title: total RNA-seq from activated B cell (ENCLB511XNC)

description:
https://www.encodeproject.org/experiments/ENCSR398REC/
***************
biological replicate number: 1
technical replicate number: 1
description: PBMCCD19+ (B cells) activatedCPG ODN2006 24h
experiment encode accession: ENCSR398REC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB511XNC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: activated B cell

value: primary cell

value: male

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS323XPY at ENCODE; https://www.encodeproject.org/ENCBS323XPY/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: total RNA-seq from A549 (ENCLB603UAC)

status: Public on Dec 04 2022

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/ENCSR155ZTO/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR155ZTO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB603UAC
size range: 200-300

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens A549 cell line treated with 1 uM AZD2906 (agonist) for 4 hours

extract_protocol:
extraction protocol: https://www.encodeproject.org/documents/e4e1b09a-8fe8-4212-9e76-a2fd6d0c8b49/@@download/attachment/supplemental%20PolyA%20plus%20RNA-seq%20library%20construction%20protocol.pdf
general protocol: https://www.encodeproject.org/documents/c2499c10-935d-4bc9-b374-5a40f69d4af9/@@download/attachment/Reddy_Lab_RNAseq_ENCODE_protocol.pdf
extraction method: Qiagen RNA extraction

tag: line

value: cell line

tag: biosample encode accession

tag: organism

value: Homo sapiens

tag: Sex

tag: dev stage

value: adult

tag: age

value: 58 year

tag: lab

value: Tim Reddy, Duke

tag: source

value: ATCC

tag: treatments

value: treatment_term_name:AZD2906; treatment_type:chemical; duration:4; duration_units:hour;

tag: link

value: ENCBS390UFY at ENCODE; https://www.encodeproject.org/ENCBS390UFY/

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


title: CRISPR RNA-seq from HepG2 (ENCLB386NQP)

description:
https://www.encodeproject.org/experiments/ENCSR153WFE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL2. (RUVBL2-BGHcLV31)
experiment encode accession: ENCSR153WFE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB386NQP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens RUVBL2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3b08c8a8-6a04-41a5-bd64-92e84a1dc59d/@@download/attachment/L-RUVBL2-BGHcLV31-21.pdf

tag: antibody

tag: description

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL2. (RUVBL2-BGHcLV31-21)

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS841DKK at ENCODE; https://www.encodeproject.org/ENCBS841DKK/

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


title: CRISPR RNA-seq from HepG2 (ENCLB135XBK)

description:
https://www.encodeproject.org/experiments/ENCSR153WFE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL2. (RUVBL2-BGHcLV31)
experiment encode accession: ENCSR153WFE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB135XBK
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/19e96fd6-1379-46f6-b150-1b65e6513f5a/@@download/attachment/L-RUVBL2-BGHcLV31-22.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL2. (RUVBL2-BGHcLV31-22)

value: male

value: ENCBS050QUI at ENCODE; https://www.encodeproject.org/ENCBS050QUI/


title: total RNA-seq from middle frontal area 46 (ENCLB142PAK)

description:
https://www.encodeproject.org/experiments/ENCSR390MBR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2351217_BS143_ENC4_cDNA693
experiment encode accession: ENCSR390MBR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB142PAK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens male adult (83 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: adult

value: 83 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS395PUX at ENCODE; https://www.encodeproject.org/ENCBS395PUX/

value: Derived from ENCODE donor ENCDO420VTI; https://www.encodeproject.org/ENCDO420VTI/


title: microRNA-seq from HL-60 (ENCLB104NSX)

description:
https://www.encodeproject.org/experiments/ENCSR350OBF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HL-60 derived M1 macrophages (differentiated 24hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR350OBF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB104NSX
size range: <30

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 100 ng/mL interferon gamma for 24 hours, 100 ng/mL lipopolysaccharide for 24 hours

value: cell line

value: HL-60 derived M1 macrophages (24hr)

value: female

value: acute promyelocytic leukemia

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P01579; treatment_term_name:interferon gamma; treatment_type:protein; duration:24; duration_units:hour; treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS970MQP at ENCODE; https://www.encodeproject.org/ENCBS970MQP/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: total RNA-seq from natural killer cell (ENCLB013LEW)

description:
https://www.encodeproject.org/experiments/ENCSR388NNP/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD56+_DONOR 2: 0 hour no activation
experiment encode accession: ENCSR388NNP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB013LEW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (47 years) natural killer primary cell

value: natural killer cell

value: primary cell

value: Homo sapiens

value: male

value: 47 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS117WPK at ENCODE; https://www.encodeproject.org/ENCBS117WPK/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: microRNA-seq from HL-60 (ENCLB216NWH)

description:
https://www.encodeproject.org/experiments/ENCSR350OBF/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation HL-60 derived M1 macrophages (differentiated 24hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR350OBF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB216NWH
size range: <30

value: cell line

value: HL-60 derived M1 macrophages (24hr)

value: female

value: adult

value: ENCBS755GCM at ENCODE; https://www.encodeproject.org/ENCBS755GCM/


title: CRISPR RNA-seq from K562 (ENCLB793XVU)

description:
https://www.encodeproject.org/experiments/ENCSR613ZVB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX17. (DDX17-BGKcLV28)
experiment encode accession: ENCSR613ZVB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB793XVU
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens DDX17

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e07cb20d-006d-4a42-be7f-b94a3f5373b8/@@download/attachment/L-DDX17-BGKcLV28-70.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX17. (DDX17-BGKcLV28-70)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS555TAR at ENCODE; https://www.encodeproject.org/ENCBS555TAR/

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


title: microRNA-seq from HL-60 (ENCLB639WSY)

description:
https://www.encodeproject.org/experiments/ENCSR350OBF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HL-60 derived M1 macrophages (differentiated 24hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR350OBF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB639WSY
size range: <30

value: Homo sapiens

value: acute promyelocytic leukemia

value: 36 year

value: Ali Mortazavi, UCI

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P01579; treatment_term_name:interferon gamma; treatment_type:protein; duration:24; duration_units:hour; treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS195FGT at ENCODE; https://www.encodeproject.org/ENCBS195FGT/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: total RNA-seq from natural killer cell (ENCLB124OSO)

description:
https://www.encodeproject.org/experiments/ENCSR388NNP/
***************
biological replicate number: 1
technical replicate number: 2
description: h.CD56+_DONOR 2: 0 hour no activation
experiment encode accession: ENCSR388NNP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB124OSO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: natural killer cell

value: primary cell

value: male

value: 47 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS117WPK at ENCODE; https://www.encodeproject.org/ENCBS117WPK/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: microRNA-seq from mesothelial cell of epicardium (ENCLB469MEY)

description:
https://www.encodeproject.org/experiments/ENCSR341PLF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation WA09-derived epicardium microRNA-seq from Mortazavi
experiment encode accession: ENCSR341PLF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB469MEY
size range: <30

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: CRISPR RNA-seq from K562 (ENCLB404UMJ)

description:
https://www.encodeproject.org/experiments/ENCSR613ZVB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX17. (DDX17-BGKcLV28)
experiment encode accession: ENCSR613ZVB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB404UMJ
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/3abf5144-5656-45c0-8bba-3d9b921ccf98/@@download/attachment/L-DDX17-BGKcLV28-69.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX17. (DDX17-BGKcLV28-69)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS535FPO at ENCODE; https://www.encodeproject.org/ENCBS535FPO/

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


title: total RNA-seq from middle frontal area 46 (ENCLB501SZW)

description:
https://www.encodeproject.org/experiments/ENCSR378WUC/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6413534_BS158_ENC4_cDNA708
experiment encode accession: ENCSR378WUC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB501SZW
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 (90 or above years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: male

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS577UDQ at ENCODE; https://www.encodeproject.org/ENCBS577UDQ/

value: Derived from ENCODE donor ENCDO607HHC; https://www.encodeproject.org/ENCDO607HHC/


title: total RNA-seq from WTC11 (ENCLB628YGV)

description:
https://www.encodeproject.org/experiments/ENCSR771NRY/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 3 days after differentiation
experiment encode accession: ENCSR771NRY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB628YGV

source_name: Homo sapiens WTC11 cell line treated with 7.5 uM IWP-2 for 24 hours, 3 days post differentiation, preserved by flash-freezing

value: cell line

value: iPSC differentiation in to cardiomycytes

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: treatment_term_id:CHEBI:125649; treatment_term_name:IWP-2; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS956LJI at ENCODE; https://www.encodeproject.org/ENCBS956LJI/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: total RNA-seq from middle frontal area 46 (ENCLB057VUN)

description:
https://www.encodeproject.org/experiments/ENCSR377MTB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8895621_BS185_ENC4_cDNA739
experiment encode accession: ENCSR377MTB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB057VUN
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 (86 years) middle frontal area 46 tissue

value: Homo sapiens

value: adult

value: 86 year

value: ENCBS077ZEW at ENCODE; https://www.encodeproject.org/ENCBS077ZEW/

value: Derived from ENCODE donor ENCDO666UNK; https://www.encodeproject.org/ENCDO666UNK/


title: CRISPR RNA-seq from K562 (ENCLB202FEW)

description:
https://www.encodeproject.org/experiments/ENCSR146YRO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGKcLV28)
experiment encode accession: ENCSR146YRO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB202FEW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8ceea794-06ed-4184-b0b4-a95bba36e7db/@@download/attachment/L-CTTN-BGKcLV28-52.pdf

value: CTTN

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGKcLV28-52)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS909SFC at ENCODE; https://www.encodeproject.org/ENCBS909SFC/

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


title: total RNA-seq from middle frontal area 46 (ENCLB628HAV)

description:
https://www.encodeproject.org/experiments/ENCSR800PJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E9254359_BS216_ENC4_cDNA771
experiment encode accession: ENCSR800PJQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB628HAV
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 adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS159MAA at ENCODE; https://www.encodeproject.org/ENCBS159MAA/

value: Derived from ENCODE donor ENCDO915WZE; https://www.encodeproject.org/ENCDO915WZE/


title: total RNA-seq from A549 (ENCLB575IJN)

description:
https://www.encodeproject.org/experiments/ENCSR155ZTO/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR155ZTO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB575IJN
size range: 200-300

value: cell line

value: Homo sapiens

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_name:AZD2906; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS724PTR at ENCODE; https://www.encodeproject.org/ENCBS724PTR/

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


title: total RNA-seq from WTC11 (ENCLB040VLT)

description:
https://www.encodeproject.org/experiments/ENCSR771NRY/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 3 days after differentiation
experiment encode accession: ENCSR771NRY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB040VLT

value: iPSC differentiation in to cardiomycytes

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: treatment_term_id:CHEBI:125649; treatment_term_name:IWP-2; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS757YGX at ENCODE; https://www.encodeproject.org/ENCBS757YGX/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: CRISPR RNA-seq from K562 (ENCLB003ECN)

description:
https://www.encodeproject.org/experiments/ENCSR608WYZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RIOK1. (RIOK1-BGKcLV30)
experiment encode accession: ENCSR608WYZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB003ECN
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens RIOK1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a50043fc-c5da-4c5f-bab8-8b66d70b2f55/@@download/attachment/L-RIOK1-BGKcLV30-33.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RIOK1. (RIOK1-BGKcLV30-33)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS394BIN at ENCODE; https://www.encodeproject.org/ENCBS394BIN/

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


title: total RNA-seq from WTC11 (ENCLB557VYR)

description:
https://www.encodeproject.org/experiments/ENCSR771DEX/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 1 days after differentiation
experiment encode accession: ENCSR771DEX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB557VYR

source_name: Homo sapiens WTC11 cell line treated with 7.5 uM CHIR 99021 for 24 hours, 1 day post differentiation, preserved by flash-freezing

value: cell line

value: Homo sapiens

value: male

value: adult

value: treatment_term_id:CHEBI:91091; treatment_term_name:CHIR 99021; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS139ZBT at ENCODE; https://www.encodeproject.org/ENCBS139ZBT/


title: microRNA-seq from HL-60 (ENCLB184MUM)

description:
https://www.encodeproject.org/experiments/ENCSR865XJM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HL-60 derived M2 macrophages (differentiated 24hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR865XJM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB184MUM
size range: <30

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 10 ng/mL interleukin-13 for 24 hours, 10 ng/mL interleukin-4 for 24 hours

value: HL-60 derived M2A macrophages (24hr)

value: acute promyelocytic leukemia

value: 36 year

value: Ali Mortazavi, UCI

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P35225; treatment_term_name:interleukin-13; treatment_type:protein; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:interleukin-4; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS379TMH at ENCODE; https://www.encodeproject.org/ENCBS379TMH/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: CRISPR RNA-seq from K562 (ENCLB543PEV)

description:
https://www.encodeproject.org/experiments/ENCSR608WYZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RIOK1. (RIOK1-BGKcLV30)
experiment encode accession: ENCSR608WYZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB543PEV
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/2b25c65b-fc14-49cc-9246-fe1aac1b0978/@@download/attachment/L-RIOK1-BGKcLV30-34.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RIOK1. (RIOK1-BGKcLV30-34)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS862EQG at ENCODE; https://www.encodeproject.org/ENCBS862EQG/


title: total RNA-seq from WTC11 (ENCLB913BBK)

description:
https://www.encodeproject.org/experiments/ENCSR758MWM/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 2 days after differentiation
experiment encode accession: ENCSR758MWM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB913BBK

source_name: Homo sapiens WTC11 cell line treated with 7.5 uM CHIR 99021 for 48 hours, 2 days post differentiation, preserved by flash-freezing

value: cell line

value: iPSC differentiation in to cardiomycytes

value: Homo sapiens

value: male

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: treatment_term_id:CHEBI:91091; treatment_term_name:CHIR 99021; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS747KRV at ENCODE; https://www.encodeproject.org/ENCBS747KRV/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: CRISPR RNA-seq from HepG2 (ENCLB079DGB)

description:
https://www.encodeproject.org/experiments/ENCSR146ITQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCTN2. (DCTN2-BGHcLV29)
experiment encode accession: ENCSR146ITQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB079DGB
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens DCTN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f12c2326-ef6b-4462-a80c-b9ce85682639/@@download/attachment/L-DCTN2-BGHcLV29-66.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCTN2. (DCTN2-BGHcLV29-66)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS535IUJ at ENCODE; https://www.encodeproject.org/ENCBS535IUJ/

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


title: total RNA-seq from middle frontal area 46 (ENCLB244MUI)

description:
https://www.encodeproject.org/experiments/ENCSR789PJB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3253149_BS96_ENC4_cDNA673
experiment encode accession: ENCSR789PJB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB244MUI
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 (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS190LXS at ENCODE; https://www.encodeproject.org/ENCBS190LXS/

value: Derived from ENCODE donor ENCDO877NVF; https://www.encodeproject.org/ENCDO877NVF/


title: total RNA-seq from A549 (ENCLB516YKQ)

description:
https://www.encodeproject.org/experiments/ENCSR155ZTO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR155ZTO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB516YKQ
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM AZD2906 (agonist) for 4 hours

value: cell line

value: Homo sapiens

value: male

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_name:AZD2906; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS993TMP at ENCODE; https://www.encodeproject.org/ENCBS993TMP/

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


title: total RNA-seq from WTC11 (ENCLB981JNE)

description:
https://www.encodeproject.org/experiments/ENCSR758MWM/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 2 days after differentiation
experiment encode accession: ENCSR758MWM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB981JNE

value: iPSC differentiation in to cardiomycytes

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: treatment_term_id:CHEBI:91091; treatment_term_name:CHIR 99021; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS270XPA at ENCODE; https://www.encodeproject.org/ENCBS270XPA/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: CRISPR RNA-seq from HepG2 (ENCLB940RPR)

description:
https://www.encodeproject.org/experiments/ENCSR146ITQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCTN2. (DCTN2-BGHcLV29)
experiment encode accession: ENCSR146ITQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB940RPR
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/cda600df-9cdf-4dc4-8d80-bd648316c0b4/@@download/attachment/L-DCTN2-BGHcLV29-65.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCTN2. (DCTN2-BGHcLV29-65)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS709SAZ at ENCODE; https://www.encodeproject.org/ENCBS709SAZ/

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


title: total RNA-seq from WTC11 (ENCLB030QXD)

description:
https://www.encodeproject.org/experiments/ENCSR771DEX/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 1 days after differentiation
experiment encode accession: ENCSR771DEX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB030QXD

value: cell line

value: Homo sapiens

value: male

value: adult

value: treatment_term_id:CHEBI:91091; treatment_term_name:CHIR 99021; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS991CMT at ENCODE; https://www.encodeproject.org/ENCBS991CMT/


title: total RNA-seq from T-cell (ENCLB186KMY)

description:
https://www.encodeproject.org/experiments/ENCSR798USR/
***************
biological replicate number: 1
technical replicate number: 1
description: CD3+_DONOR 1: 0 hour no activation
experiment encode accession: ENCSR798USR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB186KMY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (43 years) T-cell primary cell

value: T-cell

value: primary cell

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS353AGW at ENCODE; https://www.encodeproject.org/ENCBS353AGW/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: total RNA-seq from middle frontal area 46 (ENCLB617GYQ)

description:
https://www.encodeproject.org/experiments/ENCSR793SPM/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7908427_BS211_ENC4_cDNA766
experiment encode accession: ENCSR793SPM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB617GYQ
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 adult (89 years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 89 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS504PDX at ENCODE; https://www.encodeproject.org/ENCBS504PDX/

value: Derived from ENCODE donor ENCDO896WHW; https://www.encodeproject.org/ENCDO896WHW/


title: total RNA-seq from middle frontal area 46 (ENCLB559MMP)

description:
https://www.encodeproject.org/experiments/ENCSR394HJK/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8947111_BS186_ENC4_cDNA740
experiment encode accession: ENCSR394HJK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB559MMP
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 (83 years) middle frontal area 46 tissue

value: Homo sapiens

value: male

value: adult

value: 83 year

value: ENCBS317HDH at ENCODE; https://www.encodeproject.org/ENCBS317HDH/

value: Derived from ENCODE donor ENCDO736YJH; https://www.encodeproject.org/ENCDO736YJH/


title: PRO-cap from K562 (ENCLB733QLQ)

description:
https://www.encodeproject.org/experiments/ENCSR756TPG/
***************
biological replicate number: 2
technical replicate number: 2
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR756TPG
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB733QLQ

source_name: Homo sapiens K562 cell line

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Lis, Cornell

value: ATCC

value: ENCBS059DTN at ENCODE; https://www.encodeproject.org/ENCBS059DTN/

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


title: CRISPR RNA-seq from HepG2 (ENCLB346BQX)

description:
https://www.encodeproject.org/experiments/ENCSR608WXK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGHcLV24)
experiment encode accession: ENCSR608WXK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB346BQX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens EIF6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/aff709dc-f2a9-43a0-b55f-4230ac5fdf91/@@download/attachment/L-EIF6-BGHcLV24-30.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGHcLV24-30)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS044SUT at ENCODE; https://www.encodeproject.org/ENCBS044SUT/

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


title: total RNA-seq from middle frontal area 46 (ENCLB950ZNG)

description:
https://www.encodeproject.org/experiments/ENCSR363EVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E9687283_BS217_ENC4_cDNA772
experiment encode accession: ENCSR363EVQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB950ZNG
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 adult (90 or above years) with Cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS626ZIO at ENCODE; https://www.encodeproject.org/ENCBS626ZIO/

value: Derived from ENCODE donor ENCDO359XWR; https://www.encodeproject.org/ENCDO359XWR/


title: CRISPR RNA-seq from HepG2 (ENCLB486TCX)

description:
https://www.encodeproject.org/experiments/ENCSR608WXK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGHcLV24)
experiment encode accession: ENCSR608WXK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB486TCX
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/163ba6ea-3cae-4abc-b55e-c780be11783d/@@download/attachment/L-EIF6-BGHcLV24-29.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGHcLV24-29)

value: male

value: ATCC

value: ENCBS673YTO at ENCODE; https://www.encodeproject.org/ENCBS673YTO/


title: PRO-cap from K562 (ENCLB390YOT)

description:
https://www.encodeproject.org/experiments/ENCSR756TPG/
***************
biological replicate number: 1
technical replicate number: 2
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR756TPG
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB390YOT

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Lis, Cornell

value: ENCBS223MNJ at ENCODE; https://www.encodeproject.org/ENCBS223MNJ/

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


title: PRO-seq from HCT116 (ENCLB191KVF)

description:
https://www.encodeproject.org/experiments/ENCSR349AFH/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in CDK7_U
experiment encode accession: ENCSR349AFH
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB191KVF
spikeins used: The drosophila spike-in reference used for alignment

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

value: Homo sapiens

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

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


title: PRO-cap from K562 (ENCLB570VMP)

description:
https://www.encodeproject.org/experiments/ENCSR756TPG/
***************
biological replicate number: 1
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR756TPG
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB570VMP

value: cell line

value: female

value: adult


title: PRO-seq from HCT116 (ENCLB961MMD)

description:
https://www.encodeproject.org/experiments/ENCSR351QUY/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in MED14_T
experiment encode accession: ENCSR351QUY
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB961MMD
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

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

value: ENCBS447TCM at ENCODE; https://www.encodeproject.org/ENCBS447TCM/


title: PRO-seq from HCT116 (ENCLB442KRD)

description:
https://www.encodeproject.org/experiments/ENCSR349AFH/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in CDK7_U
experiment encode accession: ENCSR349AFH
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB442KRD
spikeins used: The drosophila spike-in reference used for alignment

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


title: Bru-seq from PC-9 (ENCLB629YXB)

description:
https://www.encodeproject.org/experiments/ENCSR137XKP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR137XKP
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR223GHJ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB629YXB
size range: 400-500

source_name: Homo sapiens PC-9 cell line treated with 500 rad irradiation

value: not collected

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS793NWJ at ENCODE; https://www.encodeproject.org/ENCBS793NWJ/

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


title: total RNA-seq from T-cell (ENCLB935EOE)

description:
https://www.encodeproject.org/experiments/ENCSR798USR/
***************
biological replicate number: 1
technical replicate number: 2
description: CD3+_DONOR 1: 0 hour no activation
experiment encode accession: ENCSR798USR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB935EOE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: T-cell

value: primary cell

value: Homo sapiens

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS353AGW at ENCODE; https://www.encodeproject.org/ENCBS353AGW/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: PRO-cap from K562 (ENCLB858GXI)

description:
https://www.encodeproject.org/experiments/ENCSR756TPG/
***************
biological replicate number: 2
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR756TPG
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB858GXI

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: John Lis, Cornell

value: ATCC

value: ENCBS059DTN at ENCODE; https://www.encodeproject.org/ENCBS059DTN/

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


title: PRO-seq from HCT116 (ENCLB691PCT)

description:
https://www.encodeproject.org/experiments/ENCSR351QUY/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in MED14_T
experiment encode accession: ENCSR351QUY
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB691PCT
spikeins used: The drosophila spike-in reference used for alignment

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS328JBR at ENCODE; https://www.encodeproject.org/ENCBS328JBR/

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


title: total RNA-seq from middle frontal area 46 (ENCLB828LFE)

description:
https://www.encodeproject.org/experiments/ENCSR397GDU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E9876975_BS193_ENC4_cDNA747
experiment encode accession: ENCSR397GDU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB828LFE
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 adult (90 or above years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS687KKD at ENCODE; https://www.encodeproject.org/ENCBS687KKD/

value: Derived from ENCODE donor ENCDO948PMW; https://www.encodeproject.org/ENCDO948PMW/


title: total RNA-seq from activated T-helper 2 cell (ENCLB499IUU)

description:
https://www.encodeproject.org/experiments/ENCSR341VFG/
***************
biological replicate number: 2
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th2 (aIFNg 5ug/ml+IL-4 100ng/ml)(day 13)+beads (1:3) day 1
experiment encode accession: ENCSR341VFG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB499IUU
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 (35 years) activated T-helper 2 primary cell treated with 5 ug/mL Interferon-gamma antibody for 36 hours, anti-CD3 and anti-CD28 coated beads for 24 hours, 10 ng/mL Interleukin-2 for 14 days, anti-CD3 and anti-CD28 coated bead...

value: activated T-helper 2 cell

value: primary cell

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; duration:36; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:14; duration_units:day; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:36; duration_units:hour;

value: ENCBS696MEH at ENCODE; https://www.encodeproject.org/ENCBS696MEH/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: CRISPR RNA-seq from HepG2 (ENCLB080RVZ)

description:
https://www.encodeproject.org/experiments/ENCSR608CUI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGHcLV25)
experiment encode accession: ENCSR608CUI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB080RVZ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens PSMA1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6942a524-df74-4884-93a4-2245bc308dfd/@@download/attachment/L-PSMA1-BGHcLV25-52.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGHcLV25-52)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS664UYP at ENCODE; https://www.encodeproject.org/ENCBS664UYP/

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


title: Bru-seq from PC-9 (ENCLB733FKS)

description:
https://www.encodeproject.org/experiments/ENCSR137XKP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR137XKP
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR223GHJ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB733FKS
size range: 400-500

value: Homo sapiens

value: not collected

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS350CVC at ENCODE; https://www.encodeproject.org/ENCBS350CVC/

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


title: total RNA-seq from K562 (ENCLB635SQE)

description:
https://www.encodeproject.org/experiments/ENCSR601DZY/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with DMSO for 12 hours
experiment encode accession: ENCSR601DZY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB635SQE
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 1% DMSO for 12 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:DMSO; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS186RPN at ENCODE; https://www.encodeproject.org/ENCBS186RPN/

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


title: total RNA-seq from middle frontal area 46 (ENCLB373YFF)

description:
https://www.encodeproject.org/experiments/ENCSR777KAR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5448057_BS100_ENC4_cDNA677
experiment encode accession: ENCSR777KAR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB373YFF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens female adult (81 years) with Cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 81 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS754RPU at ENCODE; https://www.encodeproject.org/ENCBS754RPU/

value: Derived from ENCODE donor ENCDO077CCP; https://www.encodeproject.org/ENCDO077CCP/


title: total RNA-seq from activated T-helper 2 cell (ENCLB013PVL)

description:
https://www.encodeproject.org/experiments/ENCSR341VFG/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th2 (aIFNg 5ug/ml+IL-4 100ng/ml)(day 13)+beads (1:3) day 1
experiment encode accession: ENCSR341VFG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB013PVL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: activated T-helper 2 cell

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; duration:36; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:14; duration_units:day; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:36; duration_units:hour;

value: ENCBS309SJI at ENCODE; https://www.encodeproject.org/ENCBS309SJI/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: total RNA-seq from WTC11 (ENCLB199KXC)

description:
https://www.encodeproject.org/experiments/ENCSR738IHB/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 5 days after differentiation
experiment encode accession: ENCSR738IHB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB199KXC

source_name: Homo sapiens WTC11 cell line, 5 days post differentiation, preserved by flash-freezing

value: cell line

value: iPSC differentiation in to cardiomycytes

value: adult

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: ENCBS715ACJ at ENCODE; https://www.encodeproject.org/ENCBS715ACJ/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: total RNA-seq from middle frontal area 46 (ENCLB445CGR)

description:
https://www.encodeproject.org/experiments/ENCSR776PQP/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8392249_BS212_ENC4_cDNA767
experiment encode accession: ENCSR776PQP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB445CGR
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 adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS322OXY at ENCODE; https://www.encodeproject.org/ENCBS322OXY/

value: Derived from ENCODE donor ENCDO075KHF; https://www.encodeproject.org/ENCDO075KHF/


title: CRISPR RNA-seq from HepG2 (ENCLB968PFX)

description:
https://www.encodeproject.org/experiments/ENCSR608CUI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGHcLV25)
experiment encode accession: ENCSR608CUI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB968PFX
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/02569197-74b6-42b7-ac6d-b7781d355c53/@@download/attachment/L-PSMA1-BGHcLV25-51.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGHcLV25-51)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS325UGX at ENCODE; https://www.encodeproject.org/ENCBS325UGX/

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


title: total RNA-seq from K562 (ENCLB864QBV)

description:
https://www.encodeproject.org/experiments/ENCSR601DZY/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with DMSO for 12 hours
experiment encode accession: ENCSR601DZY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB864QBV
size range: 300-600

value: RNA-seq on human cell line K562

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:DMSO; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS308GNV at ENCODE; https://www.encodeproject.org/ENCBS308GNV/

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


title: total RNA-seq from middle frontal area 46 (ENCLB796KGV)

description:
https://www.encodeproject.org/experiments/ENCSR339GOD/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5352389_BS201_ENC4_cDNA756
experiment encode accession: ENCSR339GOD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB796KGV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS036MOJ at ENCODE; https://www.encodeproject.org/ENCBS036MOJ/

value: Derived from ENCODE donor ENCDO343SFL; https://www.encodeproject.org/ENCDO343SFL/


title: total RNA-seq from A549 (ENCLB089MGM)

description:
https://www.encodeproject.org/experiments/ENCSR599BTG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR599BTG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB089MGM
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM GW870086 (agonist) for 4 hours

value: cell line

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_name:GW870086; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS278BSR at ENCODE; https://www.encodeproject.org/ENCBS278BSR/

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


title: total RNA-seq from A549 (ENCLB013VST)

description:
https://www.encodeproject.org/experiments/ENCSR599BTG/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR599BTG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB013VST
size range: 200-300

value: Homo sapiens

value: adult

value: ENCBS687PHC at ENCODE; https://www.encodeproject.org/ENCBS687PHC/


title: total RNA-seq from A549 (ENCLB042MFC)

description:
https://www.encodeproject.org/experiments/ENCSR599BTG/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR599BTG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB042MFC
size range: 200-300

value: ENCBS443SUX at ENCODE; https://www.encodeproject.org/ENCBS443SUX/


title: total RNA-seq from middle frontal area 46 (ENCLB607XVS)

description:
https://www.encodeproject.org/experiments/ENCSR755FNG/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7461192_BS125_ENC4_cDNA687
experiment encode accession: ENCSR755FNG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB607XVS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: ENCBS914ACI at ENCODE; https://www.encodeproject.org/ENCBS914ACI/

value: Derived from ENCODE donor ENCDO218FFZ; https://www.encodeproject.org/ENCDO218FFZ/


title: PRO-cap from K562 (ENCLB128GKT)

description:
https://www.encodeproject.org/experiments/ENCSR261KBX/
***************
biological replicate number: 1
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and PCR amplification was performed before sequencing.
experiment encode accession: ENCSR261KBX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB128GKT

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Lis, Cornell

value: ENCBS167SHL at ENCODE; https://www.encodeproject.org/ENCBS167SHL/

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


title: total RNA-seq from A549 (ENCLB997VHQ)

description:
https://www.encodeproject.org/experiments/ENCSR599BTG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR599BTG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB997VHQ
size range: 200-300

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_name:GW870086; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS039KEI at ENCODE; https://www.encodeproject.org/ENCBS039KEI/

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


title: PRO-cap from K562 (ENCLB382OOO)

description:
https://www.encodeproject.org/experiments/ENCSR261KBX/
***************
biological replicate number: 2
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and PCR amplification was performed before sequencing.
experiment encode accession: ENCSR261KBX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB382OOO

value: Homo sapiens

value: female

value: adult

value: ENCBS784DDT at ENCODE; https://www.encodeproject.org/ENCBS784DDT/


title: total RNA-seq from WTC11 (ENCLB256ZKD)

description:
https://www.encodeproject.org/experiments/ENCSR738IHB/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 5 days after differentiation
experiment encode accession: ENCSR738IHB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB256ZKD

value: cell line

value: iPSC differentiation in to cardiomycytes

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: ENCBS785JRJ at ENCODE; https://www.encodeproject.org/ENCBS785JRJ/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: total RNA-seq from A549 (ENCLB403ANB)

description:
https://www.encodeproject.org/experiments/ENCSR599BTG/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR599BTG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB403ANB
size range: 200-300

value: male

value: 58 year

value: ENCBS087PCF at ENCODE; https://www.encodeproject.org/ENCBS087PCF/


title: total RNA-seq from natural killer cell (ENCLB095AQS)

description:
https://www.encodeproject.org/experiments/ENCSR745APD/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD56+_DONOR 2: 72 hour activation IL-12+IL-15+IL-18, 100ng/ml
experiment encode accession: ENCSR745APD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB095AQS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (47 years) natural killer primary cell treated with 100 ng/mL Interleukin-12 subunit alpha for 72 hours, 100 ng/mL Interleukin-15 for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, 100 ng/mL Interleukin-18 for 7...

value: natural killer cell

value: primary cell

value: 47 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:Q14116; treatment_term_name:Interleukin-18; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS311LDY at ENCODE; https://www.encodeproject.org/ENCBS311LDY/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: microRNA-seq from HL-60 (ENCLB368INI)

description:
https://www.encodeproject.org/experiments/ENCSR645VXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HL-60 derived M0 macrophages microRNA-seq from Mortazavi
experiment encode accession: ENCSR645VXJ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB368INI
size range: <30

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours

value: cell line

value: HL-60 derived M0 macrophages

value: Homo sapiens

value: female

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour;

value: ENCBS441GXQ at ENCODE; https://www.encodeproject.org/ENCBS441GXQ/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: total RNA-seq from K562 (ENCLB328SRH)

description:
https://www.encodeproject.org/experiments/ENCSR124KOZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Galeterone for 24 hours
experiment encode accession: ENCSR124KOZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB328SRH
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 25 uM Galeterone for 24 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:Galeterone; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS271JMP at ENCODE; https://www.encodeproject.org/ENCBS271JMP/

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


title: total RNA-seq from middle frontal area 46 (ENCLB515VZS)

description:
https://www.encodeproject.org/experiments/ENCSR323YXV/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5108249_BS182_ENC4_cDNA736
experiment encode accession: ENCSR323YXV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB515VZS
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 adult (90 or above years) with Cognitive impairment, Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS305UQQ at ENCODE; https://www.encodeproject.org/ENCBS305UQQ/

value: Derived from ENCODE donor ENCDO206ZSI; https://www.encodeproject.org/ENCDO206ZSI/


title: microRNA-seq from HL-60 (ENCLB416PLB)

description:
https://www.encodeproject.org/experiments/ENCSR645VXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HL-60 derived M0 macrophages microRNA-seq from Mortazavi
experiment encode accession: ENCSR645VXJ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB416PLB
size range: <30

value: cell line

value: HL-60 derived M0 macrophages

value: female

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour;

value: ENCBS959JBS at ENCODE; https://www.encodeproject.org/ENCBS959JBS/


title: total RNA-seq from K562 (ENCLB387QVG)

description:
https://www.encodeproject.org/experiments/ENCSR124KOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Galeterone for 24 hours
experiment encode accession: ENCSR124KOZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB387QVG
size range: 300-600

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:Galeterone; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS627XLY at ENCODE; https://www.encodeproject.org/ENCBS627XLY/

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


title: total RNA-seq from middle frontal area 46 (ENCLB364UJH)

description:
https://www.encodeproject.org/experiments/ENCSR320AJD/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6422513_BS206_ENC4_cDNA761
experiment encode accession: ENCSR320AJD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB364UJH
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 adult (87 years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS375PHK at ENCODE; https://www.encodeproject.org/ENCBS375PHK/

value: Derived from ENCODE donor ENCDO063RHR; https://www.encodeproject.org/ENCDO063RHR/


title: CRISPR RNA-seq from K562 (ENCLB081FLD)

description:
https://www.encodeproject.org/experiments/ENCSR122RJE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGKcLV26)
experiment encode accession: ENCSR122RJE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB081FLD
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens ADAT1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/db5f3bcd-2347-4013-ac91-44e1091a9147/@@download/attachment/L-ADAT1-BGKcLV26-7.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGKcLV26-7)

value: female

value: adult

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS896MIR at ENCODE; https://www.encodeproject.org/ENCBS896MIR/


title: long read RNA-seq from C2C12 (ENCLB924PNJ)

description:
https://www.encodeproject.org/experiments/ENCSR418ZYU/
***************
biological replicate number: 2
technical replicate number: 1
description: Myoblast cell line derived from thigh muscle of C3H mice after crush injury
experiment encode accession: ENCSR418ZYU
assay title: long read RNA-seq
assembly: mm10
encode release date: 2019-12-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB924PNJ

organism: Mus musculus

source_name: Mus musculus C2C12 cell line

value: Mus musculus

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ENCBS670LTF at ENCODE; https://www.encodeproject.org/ENCBS670LTF/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: CRISPR RNA-seq from K562 (ENCLB324KJP)

description:
https://www.encodeproject.org/experiments/ENCSR122RJE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGKcLV26)
experiment encode accession: ENCSR122RJE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB324KJP
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/da45da11-e983-49e4-a21d-7840a8546d5f/@@download/attachment/L-ADAT1-BGKcLV26-8.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGKcLV26-8)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS223VKG at ENCODE; https://www.encodeproject.org/ENCBS223VKG/

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


title: total RNA-seq from middle frontal area 46 (ENCLB919FLD)

description:
https://www.encodeproject.org/experiments/ENCSR753BWD/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E4946143_BS152_ENC4_cDNA702
experiment encode accession: ENCSR753BWD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB919FLD
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 (87 years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: male

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS201ZQN at ENCODE; https://www.encodeproject.org/ENCBS201ZQN/

value: Derived from ENCODE donor ENCDO368JFY; https://www.encodeproject.org/ENCDO368JFY/


title: CRISPR RNA-seq from K562 (ENCLB726REY)

description:
https://www.encodeproject.org/experiments/ENCSR593NFA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DBNL. (DBNL-BGKcLV28)
experiment encode accession: ENCSR593NFA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB726REY
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/df0d39bd-9ba8-4fb4-9830-4fe89af33edc/@@download/attachment/L-DBNL-BGKcLV28-60.pdf

value: DBNL

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DBNL. (DBNL-BGKcLV28-60)

value: female

value: adult

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS969WVP at ENCODE; https://www.encodeproject.org/ENCBS969WVP/


title: long read RNA-seq from C2C12 (ENCLB124WFG)

description:
https://www.encodeproject.org/experiments/ENCSR418ZYU/
***************
biological replicate number: 1
technical replicate number: 1
description: Myoblast cell line derived from thigh muscle of C3H mice after crush injury
experiment encode accession: ENCSR418ZYU
assay title: long read RNA-seq
assembly: mm10
encode release date: 2019-12-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB124WFG

value: Mus musculus

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ENCBS351CUU at ENCODE; https://www.encodeproject.org/ENCBS351CUU/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: long read RNA-seq from forelimb (ENCLB393ATC)

description:
https://www.encodeproject.org/experiments/ENCSR804QMV/
***************
biological replicate number: 1
technical replicate number: 1
description: Mus musculus strain B6NCrl embryo (11 days) forelimb tissue
experiment encode accession: ENCSR804QMV
assay title: long read RNA-seq
assembly: mm10
encode release date: 2019-12-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB393ATC

value: forelimb

value: tissue

value: embryonic

value: 11 day

value: The Jackson Laboratory

value: ENCBS084VOL at ENCODE; https://www.encodeproject.org/ENCBS084VOL/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA-seq from HL-60 (ENCLB018LJB)

description:
https://www.encodeproject.org/experiments/ENCSR617YSI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HL-60 derived M2 macrophages (differentiated 12hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR617YSI
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB018LJB
size range: <30

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 10 ng/mL interleukin-13 for 12 hours, 10 ng/mL interleukin-4 for 12 hours

value: cell line

value: HL-60 derived M2A macrophages (12hr)

value: Homo sapiens

value: female

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P35225; treatment_term_name:interleukin-13; treatment_type:protein; duration:12; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:interleukin-4; treatment_type:protein; duration:12; duration_units:hour;

value: ENCBS982BVD at ENCODE; https://www.encodeproject.org/ENCBS982BVD/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: microRNA-seq from HL-60 (ENCLB345AWB)

description:
https://www.encodeproject.org/experiments/ENCSR645VXJ/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation HL-60 derived M0 macrophages microRNA-seq from Mortazavi
experiment encode accession: ENCSR645VXJ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB345AWB
size range: <30

value: HL-60 derived M0 macrophages

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour;

value: ENCBS042LWS at ENCODE; https://www.encodeproject.org/ENCBS042LWS/


title: total RNA-seq from middle frontal area 46 (ENCLB620MAD)

description:
https://www.encodeproject.org/experiments/ENCSR307PZR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8505753_BS213_ENC4_cDNA768
experiment encode accession: ENCSR307PZR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB620MAD
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS481KCJ at ENCODE; https://www.encodeproject.org/ENCBS481KCJ/

value: Derived from ENCODE donor ENCDO557QXE; https://www.encodeproject.org/ENCDO557QXE/


title: microRNA-seq from HL-60 (ENCLB389NCH)

description:
https://www.encodeproject.org/experiments/ENCSR617YSI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HL-60 derived M2 macrophages (differentiated 12hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR617YSI
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB389NCH
size range: <30

value: cell line

value: HL-60 derived M2A macrophages (12hr)

value: Homo sapiens

value: female

value: acute promyelocytic leukemia

value: adult

value: ENCBS756IEB at ENCODE; https://www.encodeproject.org/ENCBS756IEB/


title: total RNA-seq from middle frontal area 46 (ENCLB378ZUY)

description:
https://www.encodeproject.org/experiments/ENCSR733DBA/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E9696602_BS191_ENC4_cDNA745
experiment encode accession: ENCSR733DBA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB378ZUY
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 adult (90 or above years) with Alzheimer's disease; middle frontal area 46 tissue

value: ENCBS334NVI at ENCODE; https://www.encodeproject.org/ENCBS334NVI/

value: Derived from ENCODE donor ENCDO473TSU; https://www.encodeproject.org/ENCDO473TSU/


title: long read RNA-seq from left cerebral cortex (ENCLB872YLK)

description:
https://www.encodeproject.org/experiments/ENCSR340GWV/
***************
biological replicate number: 2
technical replicate number: 1
description: Cortex1 from 6 mo C57BL/6 male
experiment encode accession: ENCSR340GWV
assay title: long read RNA-seq
assembly: mm10
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB872YLK

source_name: Mus musculus strain B6NCrl adult (6 months) left cerebral cortex tissue

value: left cerebral cortex

value: Cortex from 6 mo C57BL/6 male

value: Mus musculus

value: not collected

value: 6 month

value: Ali Mortazavi, UCI

value: Andrea Tenner

value: ENCBS191KAZ at ENCODE; https://www.encodeproject.org/ENCBS191KAZ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: CRISPR RNA-seq from HepG2 (ENCLB683GOT)

description:
https://www.encodeproject.org/experiments/ENCSR119RXN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGHcLV32)
experiment encode accession: ENCSR119RXN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB683GOT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens RPS15A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/96c4541c-eb1e-4eba-9032-84c6910f559f/@@download/attachment/L-RPS15A-BGHcLV32-66.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGHcLV32-66)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS632MXM at ENCODE; https://www.encodeproject.org/ENCBS632MXM/

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


title: CRISPR RNA-seq from K562 (ENCLB250EKU)

description:
https://www.encodeproject.org/experiments/ENCSR593NFA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DBNL. (DBNL-BGKcLV28)
experiment encode accession: ENCSR593NFA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB250EKU
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/210a14ce-e213-428e-b3c1-8be548b7aca1/@@download/attachment/L-DBNL-BGKcLV28-59.pdf

value: DBNL

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DBNL. (DBNL-BGKcLV28-59)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS859OJC at ENCODE; https://www.encodeproject.org/ENCBS859OJC/

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


title: CRISPR RNA-seq from HepG2 (ENCLB243EBA)

description:
https://www.encodeproject.org/experiments/ENCSR119RXN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGHcLV32)
experiment encode accession: ENCSR119RXN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB243EBA
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/3626aa3d-fdb4-49ed-bf8a-d932eeabdf5b/@@download/attachment/L-RPS15A-BGHcLV32-65.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGHcLV32-65)

value: male

value: ENCBS724WJD at ENCODE; https://www.encodeproject.org/ENCBS724WJD/


title: PRO-cap from K562 (ENCLB875MQQ)

description:
https://www.encodeproject.org/experiments/ENCSR149ZRX/
***************
biological replicate number: 1
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and PCR amplification was performed before sequencing.
experiment encode accession: ENCSR149ZRX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB875MQQ

source_name: Homo sapiens K562 cell line

value: John Lis, Cornell

value: ENCBS526RIS at ENCODE; https://www.encodeproject.org/ENCBS526RIS/


title: total RNA-seq from middle frontal area 46 (ENCLB215WUR)

description:
https://www.encodeproject.org/experiments/ENCSR728FFT/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3648984_BS196_ENC4_cDNA751
experiment encode accession: ENCSR728FFT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB215WUR
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 adult (88 years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 88 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS682RDL at ENCODE; https://www.encodeproject.org/ENCBS682RDL/

value: Derived from ENCODE donor ENCDO151OJB; https://www.encodeproject.org/ENCDO151OJB/


title: CRISPR RNA-seq from K562 (ENCLB708RGM)

description:
https://www.encodeproject.org/experiments/ENCSR119PLU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGKcLV33)
experiment encode accession: ENCSR119PLU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB708RGM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens SAP30BP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/368248ee-e177-47d4-86a9-814325af953f/@@download/attachment/L-RUVBL1-BGKcLV33-24.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGKcLV33-24)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS126IJD at ENCODE; https://www.encodeproject.org/ENCBS126IJD/


title: PRO-cap from K562 (ENCLB424YOZ)

description:
https://www.encodeproject.org/experiments/ENCSR604EBH/
***************
biological replicate number: 2
technical replicate number: 2
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR604EBH
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB424YOZ

value: cell line

value: 53 year

value: John Lis, Cornell

value: ENCBS853KVF at ENCODE; https://www.encodeproject.org/ENCBS853KVF/

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


title: total RNA-seq from middle frontal area 46 (ENCLB032VNS)

description:
https://www.encodeproject.org/experiments/ENCSR693YZA/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5124249_BS200_ENC4_cDNA755
experiment encode accession: ENCSR693YZA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB032VNS
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 adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Barbara Wold, Caltech

value: ENCBS047HSL at ENCODE; https://www.encodeproject.org/ENCBS047HSL/

value: Derived from ENCODE donor ENCDO471EKG; https://www.encodeproject.org/ENCDO471EKG/


title: total RNA-seq from middle frontal area 46 (ENCLB175NLF)

description:
https://www.encodeproject.org/experiments/ENCSR318WUN/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3616882_BS195_ENC4_cDNA750
experiment encode accession: ENCSR318WUN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB175NLF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: Homo sapiens

value: female

value: Rush University

value: ENCBS301QVL at ENCODE; https://www.encodeproject.org/ENCBS301QVL/

value: Derived from ENCODE donor ENCDO033BMB; https://www.encodeproject.org/ENCDO033BMB/


title: total RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB717WFC)

description:
https://www.encodeproject.org/experiments/ENCSR317HKT/
***************
biological replicate number: 2
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th0 (no diff Cytokines)(day 14)
experiment encode accession: ENCSR317HKT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB717WFC
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 (35 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS737JKH at ENCODE; https://www.encodeproject.org/ENCBS737JKH/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: total RNA-seq from activated T-helper 17 cell (ENCLB772VBV)

description:
https://www.encodeproject.org/experiments/ENCSR265EHG/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Th17_DONOR 5: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR265EHG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB772VBV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (48 years) activated T-helper 17 primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-helper 17 cell

value: 48 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS222ZSB at ENCODE; https://www.encodeproject.org/ENCBS222ZSB/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/