title: CRISPR RNA-seq from HepG2 (ENCLB718PAE)

description:
https://www.encodeproject.org/experiments/ENCSR775ZWO/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV10)
experiment encode accession: ENCSR775ZWO
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB718PAE
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/9ebb0f0c-e7ee-4baa-b86a-477dda5086fe/@@download/attachment/L-NT-BGHcLV10-2.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV10-2)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS282MMS at ENCODE; https://www.encodeproject.org/ENCBS282MMS/

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


title: CRISPR RNA-seq from K562 (ENCLB602PPG)

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/ENCSR775USN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMYD3. (SMYD3-BGKcLV19)
experiment encode accession: ENCSR775USN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB602PPG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting SMYD3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/79becdf8-6ec9-4fcd-b7c4-b14c853ae0cd/@@download/attachment/L-SMYD3-BGKcLV19-52.pdf

tag: antibody

tag: line

value: cell line

tag: description

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMYD3. (SMYD3-BGKcLV19-52)

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

tag: source

tag: link

value: ENCBS686RDU at ENCODE; https://www.encodeproject.org/ENCBS686RDU/

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


title: CRISPR RNA-seq from K562 (ENCLB735IRF)

description:
https://www.encodeproject.org/experiments/ENCSR650GNB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF335. (ZNF335-BGKcLV17)
experiment encode accession: ENCSR650GNB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB735IRF
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 ZNF335

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/620bfab7-e61e-4539-93ab-5b2ce19168d1/@@download/attachment/L-ZNF335-BGKcLV17-58.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF335. (ZNF335-BGKcLV17-58)

value: ENCBS362YBE at ENCODE; https://www.encodeproject.org/ENCBS362YBE/


title: Control eCLIP from K562 (ENCLB426AJM)

description:
https://www.encodeproject.org/experiments/ENCSR183FVK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against MATR3
experiment encode accession: ENCSR183FVK
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB426AJM
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

tag: passage number

value: Gene Yeo, UCSD

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

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB195DSL)

description:
https://www.encodeproject.org/experiments/ENCSR659DRE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAVL1. (ELAVL1-BGHcLV14)
experiment encode accession: ENCSR659DRE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR750CPT
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB195DSL
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 ELAVL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/330e7dc8-47e9-4d7f-bc4d-55c5fb1fa892/@@download/attachment/L-ELAVL1-BGHcLV14-40.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAVL1. (ELAVL1-BGHcLV14-40)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS777RCK at ENCODE; https://www.encodeproject.org/ENCBS777RCK/


title: CRISPR RNA-seq from K562 (ENCLB999GRF)

description:
https://www.encodeproject.org/experiments/ENCSR650GNB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF335. (ZNF335-BGKcLV17)
experiment encode accession: ENCSR650GNB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB999GRF
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/50973d96-2f18-4ff4-9c76-64f353295a92/@@download/attachment/L-ZNF335-BGKcLV17-57.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF335. (ZNF335-BGKcLV17-57)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS464XQN at ENCODE; https://www.encodeproject.org/ENCBS464XQN/


title: CRISPR RNA-seq from K562 (ENCLB677HEM)

description:
https://www.encodeproject.org/experiments/ENCSR649MBU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD5. (SMAD5-BGKcLV19)
experiment encode accession: ENCSR649MBU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB677HEM
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 SMAD5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dbdb96e9-d82b-4610-9acf-8d6bbe2df8d3/@@download/attachment/L-SMAD5-BGKcLV19-48.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD5. (SMAD5-BGKcLV19-48)

value: ENCBS273YVK at ENCODE; https://www.encodeproject.org/ENCBS273YVK/

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


title: CRISPR RNA-seq from K562 (ENCLB219FBY)

description:
https://www.encodeproject.org/experiments/ENCSR649MBU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD5. (SMAD5-BGKcLV19)
experiment encode accession: ENCSR649MBU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB219FBY
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/64975513-a8b5-4f87-9998-321ccc0e8cfb/@@download/attachment/L-SMAD5-BGKcLV19-47.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMAD5. (SMAD5-BGKcLV19-47)

value: ENCBS190TOX at ENCODE; https://www.encodeproject.org/ENCBS190TOX/


title: eCLIP from HepG2 (ENCLB191OON)

description:
https://www.encodeproject.org/experiments/ENCSR256CHX/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against PCBP1
experiment encode accession: ENCSR256CHX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR825FTY
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB191OON
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: child

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/

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

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


title: BruChase-seq from K562 (ENCLB894OPO)

description:
https://www.encodeproject.org/experiments/ENCSR762OPQ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR762OPQ
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR729WFH
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB894OPO
size range: 400-500

source_name: Homo sapiens K562 cell line, subjected to a 6 hour pulse-chase

value: cell line

value: female

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS824PQT at ENCODE; https://www.encodeproject.org/ENCBS824PQT/


title: CRISPR RNA-seq from K562 (ENCLB610IIT)

description:
https://www.encodeproject.org/experiments/ENCSR644LYC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CNOT10. (CNOT10-BGKcLV21)
experiment encode accession: ENCSR644LYC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB610IIT
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 CNOT10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6afef998-1242-4dc6-82a1-f022f8f8ba63/@@download/attachment/L-CNOT10-BGKcLV21-7.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CNOT10. (CNOT10-BGKcLV21-7)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS252NYL at ENCODE; https://www.encodeproject.org/ENCBS252NYL/


title: eCLIP from HepG2 (ENCLB385ATT)

description:
https://www.encodeproject.org/experiments/ENCSR256CHX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against PCBP1
experiment encode accession: ENCSR256CHX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR825FTY
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB385ATT
fragmentation methods: see document
size range: 175-300

value: child

value: male

value: 15 year

value: ENCBS074YUC at ENCODE; https://www.encodeproject.org/ENCBS074YUC/

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB813QCU)

description:
https://www.encodeproject.org/experiments/ENCSR048ARD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR048ARD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR934ZBY
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB813QCU
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell, preserved by cryopreservation

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: CD4+ memory CD3+ CD4+ CD8- CD45RA- CD45RO+ nonTreg

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS668VBU at ENCODE; https://www.encodeproject.org/ENCBS668VBU/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: TF ChIP-seq from A549 (ENCLB790EQW)

description:
https://www.encodeproject.org/experiments/ENCSR192SKV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-HMGXB4 ChIP-seq on human A549
experiment encode accession: ENCSR192SKV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR580TXR, ENCSR542LGX
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB790EQW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting HMGXB4

value: cell line

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS644DVI at ENCODE; https://www.encodeproject.org/ENCBS644DVI/

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


title: CRISPR RNA-seq from K562 (ENCLB490YAI)

description:
https://www.encodeproject.org/experiments/ENCSR765HSN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CIZ1. (CIZ1-BGKcLV19)
experiment encode accession: ENCSR765HSN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB490YAI
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 CIZ1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0b6da6d5-62e6-4c97-86db-bc979646144d/@@download/attachment/L-CIZ1-BGKcLV19-9.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CIZ1. (CIZ1-BGKcLV19-10)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS003ASV at ENCODE; https://www.encodeproject.org/ENCBS003ASV/

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


title: Control eCLIP from K562 (ENCLB022PZI)

description:
https://www.encodeproject.org/experiments/ENCSR255PGS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against UTP18
experiment encode accession: ENCSR255PGS
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB022PZI
fragmentation methods: see document
size range: 175-300

value: Gene Yeo, UCSD

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

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

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


title: CRISPR RNA-seq from K562 (ENCLB056VMX)

description:
https://www.encodeproject.org/experiments/ENCSR765HSN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CIZ1. (CIZ1-BGKcLV19)
experiment encode accession: ENCSR765HSN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB056VMX
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/fae50ee4-b8d2-4c06-af36-9bda32c0fad9/@@download/attachment/L-CIZ1-BGKcLV19-10.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CIZ1. (CIZ1-BGKcLV19-9)

value: adult

value: ENCBS358YTN at ENCODE; https://www.encodeproject.org/ENCBS358YTN/


title: eCLIP from K562 (ENCLB991KCZ)

description:
https://www.encodeproject.org/experiments/ENCSR181NRW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against ZC3H8
experiment encode accession: ENCSR181NRW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR716DGM
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB991KCZ
fragmentation methods: see document
size range: 175-300


title: Bru-seq from Panc1 (ENCLB678RPG)

description:
https://www.encodeproject.org/experiments/ENCSR639ZOU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR639ZOU
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB678RPG
size range: 400-500

source_name: Homo sapiens Panc1 cell line

value: male

value: pancreatic carcinoma

value: 56 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS129GRW at ENCODE; https://www.encodeproject.org/ENCBS129GRW/

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


title: eCLIP from K562 (ENCLB850GSZ)

description:
https://www.encodeproject.org/experiments/ENCSR181NRW/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against ZC3H8
experiment encode accession: ENCSR181NRW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR716DGM
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB850GSZ
fragmentation methods: see document
size range: 175-300

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/


title: BruChase-seq from K562 (ENCLB428UYA)

description:
https://www.encodeproject.org/experiments/ENCSR762OPQ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR762OPQ
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR729WFH
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB428UYA
size range: 400-500

value: ENCBS220SUH at ENCODE; https://www.encodeproject.org/ENCBS220SUH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB649YCQ)

description:
https://www.encodeproject.org/experiments/ENCSR637CZY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNF187. (RNF187-BGHcLV20)
experiment encode accession: ENCSR637CZY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB649YCQ
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 RNF187

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/49727fd8-f202-4832-8222-662a58fc3cdc/@@download/attachment/L-RNF187-BGHcLV20-28.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNF187. (RNF187-BGHcLV20-28)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS493TQZ at ENCODE; https://www.encodeproject.org/ENCBS493TQZ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB504VAA)

description:
https://www.encodeproject.org/experiments/ENCSR636PNL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against THOC1. (THOC1-BGHcLV16)
experiment encode accession: ENCSR636PNL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB504VAA
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 THOC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/32bbebb3-bd0a-4fdf-b6ab-62901ad7efb5/@@download/attachment/L-THOC1-BGHcLV16-57.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against THOC1. (THOC1-BGHcLV16-57)

value: male

value: ATCC

value: ENCBS666ZDP at ENCODE; https://www.encodeproject.org/ENCBS666ZDP/


title: eCLIP from K562 (ENCLB686CTS)

description:
https://www.encodeproject.org/experiments/ENCSR249ROI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPC
experiment encode accession: ENCSR249ROI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR960OKV
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB686CTS
fragmentation methods: see document
size range: 175-300

value: HNRNPC

value: adult

value: female

value: 53 year

value: Gene Yeo, UCSD

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


title: CRISPR RNA-seq from HepG2 (ENCLB225FWQ)

description:
https://www.encodeproject.org/experiments/ENCSR636DVA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZFP106. (ZFP106-BGHcLV10)
experiment encode accession: ENCSR636DVA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB225FWQ
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 ZNF106

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/73fa8afa-cda7-42ae-b004-7ef900405e0c/@@download/attachment/L-ZFP106-BGHcLV10-56.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZFP106. (ZFP106-BGHcLV10-56)

value: ENCBS542LFH at ENCODE; https://www.encodeproject.org/ENCBS542LFH/


title: CRISPR RNA-seq from HepG2 (ENCLB384ZKO)

description:
https://www.encodeproject.org/experiments/ENCSR636PNL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against THOC1. (THOC1-BGHcLV16)
experiment encode accession: ENCSR636PNL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR964HKT
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB384ZKO
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/7c02cf08-6f95-44de-a723-95ddbae7a21d/@@download/attachment/L-THOC1-BGHcLV16-58.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against THOC1. (THOC1-BGHcLV16-58)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS730TVL at ENCODE; https://www.encodeproject.org/ENCBS730TVL/


title: CRISPR RNA-seq from HepG2 (ENCLB775QSN)

description:
https://www.encodeproject.org/experiments/ENCSR636DVA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZFP106. (ZFP106-BGHcLV10)
experiment encode accession: ENCSR636DVA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR775ZWO
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB775QSN
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/a2c47d33-d428-4576-8bd6-eae86c084bc4/@@download/attachment/L-ZFP106-BGHcLV10-55.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ZFP106. (ZFP106-BGHcLV10-55)

value: male

value: Brenton Graveley, UConn

value: ENCBS611UOT at ENCODE; https://www.encodeproject.org/ENCBS611UOT/

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


title: eCLIP from K562 (ENCLB480ZLG)

description:
https://www.encodeproject.org/experiments/ENCSR177QQY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against AKAP1
experiment encode accession: ENCSR177QQY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR544UON
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB480ZLG
fragmentation methods: see document
size range: 175-300

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/

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


title: Control eCLIP from K562 (ENCLB928RJM)

description:
https://www.encodeproject.org/experiments/ENCSR251FMT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against GRWD1
experiment encode accession: ENCSR251FMT
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB928RJM
fragmentation methods: see document
size range: 175-300

value: cell line

value: 53 year

value: Gene Yeo, UCSD

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

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB162TCY)

description:
https://www.encodeproject.org/experiments/ENCSR637CZY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNF187. (RNF187-BGHcLV20)
experiment encode accession: ENCSR637CZY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB162TCY
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/93c89f7f-b87e-40fc-b26e-0e8ed27ae2be/@@download/attachment/L-RNF187-BGHcLV20-27.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RNF187. (RNF187-BGHcLV20-27)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS320HYP at ENCODE; https://www.encodeproject.org/ENCBS320HYP/


title: BruChase-seq from K562 (ENCLB397CNU)

description:
https://www.encodeproject.org/experiments/ENCSR633UIR/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR633UIR
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR729WFH
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB397CNU
size range: 400-500

source_name: Homo sapiens K562 cell line, subjected to a 2 hour pulse-chase

value: adult

value: Mats Ljungman, UMichigan

value: ENCBS361CYI at ENCODE; https://www.encodeproject.org/ENCBS361CYI/


title: CRISPR RNA-seq from K562 (ENCLB253RUF)

description:
https://www.encodeproject.org/experiments/ENCSR635RAB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against FBL. (FBL-BGKcLV17)
experiment encode accession: ENCSR635RAB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB253RUF
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 FBL

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e0204e35-6a72-46a5-a7ed-1efcb023671e/@@download/attachment/L-FBL-BGKcLV17-19.pdf

value: FBL

value: RNA-seq on K562 cells treated with a CRISPR gRNA against FBL. (FBL-BGKcLV17-19)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS642JRY at ENCODE; https://www.encodeproject.org/ENCBS642JRY/


title: eCLIP from K562 (ENCLB793PPC)

description:
https://www.encodeproject.org/experiments/ENCSR249ROI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPC
experiment encode accession: ENCSR249ROI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR960OKV
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB793PPC
fragmentation methods: see document
size range: 175-300

value: HNRNPC

value: cell line

value: 53 year

value: Gene Yeo, UCSD

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

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

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


title: BruChase-seq from K562 (ENCLB758TWT)

description:
https://www.encodeproject.org/experiments/ENCSR633UIR/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR633UIR
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR729WFH
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB758TWT
size range: 400-500

value: ATCC

value: ENCBS413NWV at ENCODE; https://www.encodeproject.org/ENCBS413NWV/


title: CRISPR RNA-seq from K562 (ENCLB284HVU)

description:
https://www.encodeproject.org/experiments/ENCSR635RAB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against FBL. (FBL-BGKcLV17)
experiment encode accession: ENCSR635RAB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB284HVU
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/05230b71-257f-449c-b566-edf858b2b4fc/@@download/attachment/L-FBL-BGKcLV17-20.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against FBL. (FBL-BGKcLV17-20)

value: adult

value: ENCBS923WNC at ENCODE; https://www.encodeproject.org/ENCBS923WNC/


title: CRISPR RNA-seq from K562 (ENCLB746OKV)

description:
https://www.encodeproject.org/experiments/ENCSR644LYC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CNOT10. (CNOT10-BGKcLV21)
experiment encode accession: ENCSR644LYC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR854OFV
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB746OKV
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/d30498e9-b02e-49ff-a26f-5d28eaa0dcad/@@download/attachment/L-CNOT10-BGKcLV21-8.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CNOT10. (CNOT10-BGKcLV21-8)

value: ENCBS018RUQ at ENCODE; https://www.encodeproject.org/ENCBS018RUQ/


title: CRISPR RNA-seq from K562 (ENCLB937LJY)

description:
https://www.encodeproject.org/experiments/ENCSR628AFF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2AK2. (EIF2AK2-BGKcLV13)
experiment encode accession: ENCSR628AFF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB937LJY
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 EIF2AK2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/48970f4d-27b1-4de7-825a-096279e23b48/@@download/attachment/L-EIF2AK2-BGKcLV13-53.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2AK2. (EIF2AK2-BGKcLV13-53)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS183UMR at ENCODE; https://www.encodeproject.org/ENCBS183UMR/


title: CRISPR RNA-seq from HepG2 (ENCLB215INH)

description:
https://www.encodeproject.org/experiments/ENCSR750CPT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NT. (NT-BGHcLV14)
experiment encode accession: ENCSR750CPT
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB215INH
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/08d49d57-9e2a-4643-b809-00dcefe8b827/@@download/attachment/L-NT-BGHcLV14-2.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV14-2)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS363HBB at ENCODE; https://www.encodeproject.org/ENCBS363HBB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB222LZJ)

description:
https://www.encodeproject.org/experiments/ENCSR751TUX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF1. (CSTF1-BGHcLV22)
experiment encode accession: ENCSR751TUX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB222LZJ
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 CSTF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/adf7955c-b8e2-413f-a762-88d423404784/@@download/attachment/L-CSTF1-BGHcLV22-15.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF1. (CSTF1-BGHcLV22-15)

value: ATCC

value: ENCBS138BKF at ENCODE; https://www.encodeproject.org/ENCBS138BKF/


title: eCLIP from K562 (ENCLB042TSY)

description:
https://www.encodeproject.org/experiments/ENCSR069EVH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against FUS
experiment encode accession: ENCSR069EVH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR389ISM
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB042TSY
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: FUS

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/

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

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


title: eCLIP from K562 (ENCLB256JEX)

description:
https://www.encodeproject.org/experiments/ENCSR177QQY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against AKAP1
experiment encode accession: ENCSR177QQY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR544UON
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB256JEX
fragmentation methods: see document
size range: 175-300

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

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

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


title: eCLIP from K562 (ENCLB861HQF)

description:
https://www.encodeproject.org/experiments/ENCSR069EVH/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against FUS
experiment encode accession: ENCSR069EVH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR389ISM
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB861HQF
fragmentation methods: see document
size range: 175-300


title: CRISPR RNA-seq from K562 (ENCLB673GSO)

description:
https://www.encodeproject.org/experiments/ENCSR628AFF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2AK2. (EIF2AK2-BGKcLV13)
experiment encode accession: ENCSR628AFF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB673GSO
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/00971ea5-a692-450e-9bc7-bce93a74af19/@@download/attachment/L-EIF2AK2-BGKcLV13-54.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF2AK2. (EIF2AK2-BGKcLV13-54)

value: Brenton Graveley, UConn

value: ENCBS325OFK at ENCODE; https://www.encodeproject.org/ENCBS325OFK/


title: Mint-ChIP-seq from immature natural killer cell (ENCLB438RJO)

description:
https://www.encodeproject.org/experiments/ENCSR746AIX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR746AIX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR169WAD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB438RJO
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

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: Control eCLIP from K562 (ENCLB466AKC)

description:
https://www.encodeproject.org/experiments/ENCSR155XOS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SDAD1
experiment encode accession: ENCSR155XOS
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB466AKC
fragmentation methods: see document
size range: 175-300

value: cell line

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB064JKG)

description:
https://www.encodeproject.org/experiments/ENCSR751TUX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF1. (CSTF1-BGHcLV22)
experiment encode accession: ENCSR751TUX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR704VPL
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB064JKG
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/dd87edb1-6eb2-4ddd-bdca-8f04e013fc62/@@download/attachment/L-CSTF1-BGHcLV22-16.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF1. (CSTF1-BGHcLV22-16)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS830QUG at ENCODE; https://www.encodeproject.org/ENCBS830QUG/

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


title: eCLIP from K562 (ENCLB262WRA)

description:
https://www.encodeproject.org/experiments/ENCSR154CSN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against DDX52
experiment encode accession: ENCSR154CSN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR864XNB
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB262WRA
fragmentation methods: see document
size range: 175-300

value: chronic myelogenous leukemia (CML)

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB250CUE)

description:
https://www.encodeproject.org/experiments/ENCSR624YDI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MAK16. (MAK16-BGHcLV12)
experiment encode accession: ENCSR624YDI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB250CUE
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 MAK16

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/001ea761-4f27-4c46-8fc7-68030629e950/@@download/attachment/L-MAK16-BGHcLV12-44.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MAK16. (MAK16-BGHcLV12-44)

value: ENCBS833CNT at ENCODE; https://www.encodeproject.org/ENCBS833CNT/


title: Bru-seq from PC-3 (ENCLB360VVU)

description:
https://www.encodeproject.org/experiments/ENCSR622SUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR622SUM
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB360VVU
size range: 400-500

source_name: Homo sapiens PC-3 cell line

value: grade IV, adenocarcinoma

value: adult

value: 62 year

value: Mats Ljungman, UMichigan

value: ENCBS731DBV at ENCODE; https://www.encodeproject.org/ENCBS731DBV/

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


title: Control eCLIP from K562 (ENCLB278BFU)

description:
https://www.encodeproject.org/experiments/ENCSR241ALC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against UTP3
experiment encode accession: ENCSR241ALC
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB278BFU
fragmentation methods: see document
size range: 175-300

value: female

value: 53 year

value: Gene Yeo, UCSD

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

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

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


title: Bru-seq from PC-3 (ENCLB950ZKG)

description:
https://www.encodeproject.org/experiments/ENCSR622SUM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR622SUM
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB950ZKG
size range: 400-500

value: male

value: ATCC

value: ENCBS394STR at ENCODE; https://www.encodeproject.org/ENCBS394STR/


title: CRISPR RNA-seq from HepG2 (ENCLB688NYY)

description:
https://www.encodeproject.org/experiments/ENCSR624YDI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MAK16. (MAK16-BGHcLV12)
experiment encode accession: ENCSR624YDI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB688NYY
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/6113d496-6401-46e3-b19c-feb1b1b2d2ab/@@download/attachment/L-MAK16-BGHcLV12-43.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against MAK16. (MAK16-BGHcLV12-43)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS656WSC at ENCODE; https://www.encodeproject.org/ENCBS656WSC/

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


title: eCLIP from K562 (ENCLB927ETV)

description:
https://www.encodeproject.org/experiments/ENCSR154CSN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against DDX52
experiment encode accession: ENCSR154CSN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR864XNB
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB927ETV
fragmentation methods: see document
size range: 175-300

value: adult

value: female

value: chronic myelogenous leukemia (CML)

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

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


title: CRISPR RNA-seq from K562 (ENCLB193GHJ)

description:
https://www.encodeproject.org/experiments/ENCSR619GGE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against FUBP3. (FUBP3-BGKcLV08)
experiment encode accession: ENCSR619GGE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB193GHJ
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 FUBP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2b4bd45b-efcc-48b2-8975-567b2ef7d298/@@download/attachment/L-FUBP3-BGKcLV08-36.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against FUBP3. (FUBP3-BGKcLV08-36)

value: 53 year

value: ENCBS251CZU at ENCODE; https://www.encodeproject.org/ENCBS251CZU/

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


title: TF ChIP-seq from K562 (ENCLB179RYZ)

description:
https://www.encodeproject.org/experiments/ENCSR059BWP/
***************
biological replicate number: 2
technical replicate number: 1
description: PHTF2 ChIP-seq on human K562
experiment encode accession: ENCSR059BWP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR926XXG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB179RYZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting PHTF2

value: cell line

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS392EEG at ENCODE; https://www.encodeproject.org/ENCBS392EEG/


title: microRNA-seq from endodermal cell (ENCLB905OJC)

description:
https://www.encodeproject.org/experiments/ENCSR228XLW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation H9 derived endodermal cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR228XLW
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB905OJC
size range: <30

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

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/

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


title: CRISPR RNA-seq from K562 (ENCLB923MKA)

description:
https://www.encodeproject.org/experiments/ENCSR619GGE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against FUBP3. (FUBP3-BGKcLV08)
experiment encode accession: ENCSR619GGE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR015KGT
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB923MKA
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/64fc87ea-76ba-44aa-a2b5-d2bd0b6067d7/@@download/attachment/L-FUBP3-BGKcLV08-35.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against FUBP3. (FUBP3-BGKcLV08-35)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS767AXM at ENCODE; https://www.encodeproject.org/ENCBS767AXM/


title: CRISPR RNA-seq from HepG2 (ENCLB883WXM)

description:
https://www.encodeproject.org/experiments/ENCSR749QMU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIZ1. (CIZ1-BGHcLV20)
experiment encode accession: ENCSR749QMU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB883WXM
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 CIZ1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c66cdbf9-784f-4606-96a8-386ee3d3c615/@@download/attachment/L-CIZ1-BGHcLV20-4.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIZ1. (CIZ1-BGHcLV20-4)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS100NPF at ENCODE; https://www.encodeproject.org/ENCBS100NPF/

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


title: TF ChIP-seq from K562 (ENCLB094OZQ)

description:
https://www.encodeproject.org/experiments/ENCSR059BWP/
***************
biological replicate number: 1
technical replicate number: 1
description: PHTF2 ChIP-seq on human K562
experiment encode accession: ENCSR059BWP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR926XXG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB094OZQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: Michael Snyder, Stanford

value: ENCBS001UHD at ENCODE; https://www.encodeproject.org/ENCBS001UHD/

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


title: Bru-seq from K562 (ENCLB956IRQ)

description:
https://www.encodeproject.org/experiments/ENCSR729WFH/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR729WFH
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB956IRQ
size range: 400-500

source_name: Homo sapiens K562 cell line

value: female

value: chronic myelogenous leukemia (CML)

value: Mats Ljungman, UMichigan

value: ENCBS834KNC at ENCODE; https://www.encodeproject.org/ENCBS834KNC/


title: CRISPR RNA-seq from HepG2 (ENCLB838DBQ)

description:
https://www.encodeproject.org/experiments/ENCSR749QMU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIZ1. (CIZ1-BGHcLV20)
experiment encode accession: ENCSR749QMU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR306EWE
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB838DBQ
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/3e5d56dd-f6a2-4322-bd55-6fe3a1496b62/@@download/attachment/L-CIZ1-BGHcLV20-3.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CIZ1. (CIZ1-BGHcLV20-3)

value: Brenton Graveley, UConn

value: ENCBS005VFH at ENCODE; https://www.encodeproject.org/ENCBS005VFH/


title: CRISPR RNA-seq from HepG2 (ENCLB070DWE)

description:
https://www.encodeproject.org/experiments/ENCSR750CPT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NT. (NT-BGHcLV14)
experiment encode accession: ENCSR750CPT
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB070DWE
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/979eb4c6-cef4-4ebd-835d-523d9a130b88/@@download/attachment/L-NT-BGHcLV14-1.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non-target. (NT-BGHcLV14-1)

value: male

value: ENCBS223NPX at ENCODE; https://www.encodeproject.org/ENCBS223NPX/


title: Bru-seq from Panc1 (ENCLB633ZNJ)

description:
https://www.encodeproject.org/experiments/ENCSR639ZOU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639ZOU
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB633ZNJ
size range: 400-500

source_name: Homo sapiens Panc1 cell line

value: pancreatic carcinoma

value: adult

value: 56 year

value: ATCC

value: ENCBS617XWM at ENCODE; https://www.encodeproject.org/ENCBS617XWM/

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


title: eCLIP from HepG2 (ENCLB394JGD)

description:
https://www.encodeproject.org/experiments/ENCSR050BDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against SDAD1
experiment encode accession: ENCSR050BDZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR130ZDS
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB394JGD
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: child

value: 15 year

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/

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

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


title: CRISPR RNA-seq from K562 (ENCLB153UOO)

description:
https://www.encodeproject.org/experiments/ENCSR728VRY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PTGES3. (PTGES3-BGKcLV15)
experiment encode accession: ENCSR728VRY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB153UOO
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 PTGES3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ebec0536-98cd-49c8-a35b-52b88c70786b/@@download/attachment/L-PTGES3-BGKcLV15-49.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PTGES3. (PTGES3-BGKcLV15-49)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS289LMY at ENCODE; https://www.encodeproject.org/ENCBS289LMY/

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


title: Bru-seq from K562 (ENCLB496NGY)

description:
https://www.encodeproject.org/experiments/ENCSR729WFH/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR729WFH
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB496NGY
size range: 400-500

value: adult

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS364CWW at ENCODE; https://www.encodeproject.org/ENCBS364CWW/


title: CRISPR RNA-seq from K562 (ENCLB722VXR)

description:
https://www.encodeproject.org/experiments/ENCSR728VRY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PTGES3. (PTGES3-BGKcLV15)
experiment encode accession: ENCSR728VRY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB722VXR
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/c962df30-8575-43f9-9c91-dfa192633e72/@@download/attachment/L-PTGES3-BGKcLV15-50.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PTGES3. (PTGES3-BGKcLV15-50)

value: ENCBS350NXO at ENCODE; https://www.encodeproject.org/ENCBS350NXO/


title: microRNA-seq from ovary (ENCLB457ZTS)

description:
https://www.encodeproject.org/experiments/ENCSR224HDT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 ovary microRNA-seq from Mortazavi
experiment encode accession: ENCSR224HDT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB457ZTS
size range: <30

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

value: ovary

value: tissue

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS756ETL at ENCODE; https://www.encodeproject.org/ENCBS756ETL/

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


title: Bru-seq from MCF-7 (ENCLB981IRM)

description:
https://www.encodeproject.org/experiments/ENCSR727IHV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR727IHV
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB981IRM
size range: 400-500

source_name: Homo sapiens MCF-7 cell line

value: cell line

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS691MXU at ENCODE; https://www.encodeproject.org/ENCBS691MXU/

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


title: eCLIP from HepG2 (ENCLB908LJX)

description:
https://www.encodeproject.org/experiments/ENCSR050BDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against SDAD1
experiment encode accession: ENCSR050BDZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR130ZDS
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB908LJX
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS768GCL at ENCODE; https://www.encodeproject.org/ENCBS768GCL/

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


title: Control eCLIP from HepG2 (ENCLB831YTM)

description:
https://www.encodeproject.org/experiments/ENCSR145ZKN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against SSB
experiment encode accession: ENCSR145ZKN
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB831YTM
fragmentation methods: see document
size range: 175-300

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/

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


title: CRISPR RNA-seq from HepG2 (ENCLB136VWB)

description:
https://www.encodeproject.org/experiments/ENCSR723QPD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RAE1. (RAE1-BGHcLV18)
experiment encode accession: ENCSR723QPD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB136VWB
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 RAE1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ed4f2c46-8116-4db5-94b6-1fa555cc67e0/@@download/attachment/L-RAE1-BGHcLV18-39.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RAE1. (RAE1-BGHcLV18-39)

value: Brenton Graveley, UConn

value: ENCBS963YGC at ENCODE; https://www.encodeproject.org/ENCBS963YGC/


title: CRISPR RNA-seq from K562 (ENCLB949WYZ)

description:
https://www.encodeproject.org/experiments/ENCSR613LSQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CTCF. (CTCF-BGKcLV17)
experiment encode accession: ENCSR613LSQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB949WYZ
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 CTCF

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/547f37eb-e3fc-4a9c-abe4-a5c4d1f83a58/@@download/attachment/L-CTCF-BGKcLV17-6.pdf

value: CTCF

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CTCF. (CTCF-BGKcLV17-6)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS742ULM at ENCODE; https://www.encodeproject.org/ENCBS742ULM/

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


title: CRISPR RNA-seq from K562 (ENCLB937TBF)

description:
https://www.encodeproject.org/experiments/ENCSR610HJO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GSK3A. (GSK3A-BGKcLV13)
experiment encode accession: ENCSR610HJO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB937TBF
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 GSK3A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/66a1dd21-b456-4190-b460-0669d20d408f/@@download/attachment/L-GSK3A-BGKcLV13-41.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GSK3A. (GSK3A-BGKcLV13-41)

value: ATCC

value: ENCBS963NIC at ENCODE; https://www.encodeproject.org/ENCBS963NIC/


title: CRISPR RNA-seq from K562 (ENCLB846JOE)

description:
https://www.encodeproject.org/experiments/ENCSR613LSQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CTCF. (CTCF-BGKcLV17)
experiment encode accession: ENCSR613LSQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR516TLX
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB846JOE
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/8d4a650c-4707-476d-b0b5-e570d24006c6/@@download/attachment/L-CTCF-BGKcLV17-5.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CTCF. (CTCF-BGKcLV17-5)

value: ENCBS988SWN at ENCODE; https://www.encodeproject.org/ENCBS988SWN/


title: CRISPR RNA-seq from K562 (ENCLB980TTK)

description:
https://www.encodeproject.org/experiments/ENCSR610HJO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against GSK3A. (GSK3A-BGKcLV13)
experiment encode accession: ENCSR610HJO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR712CQC
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB980TTK
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/3f944ce3-3682-4138-b383-39544c664289/@@download/attachment/L-GSK3A-BGKcLV13-42.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against GSK3A. (GSK3A-BGKcLV13-42)

value: ENCBS701XJS at ENCODE; https://www.encodeproject.org/ENCBS701XJS/


title: CRISPR RNA-seq from K562 (ENCLB977HHR)

description:
https://www.encodeproject.org/experiments/ENCSR607SRH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against METTL1. (METTL1-BGKcLV23)
experiment encode accession: ENCSR607SRH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB977HHR
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 METTL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2feb9eb0-015f-4234-b3f0-7b425d2acdfe/@@download/attachment/L-METTL1-BGKcLV23-52.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against METTL1. (METTL1-BGKcLV23-52)

value: Brenton Graveley, UConn

value: ENCBS677VYZ at ENCODE; https://www.encodeproject.org/ENCBS677VYZ/


title: eCLIP from K562 (ENCLB404DZZ)

description:
https://www.encodeproject.org/experiments/ENCSR046JHH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against CPEB4
experiment encode accession: ENCSR046JHH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR533BNK
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB404DZZ
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: cell line

value: Gene Yeo, UCSD

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/

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


title: CRISPR RNA-seq from K562 (ENCLB429FQQ)

description:
https://www.encodeproject.org/experiments/ENCSR607SRH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against METTL1. (METTL1-BGKcLV23)
experiment encode accession: ENCSR607SRH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB429FQQ
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/51bd174c-6d4d-47d5-9322-cb151a424187/@@download/attachment/L-METTL1-BGKcLV23-51.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against METTL1. (METTL1-BGKcLV23-51)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS724UMH at ENCODE; https://www.encodeproject.org/ENCBS724UMH/


title: eCLIP from K562 (ENCLB448MTR)

description:
https://www.encodeproject.org/experiments/ENCSR145NLR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against DDX51
experiment encode accession: ENCSR145NLR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR268SKI
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB448MTR
fragmentation methods: see document
size range: 175-300

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

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

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


title: Bru-seq from MCF-7 (ENCLB216MDS)

description:
https://www.encodeproject.org/experiments/ENCSR727IHV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR727IHV
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB216MDS
size range: 400-500

value: breast cancer (adenocarcinoma)

value: 69 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS932AOH at ENCODE; https://www.encodeproject.org/ENCBS932AOH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB687ZQU)

description:
https://www.encodeproject.org/experiments/ENCSR606QVN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against WDR43. (WDR43-BGHcLV12)
experiment encode accession: ENCSR606QVN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB687ZQU
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 WDR43

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/16280763-8414-4236-b376-0c6f38c3deb4/@@download/attachment/L-WDR43-BGHcLV12-87.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against WDR43. (WDR43-BGHcLV12-87)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS260ZXT at ENCODE; https://www.encodeproject.org/ENCBS260ZXT/

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


title: eCLIP from K562 (ENCLB790ATE)

description:
https://www.encodeproject.org/experiments/ENCSR046JHH/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against CPEB4
experiment encode accession: ENCSR046JHH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR533BNK
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB790ATE
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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

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


title: eCLIP from K562 (ENCLB040QNY)

description:
https://www.encodeproject.org/experiments/ENCSR145NLR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against DDX51
experiment encode accession: ENCSR145NLR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR268SKI
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB040QNY
fragmentation methods: see document
size range: 175-300

value: cell line

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB094QTX)

description:
https://www.encodeproject.org/experiments/ENCSR723QPD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RAE1. (RAE1-BGHcLV18)
experiment encode accession: ENCSR723QPD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR670KAS
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB094QTX
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/8bb06171-90fd-4935-a055-96b965f65b29/@@download/attachment/L-RAE1-BGHcLV18-40.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RAE1. (RAE1-BGHcLV18-40)

value: male

value: hepatocellular carcinoma

value: ATCC

value: ENCBS244PIB at ENCODE; https://www.encodeproject.org/ENCBS244PIB/


title: CRISPR RNA-seq from K562 (ENCLB034QXG)

description:
https://www.encodeproject.org/experiments/ENCSR607RGV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RYBP. (RYBP-BGKcLV19)
experiment encode accession: ENCSR607RGV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB034QXG
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 RYBP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4bb3ea54-cb2e-41f1-ae89-654a1bdce55a/@@download/attachment/L-RYBP-BGKcLV19-44.pdf

value: RYBP

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RYBP. (RYBP-BGKcLV19-44)

value: Brenton Graveley, UConn

value: ENCBS053RXY at ENCODE; https://www.encodeproject.org/ENCBS053RXY/


title: CRISPR RNA-seq from K562 (ENCLB504QTA)

description:
https://www.encodeproject.org/experiments/ENCSR717XCO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PES1. (PES1-BGKcLV11)
experiment encode accession: ENCSR717XCO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB504QTA
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 PES1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1315f117-6f26-45bb-a241-bc848c6cf0e0/@@download/attachment/L-PES1-BGKcLV11-69.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PES1. (PES1-BGKcLV11-69)

value: female

value: adult

value: 53 year

value: ENCBS943XSM at ENCODE; https://www.encodeproject.org/ENCBS943XSM/


title: CRISPR RNA-seq from K562 (ENCLB529UWT)

description:
https://www.encodeproject.org/experiments/ENCSR717XCO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PES1. (PES1-BGKcLV11)
experiment encode accession: ENCSR717XCO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR292PXV
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB529UWT
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/cb73b467-9a4f-41f0-88c3-3ad1b37bc230/@@download/attachment/L-PES1-BGKcLV11-70.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PES1. (PES1-BGKcLV11-70)

value: chronic myelogenous leukemia (CML)

value: ENCBS434FAM at ENCODE; https://www.encodeproject.org/ENCBS434FAM/

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


title: TF ChIP-seq from A549 (ENCLB982UQA)

description:
https://www.encodeproject.org/experiments/ENCSR044RZF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-NR2E3 ChIP-seq on human A549
experiment encode accession: ENCSR044RZF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR542LGX, ENCSR689IML
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB982UQA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting NR2E3

value: male

value: 58 year

value: Michael Snyder, Stanford

value: ENCBS140TIG at ENCODE; https://www.encodeproject.org/ENCBS140TIG/

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


title: CRISPR RNA-seq from HepG2 (ENCLB717VDA)

description:
https://www.encodeproject.org/experiments/ENCSR606QVN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against WDR43. (WDR43-BGHcLV12)
experiment encode accession: ENCSR606QVN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR827PII
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB717VDA
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/e32f42e1-9a8a-4d8c-9067-e947f1ab41a6/@@download/attachment/L-WDR43-BGHcLV12-88.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against WDR43. (WDR43-BGHcLV12-88)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS795OMT at ENCODE; https://www.encodeproject.org/ENCBS795OMT/

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


title: CRISPR RNA-seq from K562 (ENCLB723AQT)

description:
https://www.encodeproject.org/experiments/ENCSR607RGV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RYBP. (RYBP-BGKcLV19)
experiment encode accession: ENCSR607RGV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR978MMZ
encode release date: 2021-02-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB723AQT
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/358d79d8-b93d-4f35-9fe5-d646e90b3a64/@@download/attachment/L-RYBP-BGKcLV19-43.pdf

value: RYBP

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RYBP. (RYBP-BGKcLV19-43)

value: female

value: adult

value: 53 year

value: ENCBS327UNO at ENCODE; https://www.encodeproject.org/ENCBS327UNO/


title: TF ChIP-seq from A549 (ENCLB531GTQ)

description:
https://www.encodeproject.org/experiments/ENCSR044RZF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-NR2E3 ChIP-seq on human A549
experiment encode accession: ENCSR044RZF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR542LGX, ENCSR689IML
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB531GTQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: 58 year

value: Michael Snyder, Stanford

value: ENCBS205MDE at ENCODE; https://www.encodeproject.org/ENCBS205MDE/


title: CRISPR RNA-seq from K562 (ENCLB754TSN)

description:
https://www.encodeproject.org/experiments/ENCSR715XCS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DICER1. (DICER1-BGKcLV15)
experiment encode accession: ENCSR715XCS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB754TSN
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 DICER1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/83daf63c-ac13-4aeb-ae64-5b8840e360c1/@@download/attachment/L-DICER1-BGKcLV15-12.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DICER1. (DICER1-BGKcLV15-12)

value: chronic myelogenous leukemia (CML)

value: ENCBS629GVA at ENCODE; https://www.encodeproject.org/ENCBS629GVA/

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


title: CRISPR RNA-seq from K562 (ENCLB645LGN)

description:
https://www.encodeproject.org/experiments/ENCSR715XCS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DICER1. (DICER1-BGKcLV15)
experiment encode accession: ENCSR715XCS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR404OHQ
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB645LGN
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/31b7a30b-2e17-4f07-a37f-3b0431ddd7dc/@@download/attachment/L-DICER1-BGKcLV15-11.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DICER1. (DICER1-BGKcLV15-11)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS524HOB at ENCODE; https://www.encodeproject.org/ENCBS524HOB/


title: CRISPR RNA-seq from HepG2 (ENCLB696VRJ)

description:
https://www.encodeproject.org/experiments/ENCSR713OTF/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV05-E)
experiment encode accession: ENCSR713OTF
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB696VRJ
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/00b3c5dc-da35-4fda-8d01-c88de256b5da/@@download/attachment/L-NT-BGHcLV05-2E.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT_BGHcLV05-2)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS901AHP at ENCODE; https://www.encodeproject.org/ENCBS901AHP/

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


title: eCLIP from K562 (ENCLB886BYY)

description:
https://www.encodeproject.org/experiments/ENCSR040QLV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against DDX21
experiment encode accession: ENCSR040QLV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR266XXD
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB886BYY
fragmentation methods: see document
size range: 175-300

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: ENCBS658KIL at ENCODE; https://www.encodeproject.org/ENCBS658KIL/

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

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


title: Control eCLIP from HepG2 (ENCLB726UDE)

description:
https://www.encodeproject.org/experiments/ENCSR138HJN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against NIP7
experiment encode accession: ENCSR138HJN
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB726UDE
fragmentation methods: see document
size range: 175-300

value: male

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/


title: CRISPR RNA-seq from K562 (ENCLB940PEV)

description:
https://www.encodeproject.org/experiments/ENCSR715GSX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGKcLV23)
experiment encode accession: ENCSR715GSX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB940PEV
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 ELAC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c8befcf0-61d8-4385-b897-570eeb00274c/@@download/attachment/L-ELAC2-BGKcLV23-41.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGKcLV23-41)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS669IHM at ENCODE; https://www.encodeproject.org/ENCBS669IHM/

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


title: CRISPR RNA-seq from K562 (ENCLB515PZV)

description:
https://www.encodeproject.org/experiments/ENCSR715GSX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGKcLV23)
experiment encode accession: ENCSR715GSX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR877JEM
encode release date: 2021-05-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB515PZV
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/ffe920a0-def4-481a-a238-37fdb19ff5ba/@@download/attachment/L-ELAC2-BGKcLV23-42.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGKcLV23-42)

value: ENCBS813KFP at ENCODE; https://www.encodeproject.org/ENCBS813KFP/


title: CRISPR RNA-seq from K562 (ENCLB232BMI)

description:
https://www.encodeproject.org/experiments/ENCSR712CQC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against NT. (NT-BGKcLV13)
experiment encode accession: ENCSR712CQC
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-10-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB232BMI
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/66552f36-ecd7-4c30-8820-e8892dc99c56/@@download/attachment/L-NT-BGKcLV13-1.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non-target. (NT-BGKcLV13-1)

value: adult

value: 53 year

value: ENCBS323JXU at ENCODE; https://www.encodeproject.org/ENCBS323JXU/


title: Control eCLIP from adrenal gland (ENCLB229VKG)

description:
https://www.encodeproject.org/experiments/ENCSR217SVF/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on adrenal gland against DGCR8
experiment encode accession: ENCSR217SVF
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB229VKG
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens adrenal gland tissue male adult (37 years)

value: adrenal gland

value: tissue

value: Adrenal Gland GTEx tissue aliquot

value: 37 year

value: Gene Yeo, UCSD

value: ENCBS168TDE at ENCODE; https://www.encodeproject.org/ENCBS168TDE/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Control eCLIP from adrenal gland (ENCLB692GSL)

description:
https://www.encodeproject.org/experiments/ENCSR217SVF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on adrenal gland against DGCR8
experiment encode accession: ENCSR217SVF
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-08-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB692GSL
fragmentation methods: see document
size range: 175-300

value: male


title: BruChase-seq from Panc1 (ENCLB782UVV)

description:
https://www.encodeproject.org/experiments/ENCSR603TYF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR603TYF
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR639ZOU
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB782UVV
size range: 400-500

source_name: Homo sapiens Panc1 cell line, subjected to a 2 hour pulse-chase

value: pancreatic carcinoma

value: 56 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS090SXQ at ENCODE; https://www.encodeproject.org/ENCBS090SXQ/

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


title: eCLIP from K562 (ENCLB362JGP)

description:
https://www.encodeproject.org/experiments/ENCSR040QLV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against DDX21
experiment encode accession: ENCSR040QLV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR266XXD
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB362JGP
fragmentation methods: see document
size range: 175-300

value: cell line

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS126AJR at ENCODE; https://www.encodeproject.org/ENCBS126AJR/

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

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

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