title: shRNA RNA-seq from K562 (ENCLB062MKT)

description:
https://www.encodeproject.org/experiments/ENCSR619PCR/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV36-C)
experiment encode accession: ENCSR619PCR
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB062MKT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/53639cd1-7f82-4a87-b7d9-b5bde3517bf7/@@download/attachment/L-NT-BGKLV36-2C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV36-2)

value: chronic myelogenous leukemia (CML)

value: ENCBS131LFM at ENCODE; https://www.encodeproject.org/ENCBS131LFM/


title: polyA plus RNA-seq from A549 (ENCLB696PBN)

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/ENCSR742VGF/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.
experiment encode accession: ENCSR742VGF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB696PBN
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 10 minutes

extract_protocol:
treatment protocol: https://www.encodeproject.org/documents/c5b10eee-de7f-4845-a387-e73980ef5a19/@@download/attachment/RNA_DEX_treatment.pdf
general protocol: https://www.encodeproject.org/documents/5533fb32-41f1-4c7a-b62d-0095a33cab20/@@download/attachment/01_RNA_HARVEST_and_ISOLATION_Reddy_GGR.pdf
extraction protocol: https://www.encodeproject.org/documents/53726435-7acc-4248-a5df-3eef6ea3b422/@@download/attachment/02_Rev%20D%20Quick%20Reference%20Card%2C%20PrepX%20PolyA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/5f9d4f74-4e39-4818-9ee9-d8e9b8004ceb/@@download/attachment/03_RevC%20Quick%20Reference%20Card%2C%20PrepX%20mRNA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/c72e898e-82c7-478d-b043-8945133a7724/@@download/attachment/04_Rev%20C%20Quick%20Reference%20Card%2C%20PrepX%20PCR%20Cleanup%2048%20Protocol.pdf
general protocol: https://www.encodeproject.org/documents/7a683e77-85ac-45f9-b1fa-b6ceb50ca1bc/@@download/attachment/05_POST_RNA_LIB_PREP_Reddy_GGR.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 58 year

tag: lab

value: Tim Reddy, Duke

tag: source

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:minute;

tag: link

value: ENCBS472MKE at ENCODE; https://www.encodeproject.org/ENCBS472MKE/

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


title: polyA plus RNA-seq from A549 (ENCLB491VHY)

description:
https://www.encodeproject.org/experiments/ENCSR742VGF/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.
experiment encode accession: ENCSR742VGF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB491VHY
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS778YOH at ENCODE; https://www.encodeproject.org/ENCBS778YOH/


title: shRNA RNA-seq from K562 (ENCLB130WZH)

description:
https://www.encodeproject.org/experiments/ENCSR629XTS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against XPO1. (XPO1-BGKLV38-C)
experiment encode accession: ENCSR629XTS
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB130WZH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting XPO1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2ac78300-1d59-487f-a133-898ff642c076/@@download/attachment/L-XPO1-BGKLV38-120C.pdf

tag: antibody

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against XPO1. (XPO1-BGKLV38-120C)

value: female

tag: health state

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS885KEV at ENCODE; https://www.encodeproject.org/ENCBS885KEV/

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


title: polyA plus RNA-seq from A549 (ENCLB925EXE)

description:
https://www.encodeproject.org/experiments/ENCSR742VGF/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.
experiment encode accession: ENCSR742VGF
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB925EXE
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS895TOZ at ENCODE; https://www.encodeproject.org/ENCBS895TOZ/


title: shRNA RNA-seq from K562 (ENCLB294JIK)

description:
https://www.encodeproject.org/experiments/ENCSR619PCR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV36-C)
experiment encode accession: ENCSR619PCR
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB294JIK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting Non-specific target control

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/902e0536-955f-40fc-b4c6-b8f634065938/@@download/attachment/L-NT-BGKLV36-1C.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV36-1)

value: chronic myelogenous leukemia (CML)

value: ENCBS405CUM at ENCODE; https://www.encodeproject.org/ENCBS405CUM/


title: shRNA RNA-seq from HepG2 (ENCLB669VDG)

description:
https://www.encodeproject.org/experiments/ENCSR736TAW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP1. (FUBP1-BGHLV37-C)
experiment encode accession: ENCSR736TAW
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB669VDG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting FUBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d3ceb457-e7a1-486d-bf08-97f8108c02fd/@@download/attachment/L-FUBP1-BGHLV37-32C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP1. (FUBP1-BGHLV37-32C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS825KVU at ENCODE; https://www.encodeproject.org/ENCBS825KVU/

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


title: shRNA RNA-seq from HepG2 (ENCLB948ZMV)

description:
https://www.encodeproject.org/experiments/ENCSR696JWA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8-BGHLV37-B)
experiment encode accession: ENCSR696JWA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR584UYK
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB948ZMV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting ZC3H8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/60688ccd-203a-4a98-b7a2-09948723903f/@@download/attachment/L-ZC3H8-BGHLV37-116B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8-BGHLV37-116B)

value: ATCC

value: ENCBS112RBO at ENCODE; https://www.encodeproject.org/ENCBS112RBO/


title: CRISPR RNA-seq from K562 (ENCLB715ELA)

description:
https://www.encodeproject.org/experiments/ENCSR642GBC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS3. (RPS3-BGKcLV04-B)
experiment encode accession: ENCSR642GBC
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR772DUM
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB715ELA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting RPS3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/57ed2092-aa19-4317-9eda-f76833cdf2db/@@download/attachment/L-RPS3-BGKcLV04-26B.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS3. (RPS3-BGKcLV04-26B)

value: female

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS515MKD at ENCODE; https://www.encodeproject.org/ENCBS515MKD/


title: CRISPR RNA-seq from K562 (ENCLB107QIU)

description:
https://www.encodeproject.org/experiments/ENCSR637EFF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CEBPZ. (CEBPZ_BGKcLV02)
experiment encode accession: ENCSR637EFF
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB107QIU
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/663dc27f-4293-4b23-9cfd-42d4f649626b/@@download/attachment/L-CEBPZ_BGKcLV02-15.pdf

value: CEBPZ

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CEBPZ. (CEBPZ_BGKcLV02-15)

value: chronic myelogenous leukemia (CML)

value: ENCBS426MFA at ENCODE; https://www.encodeproject.org/ENCBS426MFA/

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


title: shRNA RNA-seq from K562 (ENCLB055IDC)

description:
https://www.encodeproject.org/experiments/ENCSR629XTS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against XPO1. (XPO1-BGKLV38-C)
experiment encode accession: ENCSR629XTS
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB055IDC
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/77cd5bf8-ba79-42eb-996d-154150e36c36/@@download/attachment/L-XPO1-BGKLV38-119C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against XPO1. (XPO1-BGKLV38-119C)

value: ENCBS186DPZ at ENCODE; https://www.encodeproject.org/ENCBS186DPZ/


title: CRISPR RNA-seq from K562 (ENCLB592HKX)

description:
https://www.encodeproject.org/experiments/ENCSR637EFF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CEBPZ. (CEBPZ_BGKcLV02)
experiment encode accession: ENCSR637EFF
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB592HKX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/be3bd1c3-a9dd-44cd-a28f-241fe67b8701/@@download/attachment/L-CEBPZ_BGKcLV02-16.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CEBPZ. (CEBPZ_BGKcLV02-16)

value: ENCBS802AYH at ENCODE; https://www.encodeproject.org/ENCBS802AYH/


title: shRNA RNA-seq from HepG2 (ENCLB114XTP)

description:
https://www.encodeproject.org/experiments/ENCSR736TAW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP1. (FUBP1-BGHLV37-C)
experiment encode accession: ENCSR736TAW
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB114XTP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2847ba9d-8c3f-48d4-a1fe-7d0f038fd13a/@@download/attachment/L-FUBP1-BGHLV37-31C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP1. (FUBP1-BGHLV37-31C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS212XWQ at ENCODE; https://www.encodeproject.org/ENCBS212XWQ/

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


title: shRNA RNA-seq from K562 (ENCLB403KZO)

description:
https://www.encodeproject.org/experiments/ENCSR624OUI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AQR. (AQR_BGKLV38)
experiment encode accession: ENCSR624OUI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR718EWL
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB403KZO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting AQR

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ffe57f42-ea22-40ca-aaf6-3fbf2cfe9a76/@@download/attachment/L-AQR_BGKLV38-19.pdf

value: AQR

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against AQR. (AQR_BGKLV38-19)

value: female

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS037TDO at ENCODE; https://www.encodeproject.org/ENCBS037TDO/


title: CRISPR RNA-seq from HepG2 (ENCLB961UWW)

description:
https://www.encodeproject.org/experiments/ENCSR718RBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX42. (DDX42-BGHcLV05-C)
experiment encode accession: ENCSR718RBZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR834IFU
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB961UWW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting DDX42

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8eded8b9-0705-4989-b869-012818c1d60c/@@download/attachment/L-DDX42-BGHcLV05-11C.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX42. (DDX42-BGHcLV05-11C)

value: ENCBS199IOE at ENCODE; https://www.encodeproject.org/ENCBS199IOE/


title: CRISPR RNA-seq from HepG2 (ENCLB676AXT)

description:
https://www.encodeproject.org/experiments/ENCSR718RBZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX42. (DDX42-BGHcLV05-C)
experiment encode accession: ENCSR718RBZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR834IFU
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB676AXT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d38fedbd-7642-4252-8738-e333ee38b994/@@download/attachment/L-DDX42-BGHcLV05-12C.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX42. (DDX42-BGHcLV05-12C)

value: male

value: ENCBS073ZDK at ENCODE; https://www.encodeproject.org/ENCBS073ZDK/


title: shRNA RNA-seq from K562 (ENCLB213DDB)

description:
https://www.encodeproject.org/experiments/ENCSR624OUI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AQR. (AQR_BGKLV38)
experiment encode accession: ENCSR624OUI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR718EWL
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB213DDB
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d746b0a6-3ae9-489c-8b76-a13776d5732e/@@download/attachment/L-AQR_BGKLV38-20.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against AQR. (AQR_BGKLV38-20)

value: chronic myelogenous leukemia (CML)

value: ENCBS968PSV at ENCODE; https://www.encodeproject.org/ENCBS968PSV/

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


title: shRNA RNA-seq from K562 (ENCLB466UFH)

description:
https://www.encodeproject.org/experiments/ENCSR608IXR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FUBP1. (FUBP1-BGKLV38-C)
experiment encode accession: ENCSR608IXR
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB466UFH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting FUBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/89480cce-8a78-42ea-80d8-58be3f6fc3d2/@@download/attachment/L-FUBP1-BGKLV38-38C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FUBP1. (FUBP1-BGKLV38-38C)

value: ATCC

value: ENCBS407FFA at ENCODE; https://www.encodeproject.org/ENCBS407FFA/


title: shRNA RNA-seq from K562 (ENCLB059BQI)

description:
https://www.encodeproject.org/experiments/ENCSR608IXR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FUBP1. (FUBP1-BGKLV38-C)
experiment encode accession: ENCSR608IXR
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB059BQI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3aed1b05-3ff1-4e07-8044-5b0c70493c4f/@@download/attachment/L-FUBP1-BGKLV38-37C.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against FUBP1. (FUBP1-BGKLV38-37C)

value: female

value: ENCBS386NLD at ENCODE; https://www.encodeproject.org/ENCBS386NLD/


title: CRISPR RNA-seq from K562 (ENCLB412YOA)

description:
https://www.encodeproject.org/experiments/ENCSR721CNY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DGCR8 on day 30. (DGCR8-D30_BGKcLV02)
experiment encode accession: ENCSR721CNY
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR395HQT
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB412YOA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting DGCR8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b4d553c5-79e8-4d8d-8aa8-419bbce42325/@@download/attachment/L-DGCR8-D30_BGKcLV02-19.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against DGCR8 on day 30. (DGCR8-D30_BGKcLV02-19)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS998ZJJ at ENCODE; https://www.encodeproject.org/ENCBS998ZJJ/


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB378ZET)

description:
https://www.encodeproject.org/experiments/ENCSR398QLU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR398QLU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR150CMT
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB378ZET
fragmentation methods: none

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell

value: CD8-positive, alpha-beta memory T cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS144FNF at ENCODE; https://www.encodeproject.org/ENCBS144FNF/

value: Derived from ENCODE donor ENCDO258PRN; https://www.encodeproject.org/ENCDO258PRN/


title: shRNA RNA-seq from K562 (ENCLB133QPP)

description:
https://www.encodeproject.org/experiments/ENCSR718EWL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV38)
experiment encode accession: ENCSR718EWL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB133QPP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7114de81-d641-45d2-b389-3c45e9bc9922/@@download/attachment/L-NT_BGKLV38-1.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV38-1)

value: female

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS479HRC at ENCODE; https://www.encodeproject.org/ENCBS479HRC/

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


title: CRISPR RNA-seq from K562 (ENCLB194GBS)

description:
https://www.encodeproject.org/experiments/ENCSR721CNY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DGCR8 on day 30. (DGCR8-D30_BGKcLV02)
experiment encode accession: ENCSR721CNY
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR395HQT
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB194GBS
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c78fa782-1764-4a8b-a3e1-337c82a75f8b/@@download/attachment/L-DGCR8-D30_BGKcLV02-20.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against DGCR8 on day 30. (DGCR8-D30_BGKcLV02-20)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS091YRZ at ENCODE; https://www.encodeproject.org/ENCBS091YRZ/


title: CRISPR RNA-seq from K562 (ENCLB124DTE)

description:
https://www.encodeproject.org/experiments/ENCSR680OJB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SYNCRIP. (SYNCRIP-BGKcLV06)
experiment encode accession: ENCSR680OJB
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB124DTE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/de49d0db-613b-4154-bba6-5272bf96598a/@@download/attachment/L-SYNCRIP-BGKcLV06-37.pdf

value: SYNCRIP

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SYNCRIP. (SYNCRIP-BGKcLV06-37)

value: ENCBS713NAX at ENCODE; https://www.encodeproject.org/ENCBS713NAX/


title: CRISPR RNA-seq from K562 (ENCLB769OJJ)

description:
https://www.encodeproject.org/experiments/ENCSR619GAS/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 41. (NT-D41_BGKcLV02)
experiment encode accession: ENCSR619GAS
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB769OJJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B 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/83bbf93e-97ef-4c81-86be-8b4a4684b939/@@download/attachment/L-NT-D41_BGKcLV02-2.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against non -target on day 41. (NT-D41_BGKcLV02-2)

value: ENCBS345PNA at ENCODE; https://www.encodeproject.org/ENCBS345PNA/


title: shRNA RNA-seq from K562 (ENCLB178COK)

description:
https://www.encodeproject.org/experiments/ENCSR718EWL/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV38)
experiment encode accession: ENCSR718EWL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB178COK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cb72cdbb-8a6b-4566-abb9-91c7f9ec4892/@@download/attachment/L-NT_BGKLV38-2.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV38-2)

value: ENCBS865TCO at ENCODE; https://www.encodeproject.org/ENCBS865TCO/


title: CRISPR RNA-seq from HepG2 (ENCLB293XAV)

description:
https://www.encodeproject.org/experiments/ENCSR606PVX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM5. (RBM5_BGHcLV05)
experiment encode accession: ENCSR606PVX
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR481WJH
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB293XAV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting RBM5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/074fb3ab-2383-4f28-ae60-c25376714dda/@@download/attachment/L-RBM5_BGHcLV05-24.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM5. (RBM5_BGHcLV05-24)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS630WES at ENCODE; https://www.encodeproject.org/ENCBS630WES/

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


title: CRISPR RNA-seq from HepG2 (ENCLB036OZM)

description:
https://www.encodeproject.org/experiments/ENCSR606PVX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM5. (RBM5_BGHcLV05)
experiment encode accession: ENCSR606PVX
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR481WJH
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB036OZM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5e34473b-8a11-4769-b3e4-3dc54a5bc2cc/@@download/attachment/L-RBM5_BGHcLV05-23.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM5. (RBM5_BGHcLV05-23)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS826PQG at ENCODE; https://www.encodeproject.org/ENCBS826PQG/


title: CRISPR RNA-seq from K562 (ENCLB036CEZ)

description:
https://www.encodeproject.org/experiments/ENCSR395HQT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 30. (NT-D30_BGKcLV02)
experiment encode accession: ENCSR395HQT
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB036CEZ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/06c44b44-0dd0-4bf4-a08b-063b24a43e34/@@download/attachment/L-NT-D30_BGKcLV02-1.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against non -target on day 30. (NT-D30_BGKcLV02-1)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS864MCX at ENCODE; https://www.encodeproject.org/ENCBS864MCX/

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


title: CRISPR RNA-seq from K562 (ENCLB294UXD)

description:
https://www.encodeproject.org/experiments/ENCSR619GAS/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 41. (NT-D41_BGKcLV02)
experiment encode accession: ENCSR619GAS
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB294UXD
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/21acb58b-c362-4ec4-b7b3-190710685920/@@download/attachment/L-NT-D41_BGKcLV02-1.pdf

value: cell line

value: RNA-seq on k562 cells treated with an CRISPR gRNA against non -target on day 41. (NT-D41_BGKcLV02-1)

value: ENCBS411BWT at ENCODE; https://www.encodeproject.org/ENCBS411BWT/


title: CRISPR RNA-seq from K562 (ENCLB118LLJ)

description:
https://www.encodeproject.org/experiments/ENCSR599PZD/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 22. (NT-D22_BGKcLV02)
experiment encode accession: ENCSR599PZD
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB118LLJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b7e96a71-ea46-4edd-bf1b-ecd20b3605bc/@@download/attachment/L-NT-D22_BGKcLV02-2.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against non -target on day 22. (NT-D22_BGKcLV02-2)

value: ENCBS489PTQ at ENCODE; https://www.encodeproject.org/ENCBS489PTQ/


title: CRISPR RNA-seq from HepG2 (ENCLB185RVL)

description:
https://www.encodeproject.org/experiments/ENCSR599NNK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGHcLV03)
experiment encode accession: ENCSR599NNK
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB185RVL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a15a6c93-5223-489a-a6b7-95ff0b5f6636/@@download/attachment/L-HNRNPF_BGHcLV03-7.pdf

value: HNRNPF

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGHcLV03-7)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS346EFV at ENCODE; https://www.encodeproject.org/ENCBS346EFV/

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


title: total RNA-seq from placenta (ENCLB396RKH)

description:
https://www.encodeproject.org/experiments/ENCSR484WZL/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11006
experiment encode accession: ENCSR484WZL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB396RKH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens embryo placenta tissue

value: placenta

value: tissue

value: not collected

value: embryonic

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS839YIR at ENCODE; https://www.encodeproject.org/ENCBS839YIR/

value: Derived from ENCODE donor ENCDO131RJA; https://www.encodeproject.org/ENCDO131RJA/


title: polyA plus RNA-seq from A549 (ENCLB030TKL)

description:
https://www.encodeproject.org/experiments/ENCSR482TZY/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.
experiment encode accession: ENCSR482TZY
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB030TKL
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 5 minutes

extract_protocol:
treatment protocol: https://www.encodeproject.org/documents/c5b10eee-de7f-4845-a387-e73980ef5a19/@@download/attachment/RNA_DEX_treatment.pdf
general protocol: https://www.encodeproject.org/documents/5533fb32-41f1-4c7a-b62d-0095a33cab20/@@download/attachment/01_RNA_HARVEST_and_ISOLATION_Reddy_GGR.pdf
extraction protocol: https://www.encodeproject.org/documents/53726435-7acc-4248-a5df-3eef6ea3b422/@@download/attachment/02_Rev%20D%20Quick%20Reference%20Card%2C%20PrepX%20PolyA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/5f9d4f74-4e39-4818-9ee9-d8e9b8004ceb/@@download/attachment/03_RevC%20Quick%20Reference%20Card%2C%20PrepX%20mRNA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/c72e898e-82c7-478d-b043-8945133a7724/@@download/attachment/04_Rev%20C%20Quick%20Reference%20Card%2C%20PrepX%20PCR%20Cleanup%2048%20Protocol.pdf
general protocol: https://www.encodeproject.org/documents/7a683e77-85ac-45f9-b1fa-b6ceb50ca1bc/@@download/attachment/05_POST_RNA_LIB_PREP_Reddy_GGR.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

value: cell line

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:minute;

value: ENCBS336AKR at ENCODE; https://www.encodeproject.org/ENCBS336AKR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB268IKW)

description:
https://www.encodeproject.org/experiments/ENCSR715QWM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SDAD1. (SDAD1-BGHcLV07)
experiment encode accession: ENCSR715QWM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR521WAI
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB268IKW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting SDAD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2896be81-788e-449d-bd23-fc3c95141bc6/@@download/attachment/L-SDAD1-BGHcLV07-31.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SDAD1. (SDAD1-BGHcLV07-31)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS268BDM at ENCODE; https://www.encodeproject.org/ENCBS268BDM/

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


title: CRISPR RNA-seq from HepG2 (ENCLB696RSM)

description:
https://www.encodeproject.org/experiments/ENCSR599NNK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGHcLV03)
experiment encode accession: ENCSR599NNK
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB696RSM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3930267e-fe9f-42a1-9f55-711a7cae072f/@@download/attachment/L-HNRNPF_BGHcLV03-8.pdf

value: HNRNPF

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGHcLV03-8)

value: ENCBS135KID at ENCODE; https://www.encodeproject.org/ENCBS135KID/


title: CRISPR RNA-seq from K562 (ENCLB428YIP)

description:
https://www.encodeproject.org/experiments/ENCSR580TGX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against POLR2G. (POLR2G-BGKcLV06)
experiment encode accession: ENCSR580TGX
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB428YIP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting POLR2G

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e15b1dcb-4675-42ce-9912-e5dbb52ffefa/@@download/attachment/L-POLR2G-BGKcLV06-26.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against POLR2G. (POLR2G-BGKcLV06-26)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS767NRE at ENCODE; https://www.encodeproject.org/ENCBS767NRE/

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


title: CRISPR RNA-seq from K562 (ENCLB287TCX)

description:
https://www.encodeproject.org/experiments/ENCSR384LKC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGKcLV02)
experiment encode accession: ENCSR384LKC
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB287TCX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting DDX21

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0a702ce0-a305-485f-a6bf-4ca68c6a4c2d/@@download/attachment/L-DDX21_BGKcLV02-11.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGKcLV02-11)

value: ATCC

value: ENCBS549CBF at ENCODE; https://www.encodeproject.org/ENCBS549CBF/


title: CRISPR RNA-seq from K562 (ENCLB910IJD)

description:
https://www.encodeproject.org/experiments/ENCSR395HQT/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 30. (NT-D30_BGKcLV02)
experiment encode accession: ENCSR395HQT
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB910IJD
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cecc9487-e288-4559-99ae-48fc40589a53/@@download/attachment/L-NT-D30_BGKcLV02-2.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against non -target on day 30. (NT-D30_BGKcLV02-2)

value: Brenton Graveley, UConn

value: ENCBS016SET at ENCODE; https://www.encodeproject.org/ENCBS016SET/


title: CRISPR RNA-seq from K562 (ENCLB196BVI)

description:
https://www.encodeproject.org/experiments/ENCSR599PZD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq on day 22. (NT-D22_BGKcLV02)
experiment encode accession: ENCSR599PZD
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB196BVI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c86f4177-d618-4dcb-af62-f1a28fec357d/@@download/attachment/L-NT-D22_BGKcLV02-1.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against non -target on day 22. (NT-D22_BGKcLV02-1)

value: ENCBS344ZTN at ENCODE; https://www.encodeproject.org/ENCBS344ZTN/


title: CRISPR RNA-seq from K562 (ENCLB338WPN)

description:
https://www.encodeproject.org/experiments/ENCSR384LKC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGKcLV02)
experiment encode accession: ENCSR384LKC
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB338WPN
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b5c9e590-000b-4d95-9851-e6a40e965fbc/@@download/attachment/L-DDX21_BGKcLV02-12.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGKcLV02-12)

value: ENCBS177LGN at ENCODE; https://www.encodeproject.org/ENCBS177LGN/


title: shRNA RNA-seq from HepG2 (ENCLB246EQH)

description:
https://www.encodeproject.org/experiments/ENCSR584UYK/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV37-B)
experiment encode accession: ENCSR584UYK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB246EQH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens HepG2 cell line expressing RNAi

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/35f6150c-70ac-4796-bc3e-c28f16959d66/@@download/attachment/L-NT-BGHLV37-1B.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV37-1)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS496TVI at ENCODE; https://www.encodeproject.org/ENCBS496TVI/

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


title: shRNA RNA-seq from K562 (ENCLB359IBQ)

description:
https://www.encodeproject.org/experiments/ENCSR395FYF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AUH. (AUH_BGKLV38)
experiment encode accession: ENCSR395FYF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR718EWL
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB359IBQ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting AUH

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/eeb9e1a0-c964-4c97-b83e-1be0752cd1ed/@@download/attachment/L-AUH_BGKLV38-28.pdf

value: AUH

value: RNA-seq on K562 cells treated with an shRNA knockdown against AUH. (AUH_BGKLV38-28)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS806OOZ at ENCODE; https://www.encodeproject.org/ENCBS806OOZ/

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


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB936LYF)

description:
https://www.encodeproject.org/experiments/ENCSR570IJX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR570IJX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR205FKJ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB936LYF
fragmentation methods: none

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS006RRW at ENCODE; https://www.encodeproject.org/ENCBS006RRW/

value: Derived from ENCODE donor ENCDO258PRN; https://www.encodeproject.org/ENCDO258PRN/


title: total RNA-seq from placenta (ENCLB758ADE)

description:
https://www.encodeproject.org/experiments/ENCSR479MNN/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11014
experiment encode accession: ENCSR479MNN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB758ADE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male embryo placenta tissue

value: placenta

value: tissue

value: male

value: embryonic

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS769HMP at ENCODE; https://www.encodeproject.org/ENCBS769HMP/

value: Derived from ENCODE donor ENCDO868MLX; https://www.encodeproject.org/ENCDO868MLX/


title: CRISPR RNA-seq from K562 (ENCLB288KTM)

description:
https://www.encodeproject.org/experiments/ENCSR380RRP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGKcLV02)
experiment encode accession: ENCSR380RRP
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB288KTM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/18f95893-7a07-449d-829d-beb29374bda6/@@download/attachment/L-HNRNPF_BGKcLV02-9.pdf

value: HNRNPF

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGKcLV02-9)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS903OGK at ENCODE; https://www.encodeproject.org/ENCBS903OGK/

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


title: shRNA RNA-seq from HepG2 (ENCLB589ZPI)

description:
https://www.encodeproject.org/experiments/ENCSR584UYK/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV37-B)
experiment encode accession: ENCSR584UYK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB589ZPI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c8d3e17e-6036-4967-8712-8b2336e41253/@@download/attachment/L-NT-BGHLV37-2B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV37-2)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS135CDE at ENCODE; https://www.encodeproject.org/ENCBS135CDE/

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


title: CRISPR RNA-seq from HepG2 (ENCLB954QRQ)

description:
https://www.encodeproject.org/experiments/ENCSR715QWM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SDAD1. (SDAD1-BGHcLV07)
experiment encode accession: ENCSR715QWM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR521WAI
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB954QRQ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c44b173c-2419-4510-b13a-b4a385506738/@@download/attachment/L-SDAD1-BGHcLV07-32.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SDAD1. (SDAD1-BGHcLV07-32)

value: ENCBS045JKA at ENCODE; https://www.encodeproject.org/ENCBS045JKA/


title: CRISPR RNA-seq from K562 (ENCLB291MHU)

description:
https://www.encodeproject.org/experiments/ENCSR380RRP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGKcLV02)
experiment encode accession: ENCSR380RRP
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB291MHU
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f589bd65-19d3-4658-b0c3-32ece9e132cd/@@download/attachment/L-HNRNPF_BGKcLV02-10.pdf

value: HNRNPF

value: RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPF. (HNRNPF_BGKcLV02-10)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS643CHR at ENCODE; https://www.encodeproject.org/ENCBS643CHR/


title: polyA plus RNA-seq from A549 (ENCLB229NCK)

description:
https://www.encodeproject.org/experiments/ENCSR482TZY/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.
experiment encode accession: ENCSR482TZY
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB229NCK
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:minute;

value: ENCBS353WHL at ENCODE; https://www.encodeproject.org/ENCBS353WHL/

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


title: shRNA RNA-seq from K562 (ENCLB306BLZ)

description:
https://www.encodeproject.org/experiments/ENCSR473KFO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UTP3. (UTP3-BGKLV38-D)
experiment encode accession: ENCSR473KFO
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR655JYC
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB306BLZ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting UTP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/738c25c0-f537-4dac-af66-29dab0901ad5/@@download/attachment/L-UTP3-BGKLV38-104D.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UTP3. (UTP3-BGKLV38-104B)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS532TPY at ENCODE; https://www.encodeproject.org/ENCBS532TPY/

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


title: shRNA RNA-seq from K562 (ENCLB637DRP)

description:
https://www.encodeproject.org/experiments/ENCSR395FYF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AUH. (AUH_BGKLV38)
experiment encode accession: ENCSR395FYF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR718EWL
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB637DRP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/281ed78d-0206-458e-a35c-9a07a0e6fd1d/@@download/attachment/L-AUH_BGKLV38-27.pdf

value: AUH

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against AUH. (AUH_BGKLV38-27)

value: ENCBS168RTN at ENCODE; https://www.encodeproject.org/ENCBS168RTN/


title: CRISPR RNA-seq from HepG2 (ENCLB029ZCI)

description:
https://www.encodeproject.org/experiments/ENCSR481WJH/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHcLV05)
experiment encode accession: ENCSR481WJH
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB029ZCI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B 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/ec049220-4f1a-4480-834a-6291ab09769b/@@download/attachment/L-NT_BGHcLV05-2.pdf

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

value: male

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: CRISPR RNA-seq from K562 (ENCLB620XUO)

description:
https://www.encodeproject.org/experiments/ENCSR580TGX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against POLR2G. (POLR2G-BGKcLV06)
experiment encode accession: ENCSR580TGX
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB620XUO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b9e64a38-6b83-4ab1-93b2-a2301c64467d/@@download/attachment/L-POLR2G-BGKcLV06-25.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against POLR2G. (POLR2G-BGKcLV06-25)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ATCC

value: ENCBS518EXZ at ENCODE; https://www.encodeproject.org/ENCBS518EXZ/


title: total RNA-seq from placenta (ENCLB952BRY)

description:
https://www.encodeproject.org/experiments/ENCSR464VSR/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11011
experiment encode accession: ENCSR464VSR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB952BRY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: placenta

value: tissue

value: embryonic

value: not collected

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS366DUY at ENCODE; https://www.encodeproject.org/ENCBS366DUY/

value: Derived from ENCODE donor ENCDO225QCT; https://www.encodeproject.org/ENCDO225QCT/


title: shRNA RNA-seq from HepG2 (ENCLB068KGS)

description:
https://www.encodeproject.org/experiments/ENCSR466NRW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGHLV37-D)
experiment encode accession: ENCSR466NRW
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR093ERJ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB068KGS
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting PRPF4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e094256c-433b-4a37-b575-d73b231597e1/@@download/attachment/L-PRPF4-BGHLV37-41D.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGHLV37-41B)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS528KLM at ENCODE; https://www.encodeproject.org/ENCBS528KLM/


title: shRNA RNA-seq from HepG2 (ENCLB294KUJ)

description:
https://www.encodeproject.org/experiments/ENCSR466NRW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGHLV37-D)
experiment encode accession: ENCSR466NRW
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR093ERJ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB294KUJ
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/1aef3468-cf2b-4d11-a277-54c5845f163f/@@download/attachment/L-PRPF4-BGHLV37-42D.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGHLV37-42B)

value: ATCC

value: ENCBS334WBP at ENCODE; https://www.encodeproject.org/ENCBS334WBP/

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


title: CRISPR RNA-seq from HepG2 (ENCLB887ALV)

description:
https://www.encodeproject.org/experiments/ENCSR481WJH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHcLV05)
experiment encode accession: ENCSR481WJH
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB887ALV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/90950db3-b0ee-4e2b-8a6a-c3bcf8b82ca5/@@download/attachment/L-NT_BGHcLV05-1.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT_BGHcLV05-1)

value: ENCBS332SEB at ENCODE; https://www.encodeproject.org/ENCBS332SEB/


title: shRNA RNA-seq from K562 (ENCLB331KSX)

description:
https://www.encodeproject.org/experiments/ENCSR363QIA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGKLV38-C)
experiment encode accession: ENCSR363QIA
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB331KSX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting PRPF4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/52a89487-4bb6-496b-800f-56926a89dbb2/@@download/attachment/L-PRPF4-BGKLV38-63C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGKLV38-63C)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS780VTX at ENCODE; https://www.encodeproject.org/ENCBS780VTX/

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


title: shRNA RNA-seq from HepG2 (ENCLB108JIX)

description:
https://www.encodeproject.org/experiments/ENCSR438UOT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against XPO1. (XPO1-BGHLV37-C)
experiment encode accession: ENCSR438UOT
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB108JIX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting XPO1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3b6cc04d-5f07-4bd1-be56-5dfc030b1eeb/@@download/attachment/L-XPO1-BGHLV37-94C.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XPO1. (XPO1-BGHLV37-94C)

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS043LKR at ENCODE; https://www.encodeproject.org/ENCBS043LKR/


title: shRNA RNA-seq from HepG2 (ENCLB537CRC)

description:
https://www.encodeproject.org/experiments/ENCSR438UOT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against XPO1. (XPO1-BGHLV37-C)
experiment encode accession: ENCSR438UOT
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB537CRC
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bf210871-bccc-4351-9160-411413d0e0bb/@@download/attachment/L-XPO1-BGHLV37-93C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XPO1. (XPO1-BGHLV37-93C)

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS426QLM at ENCODE; https://www.encodeproject.org/ENCBS426QLM/


title: CRISPR RNA-seq from HepG2 (ENCLB590GER)

description:
https://www.encodeproject.org/experiments/ENCSR471INA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGHcLV05-B)
experiment encode accession: ENCSR471INA
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR853AOV
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB590GER
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting SRSF4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dfdb95c5-8e33-4b26-9d92-3f29d12416d0/@@download/attachment/L-SRSF4-BGHcLV05-34B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGHcLV05-34B)

value: ENCBS775SLR at ENCODE; https://www.encodeproject.org/ENCBS775SLR/

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


title: shRNA RNA-seq from K562 (ENCLB092PIG)

description:
https://www.encodeproject.org/experiments/ENCSR473KFO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UTP3. (UTP3-BGKLV38-D)
experiment encode accession: ENCSR473KFO
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR655JYC
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB092PIG
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/0a86c3da-0b4b-4b42-8ceb-32a7641dfcd6/@@download/attachment/L-UTP3-BGKLV38-103D.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UTP3. (UTP3-BGKLV38-103B)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS742THM at ENCODE; https://www.encodeproject.org/ENCBS742THM/


title: shRNA RNA-seq from K562 (ENCLB717XEG)

description:
https://www.encodeproject.org/experiments/ENCSR363QIA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGKLV38-C)
experiment encode accession: ENCSR363QIA
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB717XEG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ba6c8abb-1355-4391-942c-e308929acf21/@@download/attachment/L-PRPF4-BGKLV38-64C.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGKLV38-64C)

value: ENCBS437ESZ at ENCODE; https://www.encodeproject.org/ENCBS437ESZ/

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


title: total RNA-seq from placenta (ENCLB603CZI)

description:
https://www.encodeproject.org/experiments/ENCSR420YFF/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11007
experiment encode accession: ENCSR420YFF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB603CZI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female embryo placenta tissue

value: placenta

value: tissue

value: embryonic

value: not collected

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS753NFC at ENCODE; https://www.encodeproject.org/ENCBS753NFC/

value: Derived from ENCODE donor ENCDO412HAL; https://www.encodeproject.org/ENCDO412HAL/


title: shRNA RNA-seq from HepG2 (ENCLB867RJA)

description:
https://www.encodeproject.org/experiments/ENCSR431SXF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against AQR. (AQR-BGHLV37-C)
experiment encode accession: ENCSR431SXF
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB867RJA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting AQR

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c1d54173-d486-4168-9823-5d8cab5c1c79/@@download/attachment/L-AQR-BGHLV37-11C.pdf

value: AQR

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AQR. (AQR-BGHLV37-11C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS246WPL at ENCODE; https://www.encodeproject.org/ENCBS246WPL/

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


title: CRISPR RNA-seq from K562 (ENCLB707LPP)

description:
https://www.encodeproject.org/experiments/ENCSR376GHG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against FXR2. (FXR2_BGKcLV04)
experiment encode accession: ENCSR376GHG
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR828YEB
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB707LPP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting FXR2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4c10a6e9-a9d3-4be1-83a4-50e5eb13f269/@@download/attachment/L-FXR2_BGKcLV04_13.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against FXR2. (FXR2_BGKcLV04_13)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS460PSZ at ENCODE; https://www.encodeproject.org/ENCBS460PSZ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB799FLH)

description:
https://www.encodeproject.org/experiments/ENCSR471INA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGHcLV05-B)
experiment encode accession: ENCSR471INA
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR853AOV
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB799FLH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6b3d9d59-68fb-48fd-a92f-701f5c82899f/@@download/attachment/L-SRSF4-BGHcLV05-33B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGHcLV05-33B)

value: ENCBS284JIL at ENCODE; https://www.encodeproject.org/ENCBS284JIL/


title: CRISPR RNA-seq from K562 (ENCLB507ZED)

description:
https://www.encodeproject.org/experiments/ENCSR354RSR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPH1. (HNRNPH1-BGKcLV06)
experiment encode accession: ENCSR354RSR
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB507ZED
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting HNRNPH1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f08a4a66-fd10-4847-8ade-8f61e71a0fa6/@@download/attachment/L-HNRNPH1-BGKcLV06-16.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPH1. (HNRNPH1-BGKcLV06-16)

value: ENCBS971STX at ENCODE; https://www.encodeproject.org/ENCBS971STX/


title: polyA plus RNA-seq from A549 (ENCLB879JTV)

description:
https://www.encodeproject.org/experiments/ENCSR525HSH/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.
experiment encode accession: ENCSR525HSH
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB879JTV
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 25 minutes

extract_protocol:
treatment protocol: https://www.encodeproject.org/documents/c5b10eee-de7f-4845-a387-e73980ef5a19/@@download/attachment/RNA_DEX_treatment.pdf
general protocol: https://www.encodeproject.org/documents/5533fb32-41f1-4c7a-b62d-0095a33cab20/@@download/attachment/01_RNA_HARVEST_and_ISOLATION_Reddy_GGR.pdf
extraction protocol: https://www.encodeproject.org/documents/53726435-7acc-4248-a5df-3eef6ea3b422/@@download/attachment/02_Rev%20D%20Quick%20Reference%20Card%2C%20PrepX%20PolyA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/5f9d4f74-4e39-4818-9ee9-d8e9b8004ceb/@@download/attachment/03_RevC%20Quick%20Reference%20Card%2C%20PrepX%20mRNA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/c72e898e-82c7-478d-b043-8945133a7724/@@download/attachment/04_Rev%20C%20Quick%20Reference%20Card%2C%20PrepX%20PCR%20Cleanup%2048%20Protocol.pdf
general protocol: https://www.encodeproject.org/documents/7a683e77-85ac-45f9-b1fa-b6ceb50ca1bc/@@download/attachment/05_POST_RNA_LIB_PREP_Reddy_GGR.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

value: male

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:25; duration_units:minute;

value: ENCBS810LXW at ENCODE; https://www.encodeproject.org/ENCBS810LXW/

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


title: CRISPR RNA-seq from K562 (ENCLB451CNT)

description:
https://www.encodeproject.org/experiments/ENCSR543LCG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGKcLV02)
experiment encode accession: ENCSR543LCG
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB451CNT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting IGF2BP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1726aaf0-b934-4f5d-bdec-adbeff646b64/@@download/attachment/L-IGF2BP1_BGKcLV02-4.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGKcLV02-4)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS556RPW at ENCODE; https://www.encodeproject.org/ENCBS556RPW/


title: CRISPR RNA-seq from HepG2 (ENCLB126PXF)

description:
https://www.encodeproject.org/experiments/ENCSR437GYG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGGF1. (AGGF1-BGHcLV05-B)
experiment encode accession: ENCSR437GYG
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR853AOV
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB126PXF
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting AGGF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fe6bd315-04a1-4deb-955b-f02b02ace6e4/@@download/attachment/L-AGGF1-BGHcLV05-6B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGGF1. (AGGF1-BGHcLV05-6B)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS010LBN at ENCODE; https://www.encodeproject.org/ENCBS010LBN/

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


title: CRISPR RNA-seq from K562 (ENCLB835BAR)

description:
https://www.encodeproject.org/experiments/ENCSR376GHG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against FXR2. (FXR2_BGKcLV04)
experiment encode accession: ENCSR376GHG
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR828YEB
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB835BAR
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6f6b4f9f-caef-4a75-9b9d-8eebbbcd13f3/@@download/attachment/L-FXR2_BGKcLV04_14.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against FXR2. (FXR2_BGKcLV04_14)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS862RHQ at ENCODE; https://www.encodeproject.org/ENCBS862RHQ/

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


title: shRNA RNA-seq from K562 (ENCLB745IAP)

description:
https://www.encodeproject.org/experiments/ENCSR448JAM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8_BGKLV38)
experiment encode accession: ENCSR448JAM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR718EWL
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB745IAP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting ZC3H8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cfc8729f-15a8-4ee8-9602-ddf17a654c9f/@@download/attachment/L-ZC3H8_BGKLV38-146.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8_BGKLV38-146)

value: ENCBS106LEY at ENCODE; https://www.encodeproject.org/ENCBS106LEY/


title: shRNA RNA-seq from K562 (ENCLB095QNV)

description:
https://www.encodeproject.org/experiments/ENCSR555LCE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FMR1. (FMR1_BGKLV36)
experiment encode accession: ENCSR555LCE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB095QNV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting FMR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c101d935-e5e5-4b34-aad2-b5b0e232b7f3/@@download/attachment/L-FMR1_BGKLV36-21.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FMR1. (FMR1_BGKLV36-21)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS867LCJ at ENCODE; https://www.encodeproject.org/ENCBS867LCJ/


title: CRISPR RNA-seq from K562 (ENCLB559SJO)

description:
https://www.encodeproject.org/experiments/ENCSR341TTW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV06)
experiment encode accession: ENCSR341TTW
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB559SJO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 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/ed14e6eb-29f7-4882-aecd-9cce2e003683/@@download/attachment/L-NT-BGKcLV06-1.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT-BGKcLV06-1)

value: ENCBS280LUD at ENCODE; https://www.encodeproject.org/ENCBS280LUD/


title: shRNA RNA-seq from K562 (ENCLB473AIB)

description:
https://www.encodeproject.org/experiments/ENCSR555LCE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FMR1. (FMR1_BGKLV36)
experiment encode accession: ENCSR555LCE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB473AIB
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/42b7c0a1-6e19-4f3f-9e58-20fde3c9cfad/@@download/attachment/L-FMR1_BGKLV36-22.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FMR1. (FMR1_BGKLV36-22)

value: ENCBS162IHJ at ENCODE; https://www.encodeproject.org/ENCBS162IHJ/


title: CRISPR RNA-seq from K562 (ENCLB385YIF)

description:
https://www.encodeproject.org/experiments/ENCSR466TGH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DGCR8 on day 22. (DGCR8-D22_BGKcLV02)
experiment encode accession: ENCSR466TGH
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR599PZD
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB385YIF
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting DGCR8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7ffb94eb-5aa5-4bae-b8a2-4c9fc13e9470/@@download/attachment/L-DGCR8-D22_BGKcLV02-19.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against DGCR8 on day 22. (DGCR8-D22_BGKcLV02-19)

value: female

value: ENCBS626TPH at ENCODE; https://www.encodeproject.org/ENCBS626TPH/


title: CRISPR RNA-seq from K562 (ENCLB280VKK)

description:
https://www.encodeproject.org/experiments/ENCSR466TGH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DGCR8 on day 22. (DGCR8-D22_BGKcLV02)
experiment encode accession: ENCSR466TGH
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR599PZD
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB280VKK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/97c4f26d-29f2-440a-85db-a10f9ee49267/@@download/attachment/L-DGCR8-D22_BGKcLV02-20.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against DGCR8 on day 22. (DGCR8-D22_BGKcLV02-20)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS732IZQ at ENCODE; https://www.encodeproject.org/ENCBS732IZQ/


title: CRISPR RNA-seq from K562 (ENCLB459AVL)

description:
https://www.encodeproject.org/experiments/ENCSR341TTW/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV06)
experiment encode accession: ENCSR341TTW
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB459AVL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2a572436-4f3b-4403-87c1-c3bdf2bbb78c/@@download/attachment/L-NT-BGKcLV06-2.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT-BGKcLV06-2)

value: ENCBS044NCU at ENCODE; https://www.encodeproject.org/ENCBS044NCU/

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


title: polyA plus RNA-seq from A549 (ENCLB283EPI)

description:
https://www.encodeproject.org/experiments/ENCSR525HSH/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.
experiment encode accession: ENCSR525HSH
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB283EPI
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:25; duration_units:minute;

value: ENCBS245EST at ENCODE; https://www.encodeproject.org/ENCBS245EST/

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


title: shRNA RNA-seq from HepG2 (ENCLB281ZOM)

description:
https://www.encodeproject.org/experiments/ENCSR431SXF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against AQR. (AQR-BGHLV37-C)
experiment encode accession: ENCSR431SXF
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB281ZOM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/30f1102b-0f82-4b1a-b11b-c492033321c9/@@download/attachment/L-AQR-BGHLV37-12C.pdf

value: AQR

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AQR. (AQR-BGHLV37-12C)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS775JOM at ENCODE; https://www.encodeproject.org/ENCBS775JOM/

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


title: CRISPR RNA-seq from K562 (ENCLB333EFU)

description:
https://www.encodeproject.org/experiments/ENCSR354RSR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPH1. (HNRNPH1-BGKcLV06)
experiment encode accession: ENCSR354RSR
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB333EFU
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/69a88c6a-513c-4205-bd17-30fa91af5509/@@download/attachment/L-HNRNPH1-BGKcLV06-15.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against HNRNPH1. (HNRNPH1-BGKcLV06-15)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS333GIJ at ENCODE; https://www.encodeproject.org/ENCBS333GIJ/


title: polyA plus RNA-seq from A549 (ENCLB749UTI)

description:
https://www.encodeproject.org/experiments/ENCSR525HSH/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.
experiment encode accession: ENCSR525HSH
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB749UTI
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:25; duration_units:minute;

value: ENCBS126WEL at ENCODE; https://www.encodeproject.org/ENCBS126WEL/


title: CRISPR RNA-seq from K562 (ENCLB913WTK)

description:
https://www.encodeproject.org/experiments/ENCSR336TYW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SAFB. (SAFB-BGKcLV06)
experiment encode accession: ENCSR336TYW
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB913WTK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/646074ed-a08e-46d3-b22e-f9dfce32040a/@@download/attachment/L-SAFB-BGKcLV06-29.pdf

value: SAFB

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SAFB. (SAFB-BGKcLV06-29)

value: ENCBS936RRD at ENCODE; https://www.encodeproject.org/ENCBS936RRD/

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


title: CRISPR RNA-seq from K562 (ENCLB015UEH)

description:
https://www.encodeproject.org/experiments/ENCSR543LCG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGKcLV02)
experiment encode accession: ENCSR543LCG
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB015UEH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/aebae841-5607-49f3-959c-a8c985d116d5/@@download/attachment/L-IGF2BP1_BGKcLV02-3.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGKcLV02-3)

value: Brenton Graveley, UConn

value: ENCBS472YQF at ENCODE; https://www.encodeproject.org/ENCBS472YQF/