.org/ENCBS826MJI/


title: Bru-seq from GM12878 (ENCLB553KZR)

description:
https://www.encodeproject.org/experiments/ENCSR408AMO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR408AMO
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR267RPG
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB553KZR
size range: 400-500

source_name: Homo sapiens GM12878 cell line treated with 500 rad irradiation

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

value: Coriell

tag: treatments

value: ENCBS174KKU at ENCODE; https://www.encodeproject.org/ENCBS174KKU/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: CRISPR RNA-seq from HepG2 (ENCLB768VNU)

description:
https://www.encodeproject.org/experiments/ENCSR306EWE/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV20)
experiment encode accession: ENCSR306EWE
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB768VNU
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/8439a5cd-383c-43e3-9298-dcf0a8fa3118/@@download/attachment/L-NT-BGHcLV20-2.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV20-2)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS217OPS at ENCODE; https://www.encodeproject.org/ENCBS217OPS/

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


title: CRISPR RNA-seq from HepG2 (ENCLB125MIE)

description:
https://www.encodeproject.org/experiments/ENCSR300RMY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GSK3A. (GSK3A-BGHcLV14)
experiment encode accession: ENCSR300RMY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB125MIE
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 GSK3A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/aa854cc4-c520-4a59-96cc-f1526b1d4e57/@@download/attachment/L-GSK3A-BGHcLV14-42.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GSK3A. (GSK3A-BGHcLV14-42)

value: ENCBS560XUK at ENCODE; https://www.encodeproject.org/ENCBS560XUK/


title: CRISPR RNA-seq from K562 (ENCLB223MFL)

description:
https://www.encodeproject.org/experiments/ENCSR404OHQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGKcLV15)
experiment encode accession: ENCSR404OHQ
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB223MFL
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/ecb1b9dc-d9d4-47ec-9703-71b8445f8a94/@@download/attachment/L-NT-BGKcLV15-2.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non-target. (NT-BGKcLV15-2)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS996SVS at ENCODE; https://www.encodeproject.org/ENCBS996SVS/

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


title: CRISPR RNA-seq from K562 (ENCLB526OGT)

description:
https://www.encodeproject.org/experiments/ENCSR516EPT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against XRCC6. (XRCC6-BGKcLV15)
experiment encode accession: ENCSR516EPT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB526OGT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting XRCC6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/879fd88e-08f4-4581-b949-c2fb736d4a3f/@@download/attachment/L-XRCC6-BGKcLV15-62.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against XRCC6. (XRCC6-BGKcLV15-62)

value: ENCBS626UBX at ENCODE; https://www.encodeproject.org/ENCBS626UBX/


title: CRISPR RNA-seq from K562 (ENCLB513MBW)

description:
https://www.encodeproject.org/experiments/ENCSR404OHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGKcLV15)
experiment encode accession: ENCSR404OHQ
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB513MBW
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/087bdb79-5e50-4f2b-8231-0e4793ebdd5e/@@download/attachment/L-NT-BGKcLV15-1.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non-target. (NT-BGKcLV15-1)

value: ENCBS351RNE at ENCODE; https://www.encodeproject.org/ENCBS351RNE/


title: CRISPR RNA-seq from HepG2 (ENCLB776BXV)

description:
https://www.encodeproject.org/experiments/ENCSR323OPW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4B. (EIF4B-BGHcLV10)
experiment encode accession: ENCSR323OPW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB776BXV
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 EIF4B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9b9a6252-f501-4e07-ae26-bbf249f00511/@@download/attachment/L-EIF4B-BGHcLV10-24.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4B. (EIF4B-BGHcLV10-24)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS710LUH at ENCODE; https://www.encodeproject.org/ENCBS710LUH/


title: CRISPR RNA-seq from HepG2 (ENCLB128OBL)

description:
https://www.encodeproject.org/experiments/ENCSR312VLS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against XRCC6. (XRCC6-BGHcLV16)
experiment encode accession: ENCSR312VLS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB128OBL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting XRCC6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4a61147a-5120-4266-a6e0-20c145271400/@@download/attachment/L-XRCC6-BGHcLV16-60.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against XRCC6. (XRCC6-BGHcLV16-60)

value: ENCBS393PMQ at ENCODE; https://www.encodeproject.org/ENCBS393PMQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB514GAZ)

description:
https://www.encodeproject.org/experiments/ENCSR504CPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NSUN4. (NSUN4-BGHcLV16)
experiment encode accession: ENCSR504CPZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB514GAZ
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 NSUN4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/33097470-5617-4214-8579-20b1cdff0f5b/@@download/attachment/L-NSUN4-BGHcLV16-38.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NSUN4. (NSUN4-BGHcLV16-38)

value: ENCBS065VXB at ENCODE; https://www.encodeproject.org/ENCBS065VXB/


title: CRISPR RNA-seq from HepG2 (ENCLB714SPW)

description:
https://www.encodeproject.org/experiments/ENCSR300RMY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GSK3A. (GSK3A-BGHcLV14)
experiment encode accession: ENCSR300RMY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB714SPW
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/06ce3862-4aef-4bbd-977d-177ccc66c79e/@@download/attachment/L-GSK3A-BGHcLV14-41.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GSK3A. (GSK3A-BGHcLV14-41)

value: ENCBS840EBY at ENCODE; https://www.encodeproject.org/ENCBS840EBY/


title: CRISPR RNA-seq from HepG2 (ENCLB182BIN)

description:
https://www.encodeproject.org/experiments/ENCSR400YKV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SART1. (SART1-BGHcLV22)
experiment encode accession: ENCSR400YKV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB182BIN
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 SART1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dac37be4-3740-49ca-90f0-61dd3e5f46ea/@@download/attachment/L-SART1-BGHcLV22-50.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SART1. (SART1-BGHcLV22-50)

value: ENCBS731VZI at ENCODE; https://www.encodeproject.org/ENCBS731VZI/


title: CRISPR RNA-seq from HepG2 (ENCLB148GNM)

description:
https://www.encodeproject.org/experiments/ENCSR511QFJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PRPF39. (PRPF39-BGHcLV18)
experiment encode accession: ENCSR511QFJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB148GNM
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 PRPF39

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/899300c2-bcc6-447f-bb55-de6c76dbd38f/@@download/attachment/L-PRPF39-BGHcLV18-38.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PRPF39. (PRPF39-BGHcLV18-38)

value: male

value: ENCBS467XOJ at ENCODE; https://www.encodeproject.org/ENCBS467XOJ/


title: CRISPR RNA-seq from HepG2 (ENCLB688WVQ)

description:
https://www.encodeproject.org/experiments/ENCSR400YKV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SART1. (SART1-BGHcLV22)
experiment encode accession: ENCSR400YKV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB688WVQ
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/bf97e5a9-d814-4c4f-acfd-7a684a2ba16f/@@download/attachment/L-SART1-BGHcLV22-49.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SART1. (SART1-BGHcLV22-49)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS046YDD at ENCODE; https://www.encodeproject.org/ENCBS046YDD/


title: CRISPR RNA-seq from K562 (ENCLB809TRL)

description:
https://www.encodeproject.org/experiments/ENCSR503VIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GARS. (GARS-BGKcLV17)
experiment encode accession: ENCSR503VIZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB809TRL
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 GARS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9632da16-a81e-4283-a9fd-6f3e2f58b6d7/@@download/attachment/L-GARS-BGKcLV17-23.pdf

value: GARS

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GARS. (GARS-BGKcLV17-23)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS609YII at ENCODE; https://www.encodeproject.org/ENCBS609YII/

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


title: CRISPR RNA-seq from HepG2 (ENCLB947RPT)

description:
https://www.encodeproject.org/experiments/ENCSR400XYB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGHcLV16)
experiment encode accession: ENCSR400XYB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB947RPT
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 CD3EAP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/58adf545-3098-41e9-afaa-00d8ec96310b/@@download/attachment/L-CD3EAP-BGHcLV16-12.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGHcLV16-12)

value: male

value: ENCBS888MPT at ENCODE; https://www.encodeproject.org/ENCBS888MPT/

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


title: CRISPR RNA-seq from K562 (ENCLB129ZUM)

description:
https://www.encodeproject.org/experiments/ENCSR503VIZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GARS. (GARS-BGKcLV17)
experiment encode accession: ENCSR503VIZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB129ZUM
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/1348de16-970a-4344-8782-20dffcffca52/@@download/attachment/L-GARS-BGKcLV17-24.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GARS. (GARS-BGKcLV17-24)

value: ENCBS521NGU at ENCODE; https://www.encodeproject.org/ENCBS521NGU/


title: CRISPR RNA-seq from HepG2 (ENCLB643EOU)

description:
https://www.encodeproject.org/experiments/ENCSR400XYB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGHcLV16)
experiment encode accession: ENCSR400XYB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB643EOU
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/4dc1159e-dd79-48e8-bf02-f00fc71d6475/@@download/attachment/L-CD3EAP-BGHcLV16-11.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGHcLV16-11)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS539IKE at ENCODE; https://www.encodeproject.org/ENCBS539IKE/


title: CRISPR RNA-seq from HepG2 (ENCLB395PDQ)

description:
https://www.encodeproject.org/experiments/ENCSR323OPW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4B. (EIF4B-BGHcLV10)
experiment encode accession: ENCSR323OPW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB395PDQ
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/463ee94f-8d37-4ee4-83c1-ef44a9fee555/@@download/attachment/L-EIF4B-BGHcLV10-23.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4B. (EIF4B-BGHcLV10-23)

value: ENCBS869XGC at ENCODE; https://www.encodeproject.org/ENCBS869XGC/


title: Bru-seq from GM12878 (ENCLB157THH)

description:
https://www.encodeproject.org/experiments/ENCSR408AMO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR408AMO
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR267RPG
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB157THH
size range: 400-500

value: female

value: unknown

value: adult

value: not collected

value: Mats Ljungman, UMichigan

value: Coriell

value: ENCBS460XGH at ENCODE; https://www.encodeproject.org/ENCBS460XGH/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: CRISPR RNA-seq from HepG2 (ENCLB685RNC)

description:
https://www.encodeproject.org/experiments/ENCSR511QFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PRPF39. (PRPF39-BGHcLV18)
experiment encode accession: ENCSR511QFJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB685RNC
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/a6b22090-2e12-437b-b311-b9ddf32bdc19/@@download/attachment/L-PRPF39-BGHcLV18-37.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PRPF39. (PRPF39-BGHcLV18-37)

value: male

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS699GAM at ENCODE; https://www.encodeproject.org/ENCBS699GAM/

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


title: CRISPR RNA-seq from HepG2 (ENCLB518TBS)

description:
https://www.encodeproject.org/experiments/ENCSR308EYT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against E4F1. (E4F1-BGHcLV18)
experiment encode accession: ENCSR308EYT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB518TBS
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting E4F1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1a7fe819-c52e-4662-af4a-c14e71350329/@@download/attachment/L-E4F1-BGHcLV18-15.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against E4F1. (E4F1-BGHcLV18-15)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS074IQT at ENCODE; https://www.encodeproject.org/ENCBS074IQT/


title: CRISPR RNA-seq from HepG2 (ENCLB381USO)

description:
https://www.encodeproject.org/experiments/ENCSR298AQX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHTOP. (CHTOP-BGHcLV22)
experiment encode accession: ENCSR298AQX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB381USO
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 CHTOP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e1b803f3-e5c0-4b37-8990-68f7ee579394/@@download/attachment/L-CHTOP-BGHcLV22-8.pdf

value: CHTOP

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHTOP. (CHTOP-BGHcLV22-8)

value: ENCBS641NAE at ENCODE; https://www.encodeproject.org/ENCBS641NAE/


title: BruChase-seq from HepG2 (ENCLB054PKY)

description:
https://www.encodeproject.org/experiments/ENCSR295FEH/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR295FEH
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR974AQD
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB054PKY
size range: 400-500

source_name: Homo sapiens HepG2 cell line, subjected to a 2 hour pulse-chase

value: Mats Ljungman, UMichigan

value: ENCBS367ONT at ENCODE; https://www.encodeproject.org/ENCBS367ONT/


title: CRISPR RNA-seq from K562 (ENCLB999FUK)

description:
https://www.encodeproject.org/experiments/ENCSR292PXV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NT. (NT-BGKcLV11)
experiment encode accession: ENCSR292PXV
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB999FUK
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/aaa9a6f3-6974-4cad-9bc4-5bcbcf8c4103/@@download/attachment/L-NT-BGKcLV11-2.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non-target. (NT-BGKcLV11-2)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS390OYB at ENCODE; https://www.encodeproject.org/ENCBS390OYB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB484LAN)

description:
https://www.encodeproject.org/experiments/ENCSR504CPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NSUN4. (NSUN4-BGHcLV16)
experiment encode accession: ENCSR504CPZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB484LAN
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/d391a601-9eed-416c-b511-b0b7d011d0bf/@@download/attachment/L-NSUN4-BGHcLV16-37.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NSUN4. (NSUN4-BGHcLV16-37)

value: male

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS530BMR at ENCODE; https://www.encodeproject.org/ENCBS530BMR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB994EHQ)

description:
https://www.encodeproject.org/experiments/ENCSR400SCX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GLRX3. (GLRX3-BGHcLV12)
experiment encode accession: ENCSR400SCX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB994EHQ
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 GLRX3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/db200f5f-e9a4-4de1-ad6e-bbbf0c225cb0/@@download/attachment/L-GLRX3-BGHcLV12-78.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GLRX3. (GLRX3-BGHcLV12-78)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS869LGZ at ENCODE; https://www.encodeproject.org/ENCBS869LGZ/


title: CRISPR RNA-seq from K562 (ENCLB108KVM)

description:
https://www.encodeproject.org/experiments/ENCSR292PXV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NT. (NT-BGKcLV11)
experiment encode accession: ENCSR292PXV
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB108KVM
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/d9841217-b733-49dd-8208-0bf7ca06c7b8/@@download/attachment/L-NT-BGKcLV11-1.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non-target. (NT-BGKcLV11-1)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS421LRO at ENCODE; https://www.encodeproject.org/ENCBS421LRO/


title: CRISPR RNA-seq from HepG2 (ENCLB862YPF)

description:
https://www.encodeproject.org/experiments/ENCSR400SCX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GLRX3. (GLRX3-BGHcLV12)
experiment encode accession: ENCSR400SCX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB862YPF
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/caae6cf5-8387-4f57-914b-4b067b583f82/@@download/attachment/L-GLRX3-BGHcLV12-77.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against GLRX3. (GLRX3-BGHcLV12-77)

value: ENCBS041KFE at ENCODE; https://www.encodeproject.org/ENCBS041KFE/


title: CRISPR RNA-seq from K562 (ENCLB426ZQB)

description:
https://www.encodeproject.org/experiments/ENCSR090SBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NCBP1. (NCBP1-BGKcLV11)
experiment encode accession: ENCSR090SBZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB426ZQB
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 NCBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e446bc1f-cdd2-4323-8499-3f396cc958be/@@download/attachment/L-NCBP1-BGKcLV11-61.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NCBP1. (NCBP1-BGKcLV11-61)

value: adult

value: 53 year

value: ENCBS192AQT at ENCODE; https://www.encodeproject.org/ENCBS192AQT/

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


title: CRISPR RNA-seq from K562 (ENCLB811YQC)

description:
https://www.encodeproject.org/experiments/ENCSR298ASI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX6. (DDX6-BGKcLV08)
experiment encode accession: ENCSR298ASI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB811YQC
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 DDX6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/16ffd70f-c01e-4a6f-95a7-e0e3a0e4dd1f/@@download/attachment/L-DDX6-BGKcLV08-30.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX6. (DDX6-BGKcLV08-30)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS324CCL at ENCODE; https://www.encodeproject.org/ENCBS324CCL/


title: CRISPR RNA-seq from K562 (ENCLB218JPE)

description:
https://www.encodeproject.org/experiments/ENCSR299PRA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC10. (EXOSC10-BGKcLV21)
experiment encode accession: ENCSR299PRA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB218JPE
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 EXOSC10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/80e7c6a8-52b8-4092-9fd8-4c6417edf973/@@download/attachment/L-EXOSC10-BGKcLV21-21.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC10. (EXOSC10-BGKcLV21-21)

value: ENCBS311NMT at ENCODE; https://www.encodeproject.org/ENCBS311NMT/


title: CRISPR RNA-seq from K562 (ENCLB241CJZ)

description:
https://www.encodeproject.org/experiments/ENCSR092QTF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RAE1. (RAE1-BGKcLV17)
experiment encode accession: ENCSR092QTF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB241CJZ
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 RAE1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/039df385-1d8c-47f8-b839-f0bfada75963/@@download/attachment/L-RAE1-BGKcLV17-44.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RAE1. (RAE1-BGKcLV17-44)

value: female

value: ENCBS370MUB at ENCODE; https://www.encodeproject.org/ENCBS370MUB/


title: CRISPR RNA-seq from K562 (ENCLB410XQE)

description:
https://www.encodeproject.org/experiments/ENCSR299PRA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC10. (EXOSC10-BGKcLV21)
experiment encode accession: ENCSR299PRA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB410XQE
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/69730fe6-f58b-48c8-84c9-0df09cab51b0/@@download/attachment/L-EXOSC10-BGKcLV21-22.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC10. (EXOSC10-BGKcLV21-22)

value: chronic myelogenous leukemia (CML)

value: ENCBS470VBM at ENCODE; https://www.encodeproject.org/ENCBS470VBM/


title: CRISPR RNA-seq from K562 (ENCLB529ARE)

description:
https://www.encodeproject.org/experiments/ENCSR278CLE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGKcLV23)
experiment encode accession: ENCSR278CLE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB529ARE
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 ALKBH1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f802d822-ef6b-4a56-b48f-06a3c6839447/@@download/attachment/L-ALKBH1-BGKcLV23-13.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGKcLV23-13)

value: ENCBS103TTP at ENCODE; https://www.encodeproject.org/ENCBS103TTP/


title: CRISPR RNA-seq from K562 (ENCLB801CZM)

description:
https://www.encodeproject.org/experiments/ENCSR090SBZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NCBP1. (NCBP1-BGKcLV11)
experiment encode accession: ENCSR090SBZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB801CZM
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/6f3903f4-714e-4036-a0a5-de30251fb6c2/@@download/attachment/L-NCBP1-BGKcLV11-62.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against NCBP1. (NCBP1-BGKcLV11-62)

value: adult

value: 53 year

value: ENCBS674NPD at ENCODE; https://www.encodeproject.org/ENCBS674NPD/


title: CRISPR RNA-seq from K562 (ENCLB556NMK)

description:
https://www.encodeproject.org/experiments/ENCSR298ASI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX6. (DDX6-BGKcLV08)
experiment encode accession: ENCSR298ASI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB556NMK
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/7e86dea0-ce6e-40ab-8b6d-9bc25edaedc0/@@download/attachment/L-DDX6-BGKcLV08-29.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX6. (DDX6-BGKcLV08-29)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS099EPI at ENCODE; https://www.encodeproject.org/ENCBS099EPI/

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


title: CRISPR RNA-seq from HepG2 (ENCLB549HTS)

description:
https://www.encodeproject.org/experiments/ENCSR300EBW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV09)
experiment encode accession: ENCSR300EBW
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB549HTS
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/5ffaea81-c759-4e7e-97ad-ea7ce5ae7f4a/@@download/attachment/L-NT-BGHcLV09-1.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV09-1)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS205XWZ at ENCODE; https://www.encodeproject.org/ENCBS205XWZ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB184OXM)

description:
https://www.encodeproject.org/experiments/ENCSR294DOR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4E. (EIF4E-BGHcLV16)
experiment encode accession: ENCSR294DOR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB184OXM
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 EIF4E

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/856d8797-628b-4d58-ac4c-7c0eb45daa22/@@download/attachment/L-EIF4E-BGHcLV16-30.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4E. (EIF4E-BGHcLV16-30)

value: ENCBS865GQD at ENCODE; https://www.encodeproject.org/ENCBS865GQD/


title: CRISPR RNA-seq from K562 (ENCLB574JTF)

description:
https://www.encodeproject.org/experiments/ENCSR276GMG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against XRCC5. (XRCC5-BGKcLV11)
experiment encode accession: ENCSR276GMG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB574JTF
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 XRCC5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8e26fae4-4ce7-4b74-a0ee-f3973ff6966b/@@download/attachment/L-XRCC5-BGKcLV11-112.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against XRCC5. (XRCC5-BGKcLV11-112)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS288OPM at ENCODE; https://www.encodeproject.org/ENCBS288OPM/


title: BruChase-seq from HepG2 (ENCLB646QFM)

description:
https://www.encodeproject.org/experiments/ENCSR295FEH/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR295FEH
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR974AQD
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB646QFM
size range: 400-500

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS089YMA at ENCODE; https://www.encodeproject.org/ENCBS089YMA/


title: CRISPR RNA-seq from HepG2 (ENCLB742HUO)

description:
https://www.encodeproject.org/experiments/ENCSR298AQX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHTOP. (CHTOP-BGHcLV22)
experiment encode accession: ENCSR298AQX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB742HUO
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/3d58191d-6bcb-4d39-8e19-195c3469e510/@@download/attachment/L-CHTOP-BGHcLV22-7.pdf

value: CHTOP

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHTOP. (CHTOP-BGHcLV22-7)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS919KOR at ENCODE; https://www.encodeproject.org/ENCBS919KOR/


title: CRISPR RNA-seq from HepG2 (ENCLB195TZH)

description:
https://www.encodeproject.org/experiments/ENCSR080NRY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX51. (DDX51-BGHcLV12)
experiment encode accession: ENCSR080NRY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB195TZH
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 DDX51

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0de0c681-8b14-4434-aa59-129850c0688a/@@download/attachment/L-DDX51-BGHcLV12-30.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX51. (DDX51-BGHcLV12-30)

value: child

value: 15 year

value: ENCBS568ITW at ENCODE; https://www.encodeproject.org/ENCBS568ITW/

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


title: CRISPR RNA-seq from HepG2 (ENCLB667WSG)

description:
https://www.encodeproject.org/experiments/ENCSR080NRY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX51. (DDX51-BGHcLV12)
experiment encode accession: ENCSR080NRY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB667WSG
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/64ae4876-f686-44de-b7b7-17ce3268321c/@@download/attachment/L-DDX51-BGHcLV12-29.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX51. (DDX51-BGHcLV12-29)

value: ENCBS889KBU at ENCODE; https://www.encodeproject.org/ENCBS889KBU/


title: CRISPR RNA-seq from HepG2 (ENCLB382RMY)

description:
https://www.encodeproject.org/experiments/ENCSR294DOR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4E. (EIF4E-BGHcLV16)
experiment encode accession: ENCSR294DOR
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB382RMY
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/8e8b50c4-3baa-4fc3-858b-9a5b219b205b/@@download/attachment/L-EIF4E-BGHcLV16-29.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4E. (EIF4E-BGHcLV16-29)

value: ENCBS732KMO at ENCODE; https://www.encodeproject.org/ENCBS732KMO/


title: CRISPR RNA-seq from HepG2 (ENCLB245OWS)

description:
https://www.encodeproject.org/experiments/ENCSR266XKN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MECP2. (MECP2-BGHcLV16)
experiment encode accession: ENCSR266XKN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB245OWS
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 MECP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/88ef35ea-92f7-482a-a6c2-b3b715c50a4b/@@download/attachment/L-MECP2-BGHcLV16-33.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MECP2. (MECP2-BGHcLV16-33)

value: ATCC

value: ENCBS355HDT at ENCODE; https://www.encodeproject.org/ENCBS355HDT/


title: CRISPR RNA-seq from HepG2 (ENCLB868GAM)

description:
https://www.encodeproject.org/experiments/ENCSR290GUQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DNMT3B. (DNMT3B-BGHcLV20)
experiment encode accession: ENCSR290GUQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB868GAM
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 DNMT3B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b0b1570f-23a3-46a2-9e31-ed7f522a0db4/@@download/attachment/L-DNMT3B-BGHcLV20-6.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DNMT3B. (DNMT3B-BGHcLV20-6)

value: male

value: ENCBS350DLG at ENCODE; https://www.encodeproject.org/ENCBS350DLG/


title: CRISPR RNA-seq from K562 (ENCLB452ZRI)

description:
https://www.encodeproject.org/experiments/ENCSR264MSX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGKcLV15)
experiment encode accession: ENCSR264MSX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB452ZRI
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 EIF4A3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/598e4d62-b5a1-4998-8e30-7fab267d5133/@@download/attachment/L-EIF4A3-BGKcLV15-31.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGKcLV15-31)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS439XGT at ENCODE; https://www.encodeproject.org/ENCBS439XGT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB497GSD)

description:
https://www.encodeproject.org/experiments/ENCSR300EBW/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV09)
experiment encode accession: ENCSR300EBW
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB497GSD
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/9a3d4143-8067-47be-815f-846607a9e44c/@@download/attachment/L-NT-BGHcLV09-2.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV09-2)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS271VOS at ENCODE; https://www.encodeproject.org/ENCBS271VOS/

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


title: CRISPR RNA-seq from K562 (ENCLB669IKT)

description:
https://www.encodeproject.org/experiments/ENCSR276GMG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against XRCC5. (XRCC5-BGKcLV11)
experiment encode accession: ENCSR276GMG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB669IKT
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/572b86c2-43e2-437e-9852-cd5a5a990dde/@@download/attachment/L-XRCC5-BGKcLV11-111.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against XRCC5. (XRCC5-BGKcLV11-111)

value: ATCC

value: ENCBS567TJU at ENCODE; https://www.encodeproject.org/ENCBS567TJU/


title: polyA plus RNA-seq from foreskin keratinocyte (ENCLB028EIQ)

description:
https://www.encodeproject.org/experiments/ENCSR613SLA/
***************
biological replicate number: 2
technical replicate number: 1
description: polyA mRNA RNA-seq on primary keratinocytes in day 3 of differentiation
experiment encode accession: ENCSR613SLA
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB028EIQ
size range: >200

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 2.5 days

extract_protocol:
general protocol: https://www.encodeproject.org/documents/9021cb71-35b1-4a9a-9fcc-38c6df5e9fea/@@download/attachment/ggr.keratinocyte.snyder-lab.rna_assays.pdf
extraction method: Qiagen RNA extraction

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

value: male

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;

value: Healthy

tag: passage number

value: ENCBS299ONK at ENCODE; https://www.encodeproject.org/ENCBS299ONK/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: CRISPR RNA-seq from HepG2 (ENCLB534DAK)

description:
https://www.encodeproject.org/experiments/ENCSR279MNU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGHcLV10)
experiment encode accession: ENCSR279MNU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB534DAK
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 STAU2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/78550fbe-9aff-4b6b-b4bc-7e85bf627466/@@download/attachment/L-STAU2-BGHcLV10-45.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGHcLV10-45)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS365HBD at ENCODE; https://www.encodeproject.org/ENCBS365HBD/


title: CRISPR RNA-seq from K562 (ENCLB597TGG)

description:
https://www.encodeproject.org/experiments/ENCSR278CLE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGKcLV23)
experiment encode accession: ENCSR278CLE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB597TGG
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/4e93edc7-b343-4481-9f75-afb5eda76abc/@@download/attachment/L-ALKBH1-BGKcLV23-14.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGKcLV23-14)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS461EJN at ENCODE; https://www.encodeproject.org/ENCBS461EJN/

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


title: CRISPR RNA-seq from K562 (ENCLB066LMY)

description:
https://www.encodeproject.org/experiments/ENCSR095TFW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3A2. (SF3A2-BGKcLV21)
experiment encode accession: ENCSR095TFW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB066LMY
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 SF3A2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/217064e9-1947-43a0-a276-d5b9de4c66aa/@@download/attachment/L-SF3A2-BGKcLV21-42.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3A2. (SF3A2-BGKcLV21-42)

value: ENCBS437VMI at ENCODE; https://www.encodeproject.org/ENCBS437VMI/


title: Bru-seq from GM12878 (ENCLB550BZS)

description:
https://www.encodeproject.org/experiments/ENCSR267RPG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR267RPG
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB550BZS
size range: 400-500

source_name: Homo sapiens GM12878 cell line

value: cell line

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

value: Coriell

value: ENCBS242MBR at ENCODE; https://www.encodeproject.org/ENCBS242MBR/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: CRISPR RNA-seq from K562 (ENCLB016YAM)

description:
https://www.encodeproject.org/experiments/ENCSR092QTF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RAE1. (RAE1-BGKcLV17)
experiment encode accession: ENCSR092QTF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB016YAM
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/aff73192-d603-4801-93e8-a4b881664398/@@download/attachment/L-RAE1-BGKcLV17-43.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RAE1. (RAE1-BGKcLV17-43)

value: Brenton Graveley, UConn

value: ENCBS750NLG at ENCODE; https://www.encodeproject.org/ENCBS750NLG/


title: CRISPR RNA-seq from HepG2 (ENCLB642NGH)

description:
https://www.encodeproject.org/experiments/ENCSR290GUQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DNMT3B. (DNMT3B-BGHcLV20)
experiment encode accession: ENCSR290GUQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB642NGH
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/f458999e-fff2-4c1d-af8d-8e7c19e91c3c/@@download/attachment/L-DNMT3B-BGHcLV20-5.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DNMT3B. (DNMT3B-BGHcLV20-5)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS470NZT at ENCODE; https://www.encodeproject.org/ENCBS470NZT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB433SNT)

description:
https://www.encodeproject.org/experiments/ENCSR266XKN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MECP2. (MECP2-BGHcLV16)
experiment encode accession: ENCSR266XKN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB433SNT
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/e24b623f-6ae8-40e2-bee5-02d7eef87e9d/@@download/attachment/L-MECP2-BGHcLV16-34.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MECP2. (MECP2-BGHcLV16-34)

value: ATCC

value: ENCBS007KVT at ENCODE; https://www.encodeproject.org/ENCBS007KVT/


title: CRISPR RNA-seq from K562 (ENCLB761BSK)

description:
https://www.encodeproject.org/experiments/ENCSR095TFW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3A2. (SF3A2-BGKcLV21)
experiment encode accession: ENCSR095TFW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB761BSK
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/b5a093b2-f904-4657-b140-6421194a5ec1/@@download/attachment/L-SF3A2-BGKcLV21-41.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3A2. (SF3A2-BGKcLV21-41)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS060QUM at ENCODE; https://www.encodeproject.org/ENCBS060QUM/

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


title: polyA plus RNA-seq from foreskin keratinocyte (ENCLB479EDP)

description:
https://www.encodeproject.org/experiments/ENCSR613SLA/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA mRNA RNA-seq on primary keratinocytes in day 3 of differentiation
experiment encode accession: ENCSR613SLA
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB479EDP
size range: >200

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

value: male

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;

value: Healthy

value: ENCBS079LRU at ENCODE; https://www.encodeproject.org/ENCBS079LRU/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: polyA plus RNA-seq from foreskin keratinocyte (ENCLB581UGH)

description:
https://www.encodeproject.org/experiments/ENCSR100SIL/
***************
biological replicate number: 2
technical replicate number: 1
description: polyA mRNA RNA-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR100SIL
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB581UGH
size range: >200

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 5.5 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: polyA plus RNA-seq from foreskin keratinocyte (ENCLB638BED)

description:
https://www.encodeproject.org/experiments/ENCSR100SIL/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA mRNA RNA-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR100SIL
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB638BED
size range: >200

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/


title: CRISPR RNA-seq from HepG2 (ENCLB425ZLV)

description:
https://www.encodeproject.org/experiments/ENCSR197XHV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BAZ1A. (BAZ1A-BGHcLV18)
experiment encode accession: ENCSR197XHV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB425ZLV
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 BAZ1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/06fd14a6-e4a4-4e53-9c52-08251d054e11/@@download/attachment/L-BAZ1A-BGHcLV18-4.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BAZ1A. (BAZ1A-BGHcLV18-4)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS128GTR at ENCODE; https://www.encodeproject.org/ENCBS128GTR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB120XZV)

description:
https://www.encodeproject.org/experiments/ENCSR197XHV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BAZ1A. (BAZ1A-BGHcLV18)
experiment encode accession: ENCSR197XHV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB120XZV
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/03d113d9-f9a0-48c6-895c-1e4ffdca0b02/@@download/attachment/L-BAZ1A-BGHcLV18-3.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BAZ1A. (BAZ1A-BGHcLV18-3)

value: male

value: ENCBS257VCX at ENCODE; https://www.encodeproject.org/ENCBS257VCX/


title: CRISPR RNA-seq from K562 (ENCLB281AWX)

description:
https://www.encodeproject.org/experiments/ENCSR070AYA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against WBP11. (WBP11-BGKcLV23)
experiment encode accession: ENCSR070AYA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB281AWX
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 WBP11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6c6d6435-d702-4916-be47-de360c9e4e42/@@download/attachment/L-WBP11-BGKcLV23-66.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against WBP11. (WBP11-BGKcLV23-66)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS935HUM at ENCODE; https://www.encodeproject.org/ENCBS935HUM/

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


title: CRISPR RNA-seq from HepG2 (ENCLB274XXH)

description:
https://www.encodeproject.org/experiments/ENCSR279MNU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGHcLV10)
experiment encode accession: ENCSR279MNU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB274XXH
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/71c70c15-1d5c-4a45-a824-740007a59b1f/@@download/attachment/L-STAU2-BGHcLV10-46.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGHcLV10-46)

value: hepatocellular carcinoma

value: ENCBS219FEV at ENCODE; https://www.encodeproject.org/ENCBS219FEV/


title: CRISPR RNA-seq from K562 (ENCLB186YBO)

description:
https://www.encodeproject.org/experiments/ENCSR264MSX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGKcLV15)
experiment encode accession: ENCSR264MSX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB186YBO
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/c70f745e-c0b8-4e82-afae-0e7d1891d80b/@@download/attachment/L-EIF4A3-BGKcLV15-32.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGKcLV15-32)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS189BWL at ENCODE; https://www.encodeproject.org/ENCBS189BWL/


title: polyA plus RNA-seq from foreskin keratinocyte (ENCLB886SME)

description:
https://www.encodeproject.org/experiments/ENCSR367AIV/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA mRNA RNA-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR367AIV
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB886SME
size range: >200

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, grown in 2D culture, day 0.0

value: male

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: Healthy

value: ENCBS666IIR at ENCODE; https://www.encodeproject.org/ENCBS666IIR/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: CRISPR RNA-seq from K562 (ENCLB333ZJF)

description:
https://www.encodeproject.org/experiments/ENCSR163PNO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against YWHAG. (YWHAG-BGKcLV08)
experiment encode accession: ENCSR163PNO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB333ZJF
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/75f0f1b6-cc24-47c2-aa07-fc9b423c4f21/@@download/attachment/L-YWHAG-BGKcLV08-79.pdf

value: YWHAG

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against YWHAG. (YWHAG-BGKcLV08-79)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS587LTT at ENCODE; https://www.encodeproject.org/ENCBS587LTT/

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


title: BruChase-seq from HCT116 (ENCLB595FGQ)

description:
https://www.encodeproject.org/experiments/ENCSR263QXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR263QXD
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR799MPW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB595FGQ
size range: 400-500

source_name: Homo sapiens HCT116 cell line, subjected to a 2 hour pulse-chase

value: male

value: colorectal carcinoma

value: 48 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS351TFA at ENCODE; https://www.encodeproject.org/ENCBS351TFA/

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


title: BruChase-seq from Panc1 (ENCLB677UOJ)

description:
https://www.encodeproject.org/experiments/ENCSR069MAW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR069MAW
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR639ZOU
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB677UOJ
size range: 400-500

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

value: pancreatic carcinoma

value: 56 year

value: ENCBS174AJT at ENCODE; https://www.encodeproject.org/ENCBS174AJT/

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


title: Bru-seq from MCF-7 (ENCLB078DED)

description:
https://www.encodeproject.org/experiments/ENCSR258ARX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR258ARX
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR727IHV
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB078DED
size range: 400-500

source_name: Homo sapiens MCF-7 cell line treated with 500 rad irradiation

value: cell line

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS224HRN at ENCODE; https://www.encodeproject.org/ENCBS224HRN/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: Mint-ChIP-seq from immature natural killer cell (ENCLB297AXC)

description:
https://www.encodeproject.org/experiments/ENCSR245KON/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR245KON
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR169WAD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB297AXC
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

library_source: genomic

molecule: genomic DNA

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

value: immature natural killer cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB425VCB)

description:
https://www.encodeproject.org/experiments/ENCSR175OSV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX39B. (DDX39B-BGHcLV18)
experiment encode accession: ENCSR175OSV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB425VCB
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 DDX39B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7f68f06d-0540-46d3-95a8-be919297f6e2/@@download/attachment/L-DDX39B-BGHcLV18-9.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX39B. (DDX39B-BGHcLV18-10)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS277BUX at ENCODE; https://www.encodeproject.org/ENCBS277BUX/

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


title: CRISPR RNA-seq from K562 (ENCLB561VMV)

description:
https://www.encodeproject.org/experiments/ENCSR162HOU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGKcLV23)
experiment encode accession: ENCSR162HOU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB561VMV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting BRIX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cf2b8c94-1d89-4fdc-8e1f-608b342ed2a9/@@download/attachment/L-BRIX1-BGKcLV23-24.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGKcLV23-24)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS846ABT at ENCODE; https://www.encodeproject.org/ENCBS846ABT/

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


title: CRISPR RNA-seq from K562 (ENCLB643SPT)

description:
https://www.encodeproject.org/experiments/ENCSR070AYA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against WBP11. (WBP11-BGKcLV23)
experiment encode accession: ENCSR070AYA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB643SPT
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/9bb85127-66e3-4b0a-acde-0579b4f44f81/@@download/attachment/L-WBP11-BGKcLV23-65.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against WBP11. (WBP11-BGKcLV23-65)

value: ENCBS242DYL at ENCODE; https://www.encodeproject.org/ENCBS242DYL/


title: eCLIP from HepG2 (ENCLB026DPK)

description:
https://www.encodeproject.org/experiments/ENCSR061SZV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against DGCR8
experiment encode accession: ENCSR061SZV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR298SAD
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB026DPK
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: male

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

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


title: Bru-seq from MCF-7 (ENCLB274AUU)

description:
https://www.encodeproject.org/experiments/ENCSR258ARX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR258ARX
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR727IHV
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB274AUU
size range: 400-500

value: breast cancer (adenocarcinoma)

value: 69 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS679DXX at ENCODE; https://www.encodeproject.org/ENCBS679DXX/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: polyA plus RNA-seq from foreskin keratinocyte (ENCLB367IIC)

description:
https://www.encodeproject.org/experiments/ENCSR367AIV/
***************
biological replicate number: 2
technical replicate number: 1
description: polyA mRNA RNA-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR367AIV
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB367IIC
size range: >200

extract_protocol:
general protocol: https://www.encodeproject.org/documents/9021cb71-35b1-4a9a-9fcc-38c6df5e9fea/@@download/attachment/ggr.keratinocyte.snyder-lab.rna_assays.pdf
extraction method: Qiagen RNA extraction

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.0

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: Healthy

value: ENCBS538XZS at ENCODE; https://www.encodeproject.org/ENCBS538XZS/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: BruChase-seq from HCT116 (ENCLB571QGR)

description:
https://www.encodeproject.org/experiments/ENCSR263QXD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR263QXD
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR799MPW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB571QGR
size range: 400-500

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: ENCBS513TRO at ENCODE; https://www.encodeproject.org/ENCBS513TRO/

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


title: CRISPR RNA-seq from K562 (ENCLB950IDL)

description:
https://www.encodeproject.org/experiments/ENCSR064VKV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF574. (ZNF574-BGKcLV17)
experiment encode accession: ENCSR064VKV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB950IDL
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 ZNF574

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4da397c2-9f15-47fb-a572-02b62176622c/@@download/attachment/L-ZNF574-BGKcLV17-59.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF574. (ZNF574-BGKcLV17-59)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS357BKM at ENCODE; https://www.encodeproject.org/ENCBS357BKM/

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


title: CRISPR RNA-seq from HepG2 (ENCLB999KMV)

description:
https://www.encodeproject.org/experiments/ENCSR175OSV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX39B. (DDX39B-BGHcLV18)
experiment encode accession: ENCSR175OSV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB999KMV
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/c4d2020e-a850-4eb6-9613-1d273b28ba2c/@@download/attachment/L-DDX39B-BGHcLV18-10.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX39B. (DDX39B-BGHcLV18-9)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS269WJT at ENCODE; https://www.encodeproject.org/ENCBS269WJT/

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


title: eCLIP from HepG2 (ENCLB909IOJ)

description:
https://www.encodeproject.org/experiments/ENCSR061SZV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against DGCR8
experiment encode accession: ENCSR061SZV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR298SAD
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB909IOJ
fragmentation methods: see document
size range: 175-300

value: cell line

value: male

value: Gene Yeo, UCSD

value: ENCBS362ASG at ENCODE; https://www.encodeproject.org/ENCBS362ASG/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

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


title: CRISPR RNA-seq from K562 (ENCLB725NNA)

description:
https://www.encodeproject.org/experiments/ENCSR066ZMF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ETF1. (ETF1-BGKcLV08)
experiment encode accession: ENCSR066ZMF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB725NNA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting ETF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9209a0cc-1ad1-4f36-842c-846fbf538981/@@download/attachment/L-ETF1-BGKcLV08-34.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ETF1. (ETF1-BGKcLV08-34)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS355TWU at ENCODE; https://www.encodeproject.org/ENCBS355TWU/


title: CRISPR RNA-seq from K562 (ENCLB855VYU)

description:
https://www.encodeproject.org/experiments/ENCSR064VKV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF574. (ZNF574-BGKcLV17)
experiment encode accession: ENCSR064VKV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB855VYU
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/50a25a0d-35ae-47bb-81d3-6c0b9285c889/@@download/attachment/L-ZNF574-BGKcLV17-60.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF574. (ZNF574-BGKcLV17-60)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS584XDN at ENCODE; https://www.encodeproject.org/ENCBS584XDN/

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


title: Bru-seq from GM12878 (ENCLB074BYB)

description:
https://www.encodeproject.org/experiments/ENCSR267RPG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR267RPG
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB074BYB
size range: 400-500

value: cell line

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

value: Coriell

value: ENCBS835BTY at ENCODE; https://www.encodeproject.org/ENCBS835BTY/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: BruChase-seq from PC-3 (ENCLB277WLR)

description:
https://www.encodeproject.org/experiments/ENCSR155GYW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR155GYW
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR622SUM
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB277WLR
size range: 400-500

source_name: Homo sapiens PC-3 cell line, subjected to a 6 hour pulse-chase

value: male

value: grade IV, adenocarcinoma

value: 62 year

value: ENCBS942SGC at ENCODE; https://www.encodeproject.org/ENCBS942SGC/

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


title: BruChase-seq from PC-3 (ENCLB398RJS)

description:
https://www.encodeproject.org/experiments/ENCSR155GYW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR155GYW
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR622SUM
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB398RJS
size range: 400-500

value: adult

value: ENCBS103MXV at ENCODE; https://www.encodeproject.org/ENCBS103MXV/


title: Control eCLIP from HepG2 (ENCLB745ADQ)

description:
https://www.encodeproject.org/experiments/ENCSR298SAD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DGCR8
experiment encode accession: ENCSR298SAD
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB745ADQ
fragmentation methods: see document
size range: 175-300

value: child

value: 15 year

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS362ASG at ENCODE; https://www.encodeproject.org/ENCBS362ASG/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

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