title: CRISPR RNA-seq from HepG2 (ENCLB041STX)

description:
https://www.encodeproject.org/experiments/ENCSR437GYG/
***************
biological replicate number: 1
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: ENCLB041STX
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/81f254a2-2fb6-49af-9536-9ed85a394dc3/@@download/attachment/L-AGGF1-BGHcLV05-5B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGGF1. (AGGF1-BGHcLV05-5B)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS048KGW at ENCODE; https://www.encodeproject.org/ENCBS048KGW/

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


title: shRNA RNA-seq from K562 (ENCLB377LJT)

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/ENCSR448JAM/
***************
biological replicate number: 1
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: ENCLB377LJT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line expressing RNAi targeting ZC3H8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/080ab1c2-b13c-44e0-8bb2-4fa54fc2217b/@@download/attachment/L-ZC3H8_BGKLV38-145.pdf

tag: antibody

tag: line

value: cell line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8_BGKLV38-145)

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Brenton Graveley, UConn

tag: source

value: ATCC

tag: link

value: ENCBS010AAK at ENCODE; https://www.encodeproject.org/ENCBS010AAK/

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


title: CRISPR RNA-seq from HepG2 (ENCLB007ZWT)

description:
https://www.encodeproject.org/experiments/ENCSR521WAI/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV07)
experiment encode accession: ENCSR521WAI
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB007ZWT
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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e6265f3e-0550-4e24-b9ee-58b9c5d56fc6/@@download/attachment/L-NT-BGHcLV07-1.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT-BGHcLV07-1)

value: male

value: ENCBS058XCC at ENCODE; https://www.encodeproject.org/ENCBS058XCC/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB356AQP)

description:
https://www.encodeproject.org/experiments/ENCSR297FIU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR297FIU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310WXY
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB356AQP
fragmentation methods: none

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens CD14-positive monocyte primary cell

value: CD14-positive monocyte

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: ENCBS950WTC at ENCODE; https://www.encodeproject.org/ENCBS950WTC/

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


title: CRISPR RNA-seq from K562 (ENCLB411TOM)

description:
https://www.encodeproject.org/experiments/ENCSR415DJT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PTBP1. (PTBP1_BGKcLV02)
experiment encode accession: ENCSR415DJT
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB411TOM
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 PTBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/beb299f1-9588-45fc-860b-f1008dc156ba/@@download/attachment/L-PTBP1_BGKcLV02-7.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PTBP1. (PTBP1_BGKcLV02-7)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS017GMY at ENCODE; https://www.encodeproject.org/ENCBS017GMY/


title: total RNA-seq from placenta (ENCLB542TEM)

description:
https://www.encodeproject.org/experiments/ENCSR288RRZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11005
experiment encode accession: ENCSR288RRZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB542TEM
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: ENCBS928SLW at ENCODE; https://www.encodeproject.org/ENCBS928SLW/

value: Derived from ENCODE donor ENCDO384FEJ; https://www.encodeproject.org/ENCDO384FEJ/


title: total RNA-seq from placenta (ENCLB136WOV)

description:
https://www.encodeproject.org/experiments/ENCSR308XAR/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11013
experiment encode accession: ENCSR308XAR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB136WOV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: not collected

value: ENCBS346GTO at ENCODE; https://www.encodeproject.org/ENCBS346GTO/

value: Derived from ENCODE donor ENCDO023YQQ; https://www.encodeproject.org/ENCDO023YQQ/


title: shRNA RNA-seq from HepG2 (ENCLB048MFZ)

description:
https://www.encodeproject.org/experiments/ENCSR289HOV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2-BGHLV37-C)
experiment encode accession: ENCSR289HOV
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB048MFZ
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 YTHDC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/090ef43a-abb0-47e3-9bd1-951ee542114b/@@download/attachment/L-YTHDC2-BGHLV37-106C.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2-BGHLV37-106C)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS783JOY at ENCODE; https://www.encodeproject.org/ENCBS783JOY/

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


title: shRNA RNA-seq from K562 (ENCLB995VIM)

description:
https://www.encodeproject.org/experiments/ENCSR324WIS/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV36-B)
experiment encode accession: ENCSR324WIS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB995VIM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

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/76e419d9-9901-46b5-91bc-021bd64ada15/@@download/attachment/L-NT-BGKLV36-2B.pdf

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

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB400TDP)

description:
https://www.encodeproject.org/experiments/ENCSR521WAI/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV07)
experiment encode accession: ENCSR521WAI
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB400TDP
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/6b48abbf-db62-4786-a60a-8dcb983d77e8/@@download/attachment/L-NT-BGHcLV07-2.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT-BGHcLV07-2)

value: male

value: ENCBS914MWE at ENCODE; https://www.encodeproject.org/ENCBS914MWE/


title: shRNA RNA-seq from HepG2 (ENCLB715JET)

description:
https://www.encodeproject.org/experiments/ENCSR409CSO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against AUH. (AUH_BGHLV37)
experiment encode accession: ENCSR409CSO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB715JET
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 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/8b37c0c7-a9c8-4d98-a973-a80a85b8fe94/@@download/attachment/L-AUH_BGHLV37-14.pdf

value: AUH

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AUH. (AUH_BGHLV37-14)

value: hepatocellular carcinoma

value: ENCBS940BKH at ENCODE; https://www.encodeproject.org/ENCBS940BKH/


title: shRNA RNA-seq from K562 (ENCLB059RKL)

description:
https://www.encodeproject.org/experiments/ENCSR324WIS/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV36-B)
experiment encode accession: ENCSR324WIS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB059RKL
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/7af8e759-08ad-4201-aefb-e6501e564f81/@@download/attachment/L-NT-BGKLV36-1B.pdf

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

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


title: shRNA RNA-seq from HepG2 (ENCLB502ADY)

description:
https://www.encodeproject.org/experiments/ENCSR330KHN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM22. (RBM22_BGHLV37)
experiment encode accession: ENCSR330KHN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB502ADY
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting RBM22

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a3a84b3e-0178-4d23-a9f6-7ebb8b9ea86a/@@download/attachment/L-RBM22_BGHLV37-50.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM22. (RBM22_BGHLV37-50)

value: child

value: 15 year

value: ATCC

value: ENCBS454CXD at ENCODE; https://www.encodeproject.org/ENCBS454CXD/

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


title: CRISPR RNA-seq from HepG2 (ENCLB909PXV)

description:
https://www.encodeproject.org/experiments/ENCSR094HEU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPH1. (HNRNPH1-BGHcLV07-B)
experiment encode accession: ENCSR094HEU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR194SPW
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB909PXV
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 HNRNPH1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2ef4328b-f361-455a-9b15-39de011ae176/@@download/attachment/L-HNRNPH1-BGHcLV07-15B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPH1. (HNRNPH1-BGHcLV07-15B)

value: Brenton Graveley, UConn

value: ENCBS388SIY at ENCODE; https://www.encodeproject.org/ENCBS388SIY/


title: shRNA RNA-seq from HepG2 (ENCLB849ENV)

description:
https://www.encodeproject.org/experiments/ENCSR093ERJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV37-D)
experiment encode accession: ENCSR093ERJ
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB849ENV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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/80f1527c-5716-4576-8914-e804b9e56252/@@download/attachment/L-NT-BGHLV37-1D.pdf

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

value: male

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


title: shRNA RNA-seq from HepG2 (ENCLB982BCI)

description:
https://www.encodeproject.org/experiments/ENCSR330KHN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM22. (RBM22_BGHLV37)
experiment encode accession: ENCSR330KHN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB982BCI
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/7849df76-6f82-4c0e-a2ee-3f54213a9aa4/@@download/attachment/L-RBM22_BGHLV37-49.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM22. (RBM22_BGHLV37-49)

value: ENCBS929QEJ at ENCODE; https://www.encodeproject.org/ENCBS929QEJ/


title: shRNA RNA-seq from HepG2 (ENCLB652SCH)

description:
https://www.encodeproject.org/experiments/ENCSR093FHC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against WRN. (WRN-BGHLV37-C)
experiment encode accession: ENCSR093FHC
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB652SCH
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 WRN

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b13cb09f-f7a7-4561-aeb3-b63cf463ea7d/@@download/attachment/L-WRN-BGHLV37-87C.pdf

value: WRN

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against WRN. (WRN-BGHLV37-87C)

value: hepatocellular carcinoma

value: ENCBS209JZM at ENCODE; https://www.encodeproject.org/ENCBS209JZM/


title: CRISPR RNA-seq from K562 (ENCLB174HWB)

description:
https://www.encodeproject.org/experiments/ENCSR406SEH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC5. (EXOSC5-BGKcLV06)
experiment encode accession: ENCSR406SEH
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB174HWB
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 EXOSC5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/949fba95-a0b4-4235-b06e-426addad0113/@@download/attachment/L-EXOSC5-BGKcLV06-13.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC5. (EXOSC5-BGKcLV06-13)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS739CIR at ENCODE; https://www.encodeproject.org/ENCBS739CIR/

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


title: CRISPR RNA-seq from K562 (ENCLB039SBE)

description:
https://www.encodeproject.org/experiments/ENCSR336TYW/
***************
biological replicate number: 2
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: ENCLB039SBE
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/022a17d9-1061-41c7-89c2-43328c880402/@@download/attachment/L-SAFB-BGKcLV06-30.pdf

value: SAFB

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SAFB. (SAFB-BGKcLV06-30)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS454ABX at ENCODE; https://www.encodeproject.org/ENCBS454ABX/


title: CRISPR RNA-seq from K562 (ENCLB318IEX)

description:
https://www.encodeproject.org/experiments/ENCSR406SEH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC5. (EXOSC5-BGKcLV06)
experiment encode accession: ENCSR406SEH
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB318IEX
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/f2164038-da6f-4245-b8c5-a18e6d9ef4d4/@@download/attachment/L-EXOSC5-BGKcLV06-14.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EXOSC5. (EXOSC5-BGKcLV06-14)

value: ENCBS317DNC at ENCODE; https://www.encodeproject.org/ENCBS317DNC/


title: shRNA RNA-seq from HepG2 (ENCLB861KBS)

description:
https://www.encodeproject.org/experiments/ENCSR093FHC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against WRN. (WRN-BGHLV37-C)
experiment encode accession: ENCSR093FHC
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB861KBS
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/f81e9aa1-de5c-4b86-8c05-d0e997f091f9/@@download/attachment/L-WRN-BGHLV37-88C.pdf

value: WRN

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against WRN. (WRN-BGHLV37-88C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS466LQV at ENCODE; https://www.encodeproject.org/ENCBS466LQV/

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


title: shRNA RNA-seq from HepG2 (ENCLB034XYV)

description:
https://www.encodeproject.org/experiments/ENCSR289HOV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2-BGHLV37-C)
experiment encode accession: ENCSR289HOV
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB034XYV
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/b4fb3a34-1216-486c-a114-a6da99b55e4b/@@download/attachment/L-YTHDC2-BGHLV37-105C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2-BGHLV37-105C)

value: ENCBS021BDR at ENCODE; https://www.encodeproject.org/ENCBS021BDR/


title: shRNA RNA-seq from HepG2 (ENCLB193FKR)

description:
https://www.encodeproject.org/experiments/ENCSR093ERJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV37-D)
experiment encode accession: ENCSR093ERJ
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB193FKR
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/86bf40c2-23b9-4885-8d05-ff6c212cd8ac/@@download/attachment/L-NT-BGHLV37-2D.pdf

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

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


title: CRISPR RNA-seq from K562 (ENCLB436SLR)

description:
https://www.encodeproject.org/experiments/ENCSR096WVE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF3H. (EIF3H_BGKcLV04)
experiment encode accession: ENCSR096WVE
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR226KWO
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB436SLR
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 EIF3H

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1714c889-4d3d-4d58-8aa9-47e55931f683/@@download/attachment/L-EIF3H_BGKcLV04_11B.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF3H. (EIF3H_BGKcLV04_11B)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS265REC at ENCODE; https://www.encodeproject.org/ENCBS265REC/

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


title: CRISPR RNA-seq from HepG2 (ENCLB598XVU)

description:
https://www.encodeproject.org/experiments/ENCSR284SZO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC5. (EXOSC5-BGHcLV07)
experiment encode accession: ENCSR284SZO
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR521WAI
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB598XVU
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 EXOSC5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/43d409e1-ae6d-478f-8bbe-1febc4bb589f/@@download/attachment/L-EXOSC5-BGHcLV07-13.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC5. (EXOSC5-BGHcLV07-13)

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS987FUO at ENCODE; https://www.encodeproject.org/ENCBS987FUO/


title: CRISPR RNA-seq from K562 (ENCLB951KDT)

description:
https://www.encodeproject.org/experiments/ENCSR096WVE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF3H. (EIF3H_BGKcLV04)
experiment encode accession: ENCSR096WVE
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR226KWO
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB951KDT
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/14b890d7-5b20-48a1-bdc5-0ad7d7f57e99/@@download/attachment/L-EIF3H_BGKcLV04_12B.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against EIF3H. (EIF3H_BGKcLV04_12B)

value: ENCBS691KCY at ENCODE; https://www.encodeproject.org/ENCBS691KCY/


title: shRNA RNA-seq from HepG2 (ENCLB369JDZ)

description:
https://www.encodeproject.org/experiments/ENCSR409CSO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against AUH. (AUH_BGHLV37)
experiment encode accession: ENCSR409CSO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB369JDZ
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/dba88f30-17a9-4c74-9917-e7a121e02c73/@@download/attachment/L-AUH_BGHLV37-13.pdf

value: AUH

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AUH. (AUH_BGHLV37-13)

value: 15 year

value: ENCBS814XKA at ENCODE; https://www.encodeproject.org/ENCBS814XKA/

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


title: CRISPR RNA-seq from HepG2 (ENCLB498DRD)

description:
https://www.encodeproject.org/experiments/ENCSR284SZO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC5. (EXOSC5-BGHcLV07)
experiment encode accession: ENCSR284SZO
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR521WAI
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB498DRD
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/b353db09-0b57-4a75-954a-d79f07c98e20/@@download/attachment/L-EXOSC5-BGHcLV07-14.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EXOSC5. (EXOSC5-BGHcLV07-14)

value: Brenton Graveley, UConn

value: ENCBS743WLN at ENCODE; https://www.encodeproject.org/ENCBS743WLN/


title: CRISPR RNA-seq from K562 (ENCLB127PMC)

description:
https://www.encodeproject.org/experiments/ENCSR415DJT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PTBP1. (PTBP1_BGKcLV02)
experiment encode accession: ENCSR415DJT
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB127PMC
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/ff19b87f-ac81-4a11-b0c6-1d5a477f5564/@@download/attachment/L-PTBP1_BGKcLV02-8.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PTBP1. (PTBP1_BGKcLV02-8)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS829QEL at ENCODE; https://www.encodeproject.org/ENCBS829QEL/

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


title: shRNA RNA-seq from K562 (ENCLB911HYZ)

description:
https://www.encodeproject.org/experiments/ENCSR260BQC/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV38-C)
experiment encode accession: ENCSR260BQC
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB911HYZ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 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/874068fc-3c76-4e7a-a9ed-8674c77178f6/@@download/attachment/L-NT-BGKLV38-2C.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: shRNA RNA-seq from K562 (ENCLB341NEH)

description:
https://www.encodeproject.org/experiments/ENCSR260BQC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV38-C)
experiment encode accession: ENCSR260BQC
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB341NEH
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/d23c1c43-af0e-4b8d-9c2c-29655a4ce71e/@@download/attachment/L-NT-BGKLV38-1C.pdf

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB135VBI)

description:
https://www.encodeproject.org/experiments/ENCSR094HEU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPH1. (HNRNPH1-BGHcLV07-B)
experiment encode accession: ENCSR094HEU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR194SPW
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB135VBI
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/497b3164-c54a-4929-9b13-e9b0fd05aed8/@@download/attachment/L-HNRNPH1-BGHcLV07-16B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against HNRNPH1. (HNRNPH1-BGHcLV07-16B)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS381JXX at ENCODE; https://www.encodeproject.org/ENCBS381JXX/

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


title: Mint-ChIP-seq from immature natural killer cell (ENCLB851GWK)

description:
https://www.encodeproject.org/experiments/ENCSR187MVB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR187MVB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR571SOT
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB851GWK
fragmentation methods: none

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer 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: ENCBS493KVP at ENCODE; https://www.encodeproject.org/ENCBS493KVP/

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


title: CRISPR RNA-seq from HepG2 (ENCLB517HLA)

description:
https://www.encodeproject.org/experiments/ENCSR194SPW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV07-B)
experiment encode accession: ENCSR194SPW
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB517HLA
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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7916ec9c-8a16-4de4-b0ed-02fc81653b22/@@download/attachment/L-NT-BGHcLV07-1B.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT-BGHcLV07-1)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS058XCC at ENCODE; https://www.encodeproject.org/ENCBS058XCC/


title: CRISPR RNA-seq from HepG2 (ENCLB234ZYV)

description:
https://www.encodeproject.org/experiments/ENCSR278NFF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDC40. (CDC40_BGHcLV05)
experiment encode accession: ENCSR278NFF
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR481WJH
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB234ZYV
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 CDC40

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0fa3871c-7620-4419-9900-c711b3721e4c/@@download/attachment/L-CDC40_BGHcLV05_8.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDC40. (CDC40_BGHcLV05_8)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS270SQR at ENCODE; https://www.encodeproject.org/ENCBS270SQR/


title: CRISPR RNA-seq from HepG2 (ENCLB044HQZ)

description:
https://www.encodeproject.org/experiments/ENCSR278NFF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDC40. (CDC40_BGHcLV05)
experiment encode accession: ENCSR278NFF
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR481WJH
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB044HQZ
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/4216598b-1f97-4c22-bae1-dd9273da3c6a/@@download/attachment/L-CDC40_BGHcLV05_7.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDC40. (CDC40_BGHcLV05_7)

value: ENCBS298YPF at ENCODE; https://www.encodeproject.org/ENCBS298YPF/

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


title: CRISPR RNA-seq from HepG2 (ENCLB149TWK)

description:
https://www.encodeproject.org/experiments/ENCSR194SPW/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV07-B)
experiment encode accession: ENCSR194SPW
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB149TWK
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/c5df3410-7990-49ce-9582-d54b77faf76f/@@download/attachment/L-NT-BGHcLV07-2B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT-BGHcLV07-2)

value: ENCBS914MWE at ENCODE; https://www.encodeproject.org/ENCBS914MWE/


title: shRNA RNA-seq from HepG2 (ENCLB426NWV)

description:
https://www.encodeproject.org/experiments/ENCSR184YDW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8-BGHLV37-D)
experiment encode accession: ENCSR184YDW
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR093ERJ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB426NWV
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 ZC3H8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/582bb9f4-fae9-47d0-8674-64ac367616e4/@@download/attachment/L-ZC3H8-BGHLV37-115D.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8-BGHLV37-115B)

value: ENCBS699OQY at ENCODE; https://www.encodeproject.org/ENCBS699OQY/


title: total RNA-seq from mesothelial cell of epicardium (ENCLB556TQU)

description:
https://www.encodeproject.org/experiments/ENCSR168PXI/
***************
biological replicate number: 1
technical replicate number: 1
description: WA09 derived epicardium (mesothelium)
experiment encode accession: ENCSR168PXI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB556TQU
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 (5 days) mesothelial of epicardium in vitro differentiated cells

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS813HJL at ENCODE; https://www.encodeproject.org/ENCBS813HJL/

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


title: shRNA RNA-seq from HepG2 (ENCLB551FBN)

description:
https://www.encodeproject.org/experiments/ENCSR184YDW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8-BGHLV37-D)
experiment encode accession: ENCSR184YDW
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR093ERJ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB551FBN
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/3f183c60-f694-41ab-a5cf-4f7be854adda/@@download/attachment/L-ZC3H8-BGHLV37-116D.pdf

value: cell line

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

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

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


title: shRNA RNA-seq from HepG2 (ENCLB791GRM)

description:
https://www.encodeproject.org/experiments/ENCSR278CHI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SSB. (SSB_BGHLV37)
experiment encode accession: ENCSR278CHI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB791GRM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting SSB

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/37c6ca36-f63d-46fc-81a7-2f8ce7f31722/@@download/attachment/L-SSB_BGHLV37-61.pdf

value: SSB

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SSB. (SSB_BGHLV37-61)

value: ENCBS665EFH at ENCODE; https://www.encodeproject.org/ENCBS665EFH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB697TUE)

description:
https://www.encodeproject.org/experiments/ENCSR268XHM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGHcLV03)
experiment encode accession: ENCSR268XHM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB697TUE
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 IGF2BP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b2114659-5560-441d-bafe-2afc9a169169/@@download/attachment/L-IGF2BP1_BGHcLV03-4.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGHcLV03-4)

value: ENCBS038ZQB at ENCODE; https://www.encodeproject.org/ENCBS038ZQB/


title: total RNA-seq from F121-9 (ENCLB712WFJ)

description:
https://www.encodeproject.org/experiments/ENCSR982PLD/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP_mouse ES
experiment encode accession: ENCSR982PLD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-05-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB712WFJ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

organism: Mus musculus

source_name: Mus musculus F121-9 cell line

value: Cast X 129 F121-9 hybrid mouse ES cells R2 p14

value: not collected

value: unknown

value: Barbara Wold, Caltech

value: David Gilbert

value: ENCBS951CRC at ENCODE; https://www.encodeproject.org/ENCBS951CRC/

value: Derived from ENCODE donor ENCDO817NHY; https://www.encodeproject.org/ENCDO817NHY/


title: total RNA-seq from F121-9 (ENCLB677CPD)

description:
https://www.encodeproject.org/experiments/ENCSR982PLD/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP_mouse ES
experiment encode accession: ENCSR982PLD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-05-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB677CPD
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

value: cell line

value: Cast X 129 F121-9 hybrid mouse ES cells R1 p14

value: ENCBS648HXY at ENCODE; https://www.encodeproject.org/ENCBS648HXY/


title: total RNA-seq from mesothelial cell of epicardium (ENCLB657TWS)

description:
https://www.encodeproject.org/experiments/ENCSR168PXI/
***************
biological replicate number: 2
technical replicate number: 1
description: WA09 derived epicardium (mesothelium)
experiment encode accession: ENCSR168PXI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB657TWS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS918RHD at ENCODE; https://www.encodeproject.org/ENCBS918RHD/

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


title: total RNA-seq from F121-9 (ENCLB588OJP)

description:
https://www.encodeproject.org/experiments/ENCSR982PLD/
***************
biological replicate number: 3
technical replicate number: 1
description: LRGASP_mouse ES
experiment encode accession: ENCSR982PLD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-05-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB588OJP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

value: Cast X 129 F121-9 hybrid mouse ES cells R3 p14

value: not collected

value: unknown

value: Barbara Wold, Caltech

value: David Gilbert

value: ENCBS418RDP at ENCODE; https://www.encodeproject.org/ENCBS418RDP/


title: shRNA RNA-seq from K562 (ENCLB714UVV)

description:
https://www.encodeproject.org/experiments/ENCSR193CCY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RPS11. (RPS11-BGKLV34-B)
experiment encode accession: ENCSR193CCY
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR774AEQ
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB714UVV
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 RPS11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/93375323-3abb-4f8d-b80f-c5345720cc4e/@@download/attachment/L-RPS11-BGKLV34-33B.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS11. (RPS11-BGKLV34-33B)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS518YFZ at ENCODE; https://www.encodeproject.org/ENCBS518YFZ/

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


title: total RNA-seq from mesothelial cell of epicardium (ENCLB076XKH)

description:
https://www.encodeproject.org/experiments/ENCSR168PXI/
***************
biological replicate number: 3
technical replicate number: 1
description: WA09 derived epicardium (mesothelium)
experiment encode accession: ENCSR168PXI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB076XKH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS892PZZ at ENCODE; https://www.encodeproject.org/ENCBS892PZZ/


title: shRNA RNA-seq from HepG2 (ENCLB926HOX)

description:
https://www.encodeproject.org/experiments/ENCSR278CHI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SSB. (SSB_BGHLV37)
experiment encode accession: ENCSR278CHI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB926HOX
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/41b0cd22-0c30-4203-bff0-3524dc5699f1/@@download/attachment/L-SSB_BGHLV37-62.pdf

value: SSB

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SSB. (SSB_BGHLV37-62)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS810CIP at ENCODE; https://www.encodeproject.org/ENCBS810CIP/

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


title: shRNA RNA-seq from K562 (ENCLB147HTJ)

description:
https://www.encodeproject.org/experiments/ENCSR193CCY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RPS11. (RPS11-BGKLV34-B)
experiment encode accession: ENCSR193CCY
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR774AEQ
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB147HTJ
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/50f65c2d-2d9f-4034-a77a-5356099fbcea/@@download/attachment/L-RPS11-BGKLV34-34B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS11. (RPS11-BGKLV34-34B)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS369TEV at ENCODE; https://www.encodeproject.org/ENCBS369TEV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB894GPA)

description:
https://www.encodeproject.org/experiments/ENCSR147RTA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against FXR2. (FXR2-BGHcLV05)
experiment encode accession: ENCSR147RTA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR834IFU
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB894GPA
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 FXR2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d5b312ad-5d85-49bc-9e46-00abce257d99/@@download/attachment/L-FXR2-BGHcLV05-17.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against FXR2. (FXR2-BGHcLV05-17)

value: ENCBS752KDK at ENCODE; https://www.encodeproject.org/ENCBS752KDK/


title: microRNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB503AVN)

description:
https://www.encodeproject.org/experiments/ENCSR898GHF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human CD4+ T cells (activated day 7) microRNA-seq from Mortazavi
experiment encode accession: ENCSR898GHF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-06-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB503AVN
size range: <30

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS456ENT at ENCODE; https://www.encodeproject.org/ENCBS456ENT/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: total RNA-seq from placenta (ENCLB462YMC)

description:
https://www.encodeproject.org/experiments/ENCSR244HHV/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11015
experiment encode accession: ENCSR244HHV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB462YMC
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: not collected

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS360CIV at ENCODE; https://www.encodeproject.org/ENCBS360CIV/

value: Derived from ENCODE donor ENCDO442GWY; https://www.encodeproject.org/ENCDO442GWY/


title: shRNA RNA-seq from K562 (ENCLB461NSM)

description:
https://www.encodeproject.org/experiments/ENCSR165BCF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against WRN. (WRN_BGKLV38)
experiment encode accession: ENCSR165BCF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR718EWL
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB461NSM
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 WRN

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c3cb5843-f617-4815-80ba-e2b120201c90/@@download/attachment/L-WRN_BGKLV38-109.pdf

value: WRN

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against WRN. (WRN_BGKLV38-109)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS789DIB at ENCODE; https://www.encodeproject.org/ENCBS789DIB/

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


title: CRISPR RNA-seq from K562 (ENCLB193ROP)

description:
https://www.encodeproject.org/experiments/ENCSR163JUC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV02)
experiment encode accession: ENCSR163JUC
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB193ROP
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/acf8d36d-614d-4f8f-8425-145b34b4abf3/@@download/attachment/L-NT_BGKcLV02-1.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT_BGKcLV02-1)

value: ENCBS360YEH at ENCODE; https://www.encodeproject.org/ENCBS360YEH/


title: CRISPR RNA-seq from HepG2 (ENCLB072UCR)

description:
https://www.encodeproject.org/experiments/ENCSR268XHM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGHcLV03)
experiment encode accession: ENCSR268XHM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB072UCR
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/948cf61c-fbec-411c-ba83-72bd617b54af/@@download/attachment/L-IGF2BP1_BGHcLV03-3.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against IGF2BP1. (IGF2BP1_BGHcLV03-3)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS060DQW at ENCODE; https://www.encodeproject.org/ENCBS060DQW/

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


title: shRNA RNA-seq from K562 (ENCLB901YFN)

description:
https://www.encodeproject.org/experiments/ENCSR244SIO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against KRR1. (KRR1_BGKLV36)
experiment encode accession: ENCSR244SIO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB901YFN
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 KRR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/109a2ba1-c4c9-47ca-b689-fbb8e7ba9788/@@download/attachment/L-KRR1_BGKLV36-31.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against KRR1. (KRR1_BGKLV36-31)

value: female

value: ENCBS033HEY at ENCODE; https://www.encodeproject.org/ENCBS033HEY/


title: microRNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB309FLH)

description:
https://www.encodeproject.org/experiments/ENCSR898GHF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human CD4+ T cells (activated day 7) microRNA-seq from Mortazavi
experiment encode accession: ENCSR898GHF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-06-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB309FLH
size range: <30

value: primary cell

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS081TPG at ENCODE; https://www.encodeproject.org/ENCBS081TPG/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: CRISPR RNA-seq from K562 (ENCLB100WJC)

description:
https://www.encodeproject.org/experiments/ENCSR163JUC/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV02)
experiment encode accession: ENCSR163JUC
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB100WJC
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/eafdbfc7-8b8c-4c2c-8f08-20a4312147f0/@@download/attachment/L-NT_BGKcLV02-2.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT_BGKcLV02-2)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS489AXI at ENCODE; https://www.encodeproject.org/ENCBS489AXI/

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


title: shRNA RNA-seq from K562 (ENCLB139HLH)

description:
https://www.encodeproject.org/experiments/ENCSR165BCF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against WRN. (WRN_BGKLV38)
experiment encode accession: ENCSR165BCF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR718EWL
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB139HLH
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/4fb5a300-3486-4a40-8cda-c00f99f06c50/@@download/attachment/L-WRN_BGKLV38-110.pdf

value: WRN

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against WRN. (WRN_BGKLV38-110)

value: female

value: ENCBS761QSE at ENCODE; https://www.encodeproject.org/ENCBS761QSE/


title: shRNA RNA-seq from K562 (ENCLB928PAC)

description:
https://www.encodeproject.org/experiments/ENCSR244SIO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against KRR1. (KRR1_BGKLV36)
experiment encode accession: ENCSR244SIO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB928PAC
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/d6efe2bf-90a9-438d-8cb9-ef24bbdf71d0/@@download/attachment/L-KRR1_BGKLV36-32.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against KRR1. (KRR1_BGKLV36-32)

value: adult

value: ENCBS375UEO at ENCODE; https://www.encodeproject.org/ENCBS375UEO/


title: shRNA RNA-seq from K562 (ENCLB914SSP)

description:
https://www.encodeproject.org/experiments/ENCSR233UVM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ABT1. (ABT1-BGKLV38-C)
experiment encode accession: ENCSR233UVM
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB914SSP
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 ABT1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7c0d1e04-0340-4289-a494-0a03f2c98432/@@download/attachment/L-ABT1-BGKLV38-6C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ABT1. (ABT1-BGKLV38-6C)

value: ENCBS711MRV at ENCODE; https://www.encodeproject.org/ENCBS711MRV/


title: CRISPR RNA-seq from K562 (ENCLB893YIW)

description:
https://www.encodeproject.org/experiments/ENCSR865UKM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS3. (RPS3-BGKcLV04-C)
experiment encode accession: ENCSR865UKM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR005JBU
encode release date: 2021-04-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB893YIW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/79d12c4b-121f-4d4b-8777-6bf554cfd27c/@@download/attachment/L-RPS3-BGKcLV04-26C.pdf

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

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


title: shRNA RNA-seq from K562 (ENCLB237JDR)

description:
https://www.encodeproject.org/experiments/ENCSR233UVM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ABT1. (ABT1-BGKLV38-C)
experiment encode accession: ENCSR233UVM
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB237JDR
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/aa58eebc-ad77-4cb0-85fe-2050566a6d94/@@download/attachment/L-ABT1-BGKLV38-5C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ABT1. (ABT1-BGKLV38-5C)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS886EYT at ENCODE; https://www.encodeproject.org/ENCBS886EYT/


title: CRISPR RNA-seq from K562 (ENCLB729NVA)

description:
https://www.encodeproject.org/experiments/ENCSR148UGK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DGCR8 on day 41. (DGCR8-D41_BGKcLV02)
experiment encode accession: ENCSR148UGK
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR619GAS
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB729NVA
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/7cf34029-3147-43e3-b91e-b676736958c8/@@download/attachment/L-DGCR8-D41_BGKcLV02-20.pdf

value: RNA-seq on k562 cells treated with an CRISPR gRNA against DGCR8 on day 41. (DGCR8-D41_BGKcLV02-20)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS637RKV at ENCODE; https://www.encodeproject.org/ENCBS637RKV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB284TXR)

description:
https://www.encodeproject.org/experiments/ENCSR166MWM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM14. (RBM14-BGHcLV07)
experiment encode accession: ENCSR166MWM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR521WAI
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB284TXR
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 RBM14

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d54a7ff9-05e1-49bb-8186-006d934d1f75/@@download/attachment/L-RBM14-BGHcLV07-27.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM14. (RBM14-BGHcLV07-27)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS278AVW at ENCODE; https://www.encodeproject.org/ENCBS278AVW/

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


title: CRISPR RNA-seq from HepG2 (ENCLB890LXT)

description:
https://www.encodeproject.org/experiments/ENCSR147RTA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against FXR2. (FXR2-BGHcLV05)
experiment encode accession: ENCSR147RTA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR834IFU
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB890LXT
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/ca021d6a-e0cb-4b0a-a026-2b7b0d822b59/@@download/attachment/L-FXR2-BGHcLV05-18.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against FXR2. (FXR2-BGHcLV05-18)

value: ENCBS661LCS at ENCODE; https://www.encodeproject.org/ENCBS661LCS/


title: shRNA RNA-seq from HepG2 (ENCLB458NWW)

description:
https://www.encodeproject.org/experiments/ENCSR153GKS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGHLV37)
experiment encode accession: ENCSR153GKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB458NWW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting SRFBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/36737537-ca57-4768-82ac-d33afe388fdd/@@download/attachment/L-SRFBP1_BGHLV37-58.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGHLV37-58)

value: ENCBS447BKF at ENCODE; https://www.encodeproject.org/ENCBS447BKF/


title: microRNA-seq from lower lobe of left lung (ENCLB912NUM)

description:
https://www.encodeproject.org/experiments/ENCSR877HZT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 lower lobe of left lung microRNA-seq from Mortazavi
experiment encode accession: ENCSR877HZT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB912NUM
size range: <30

source_name: Homo sapiens male adult (60 years) lower lobe of left lung tissue, preserved by flash-freezing

value: lower lobe of left lung

value: tissue

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS559YLX at ENCODE; https://www.encodeproject.org/ENCBS559YLX/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: CRISPR RNA-seq from K562 (ENCLB378QPE)

description:
https://www.encodeproject.org/experiments/ENCSR865UKM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS3. (RPS3-BGKcLV04-C)
experiment encode accession: ENCSR865UKM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR005JBU
encode release date: 2021-04-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB378QPE
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/41e41a0b-b0e4-4e65-8542-7aa92ebf2976/@@download/attachment/L-RPS3-BGKcLV04-25C.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS3. (RPS3-BGKcLV04-25B)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS640DOL at ENCODE; https://www.encodeproject.org/ENCBS640DOL/

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


title: shRNA RNA-seq from HepG2 (ENCLB319GBI)

description:
https://www.encodeproject.org/experiments/ENCSR153GKS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGHLV37)
experiment encode accession: ENCSR153GKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB319GBI
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/e9d1f78e-818f-448b-82e8-1a881237d293/@@download/attachment/L-SRFBP1_BGHLV37-57.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGHLV37-57)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS971IZW at ENCODE; https://www.encodeproject.org/ENCBS971IZW/

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


title: shRNA RNA-seq from K562 (ENCLB835DSY)

description:
https://www.encodeproject.org/experiments/ENCSR047QHX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGKLV36)
experiment encode accession: ENCSR047QHX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB835DSY
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 SF3B1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0a19627f-649e-489c-824b-7fe27d50f780/@@download/attachment/L-SF3B1_BGKLV36-44.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGKLV36-44)

value: adult

value: ENCBS357WVC at ENCODE; https://www.encodeproject.org/ENCBS357WVC/


title: CRISPR RNA-seq from K562 (ENCLB130SJA)

description:
https://www.encodeproject.org/experiments/ENCSR148UGK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DGCR8 on day 41. (DGCR8-D41_BGKcLV02)
experiment encode accession: ENCSR148UGK
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR619GAS
encode release date: 2016-03-23
lab: Brenton Graveley, UConn
library encode accession: ENCLB130SJA
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/54647754-ce29-4777-9e8b-096fd887774c/@@download/attachment/L-DGCR8-D41_BGKcLV02-19.pdf

value: cell line

value: RNA-seq on k562 cells treated with an CRISPR gRNA against DGCR8 on day 41. (DGCR8-D41_BGKcLV02-19)

value: female

value: ENCBS008XYP at ENCODE; https://www.encodeproject.org/ENCBS008XYP/


title: CRISPR RNA-seq from HepG2 (ENCLB726NES)

description:
https://www.encodeproject.org/experiments/ENCSR166MWM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM14. (RBM14-BGHcLV07)
experiment encode accession: ENCSR166MWM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR521WAI
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB726NES
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/29b5b712-e5e4-4a90-a078-06f867762fae/@@download/attachment/L-RBM14-BGHcLV07-28.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM14. (RBM14-BGHcLV07-28)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS781PCX at ENCODE; https://www.encodeproject.org/ENCBS781PCX/


title: microRNA-seq from right lobe of liver (ENCLB160WSK)

description:
https://www.encodeproject.org/experiments/ENCSR895DRP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 right lobe liver microRNA-seq from Mortazavi
experiment encode accession: ENCSR895DRP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-03-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB160WSK
size range: <30

source_name: Homo sapiens female adult (41 years) right lobe of liver tissue, preserved by flash-freezing

value: right lobe of liver

value: tissue

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS823URA at ENCODE; https://www.encodeproject.org/ENCBS823URA/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: shRNA RNA-seq from K562 (ENCLB801RLY)

description:
https://www.encodeproject.org/experiments/ENCSR231PWH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NKRF. (NKRF-BGKLV36-C)
experiment encode accession: ENCSR231PWH
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR619PCR
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB801RLY
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 NKRF

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/686918ed-f73c-44b0-ab47-71e682045246/@@download/attachment/L-NKRF-BGKLV36-39.pdf

value: NKRF

value: RNA-seq on K562 cells treated with an shRNA knockdown against NKRF. (NKRF-BGKLV36-39)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS199CIR at ENCODE; https://www.encodeproject.org/ENCBS199CIR/

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


title: total RNA-seq from astrocyte (ENCLB404DIP)

description:
https://www.encodeproject.org/experiments/ENCSR129VBC/
***************
biological replicate number: 1
technical replicate number: 1
description: PGP1 derived astrocytes
experiment encode accession: ENCSR129VBC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB404DIP
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 adult (53 years) astrocyte in vitro differentiated cells

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: male

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS372XQF at ENCODE; https://www.encodeproject.org/ENCBS372XQF/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: shRNA RNA-seq from HepG2 (ENCLB705YFN)

description:
https://www.encodeproject.org/experiments/ENCSR225PRV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV37-C)
experiment encode accession: ENCSR225PRV
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB705YFN
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

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/86de00d3-323c-4f83-85e0-2ea17e2a9f4b/@@download/attachment/L-non-target-BGHLV37-1C.pdf

value: cell line

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

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

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 HepG2 (ENCLB285DBR)

description:
https://www.encodeproject.org/experiments/ENCSR225PRV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV37-C)
experiment encode accession: ENCSR225PRV
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB285DBR
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/7e6c75fd-d250-4429-bee8-fec067001712/@@download/attachment/L-non-target-BGHLV37-2C.pdf

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

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


title: total RNA-seq from astrocyte (ENCLB693TEO)

description:
https://www.encodeproject.org/experiments/ENCSR129VBC/
***************
biological replicate number: 2
technical replicate number: 1
description: PGP1 derived astrocytes
experiment encode accession: ENCSR129VBC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB693TEO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: adult

value: 53 year

value: ENCBS100HNS at ENCODE; https://www.encodeproject.org/ENCBS100HNS/


title: microRNA-seq from ovary (ENCLB838CXK)

description:
https://www.encodeproject.org/experiments/ENCSR957UVO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W80 ovary microRNA-seq from Mortazavi
experiment encode accession: ENCSR957UVO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB838CXK
size range: <30

source_name: Homo sapiens female adult (61 years) ovary tissue, preserved by flash-freezing

value: ovary

value: tissue

value: female

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: ENCBS250FEP at ENCODE; https://www.encodeproject.org/ENCBS250FEP/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: CRISPR RNA-seq from K562 (ENCLB915BOD)

description:
https://www.encodeproject.org/experiments/ENCSR139LOF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGKcLV02)
experiment encode accession: ENCSR139LOF
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB915BOD
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 SRSF7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/108b1ee7-eb6c-4299-ab1a-74c83aa33a10/@@download/attachment/L-SRSF7_BGKcLV02-5.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGKcLV02-5)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS026LKC at ENCODE; https://www.encodeproject.org/ENCBS026LKC/

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


title: CRISPR RNA-seq from HepG2 (ENCLB918RSA)

description:
https://www.encodeproject.org/experiments/ENCSR929JKA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGHcLV05-D)
experiment encode accession: ENCSR929JKA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR805TIZ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB918RSA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dceeef13-e1e1-4766-9288-3d0dd34acadc/@@download/attachment/L-SRSF4-BGHcLV05-33D.pdf

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

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB023KAL)

description:
https://www.encodeproject.org/experiments/ENCSR231RKU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGHcLV03)
experiment encode accession: ENCSR231RKU
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB023KAL
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 DDX21

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c2d6e34d-5cc3-4869-bce3-81f6ae1ece0a/@@download/attachment/L-DDX21_BGHcLV03-10.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGHcLV03-10)

value: ENCBS337WWP at ENCODE; https://www.encodeproject.org/ENCBS337WWP/


title: CRISPR RNA-seq from HepG2 (ENCLB314ELS)

description:
https://www.encodeproject.org/experiments/ENCSR929JKA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGHcLV05-D)
experiment encode accession: ENCSR929JKA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR805TIZ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB314ELS
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/73ad0487-2c26-46d3-b81e-7b360005cd6b/@@download/attachment/L-SRSF4-BGHcLV05-34D.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/


title: CRISPR RNA-seq from K562 (ENCLB194BVT)

description:
https://www.encodeproject.org/experiments/ENCSR139LOF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGKcLV02)
experiment encode accession: ENCSR139LOF
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR163JUC
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB194BVT
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/dc5fd3ca-fa55-465f-aedd-edd830e568aa/@@download/attachment/L-SRSF7_BGKcLV02-6.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGKcLV02-6)

value: female

value: adult

value: 53 year

value: ENCBS158FRU at ENCODE; https://www.encodeproject.org/ENCBS158FRU/


title: shRNA RNA-seq from K562 (ENCLB240VJU)

description:
https://www.encodeproject.org/experiments/ENCSR047QHX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGKLV36)
experiment encode accession: ENCSR047QHX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB240VJU
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)

value: RNA-seq on K562 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGKLV36-43)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS389KTJ at ENCODE; https://www.encodeproject.org/ENCBS389KTJ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB166ZLQ)

description:
https://www.encodeproject.org/experiments/ENCSR231RKU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGHcLV03)
experiment encode accession: ENCSR231RKU
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB166ZLQ
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/964674e6-fbe0-4c5c-8b11-22ae3f3c02a5/@@download/attachment/L-DDX21_BGHcLV03-9.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DDX21. (DDX21_BGHcLV03-9)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS009AVS at ENCODE; https://www.encodeproject.org/ENCBS009AVS/

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


title: microRNA-seq from progenitor cell of endocrine pancreas (ENCLB602WDZ)

description:
https://www.encodeproject.org/experiments/ENCSR931OFX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation H9 derived pancreatic progenitor cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR931OFX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB602WDZ
size range: <30

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: healthy

value: ENCBS832MSN at ENCODE; https://www.encodeproject.org/ENCBS832MSN/

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