title: CRISPR RNA-seq from HepG2 (ENCLB064OBF)

description:
https://www.encodeproject.org/experiments/ENCSR051LWN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGHcLV25)
experiment encode accession: ENCSR051LWN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB064OBF
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/a5b20039-31c9-4f13-bb1e-9d0691eaf7b9/@@download/attachment/L-ADAT1-BGHcLV25-11.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGHcLV25-11)

value: Homo sapiens

value: male

value: ENCBS413SQG at ENCODE; https://www.encodeproject.org/ENCBS413SQG/


title: total RNA-seq from middle frontal area 46 (ENCLB472NAO)

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/ENCSR530OOO/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8243181_BS167_ENC4_cDNA717
experiment encode accession: ENCSR530OOO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB472NAO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens male adult (90 or above years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

tag: description

tag: biosample encode accession

tag: organism

tag: Sex

tag: dev stage

value: adult

tag: age

value: 90 or above year

tag: lab

value: Barbara Wold, Caltech

tag: source

value: Rush University

tag: link

value: ENCBS876ZME at ENCODE; https://www.encodeproject.org/ENCBS876ZME/

value: Derived from ENCODE donor ENCDO228WQW; https://www.encodeproject.org/ENCDO228WQW/


title: PRO-seq from HCT116 (ENCLB804TAX)

description:
https://www.encodeproject.org/experiments/ENCSR019RWT/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in MED14_U
experiment encode accession: ENCSR019RWT
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB804TAX
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

tag: line

value: cell line

tag: health state

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS904RVQ at ENCODE; https://www.encodeproject.org/ENCBS904RVQ/

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


title: total RNA-seq from middle frontal area 46 (ENCLB705OVS)

description:
https://www.encodeproject.org/experiments/ENCSR025BZY/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5374703_BS155_ENC4_cDNA705
experiment encode accession: ENCSR025BZY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB705OVS
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 (82 years) middle frontal area 46 tissue

value: Homo sapiens

value: female

value: 82 year

value: ENCBS771BVR at ENCODE; https://www.encodeproject.org/ENCBS771BVR/

value: Derived from ENCODE donor ENCDO377QXX; https://www.encodeproject.org/ENCDO377QXX/


title: CRISPR RNA-seq from K562 (ENCLB815AWZ)

description:
https://www.encodeproject.org/experiments/ENCSR049YEZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGKcLV28)
experiment encode accession: ENCSR049YEZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB815AWZ
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 CDK9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/617a0f31-13e3-4fc8-82fe-82fe83a488d6/@@download/attachment/L-CDK9-BGKcLV28-13.pdf

tag: antibody

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGKcLV28-13)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS426GBU at ENCODE; https://www.encodeproject.org/ENCBS426GBU/

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


title: total RNA-seq from middle frontal area 46 (ENCLB725LZC)

description:
https://www.encodeproject.org/experiments/ENCSR530ESE/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7286104_BS208_ENC4_cDNA763
experiment encode accession: ENCSR530ESE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB725LZC
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 (84 years) with Cognitive impairment, Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: male

value: 84 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS275EQQ at ENCODE; https://www.encodeproject.org/ENCBS275EQQ/

value: Derived from ENCODE donor ENCDO284KGV; https://www.encodeproject.org/ENCDO284KGV/


title: CRISPR RNA-seq from HepG2 (ENCLB709QSN)

description:
https://www.encodeproject.org/experiments/ENCSR051BQF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAT. (CAT-BGHcLV27)
experiment encode accession: ENCSR051BQF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB709QSN
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 CAT

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bbd57f47-6cbd-4265-814e-8695a53bdc13/@@download/attachment/L-CAT-BGHcLV27-43.pdf

value: CAT

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAT. (CAT-BGHcLV27-43)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS659OBX at ENCODE; https://www.encodeproject.org/ENCBS659OBX/

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


title: total RNA-seq from middle frontal area 46 (ENCLB657PGH)

description:
https://www.encodeproject.org/experiments/ENCSR015SAL/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E4638217_BS98_ENC4_cDNA675
experiment encode accession: ENCSR015SAL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB657PGH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

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: female

value: adult

value: 90 or above year

value: ENCBS129NMG at ENCODE; https://www.encodeproject.org/ENCBS129NMG/

value: Derived from ENCODE donor ENCDO305GYI; https://www.encodeproject.org/ENCDO305GYI/


title: PRO-seq from HCT116 (ENCLB359VMQ)

description:
https://www.encodeproject.org/experiments/ENCSR545GXL/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in POLR2A_U
experiment encode accession: ENCSR545GXL
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB359VMQ
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 POLR2A

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS729ZZV at ENCODE; https://www.encodeproject.org/ENCBS729ZZV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB087HQC)

description:
https://www.encodeproject.org/experiments/ENCSR051BQF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAT. (CAT-BGHcLV27)
experiment encode accession: ENCSR051BQF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB087HQC
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/c0ee5f6e-f415-4a07-be11-e0da0745eb0f/@@download/attachment/L-CAT-BGHcLV27-44.pdf

value: CAT

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAT. (CAT-BGHcLV27-44)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS956SJA at ENCODE; https://www.encodeproject.org/ENCBS956SJA/


title: PRO-seq from HCT116 (ENCLB156QHN)

description:
https://www.encodeproject.org/experiments/ENCSR516VKD/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in SUPT16H_T
experiment encode accession: ENCSR516VKD
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB156QHN
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 SUPT16H treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: adult

tag: treatments

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

value: ENCBS081HJW at ENCODE; https://www.encodeproject.org/ENCBS081HJW/


title: CRISPR RNA-seq from K562 (ENCLB744MWI)

description:
https://www.encodeproject.org/experiments/ENCSR049YEZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGKcLV28)
experiment encode accession: ENCSR049YEZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB744MWI
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/6ebec586-532b-4055-bd50-03ee4a764ea8/@@download/attachment/L-CDK9-BGKcLV28-14.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGKcLV28-14)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS853HUJ at ENCODE; https://www.encodeproject.org/ENCBS853HUJ/

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


title: total RNA-seq from middle frontal area 46 (ENCLB587LXJ)

description:
https://www.encodeproject.org/experiments/ENCSR521ZFP/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6264119_BS159_ENC4_cDNA709
experiment encode accession: ENCSR521ZFP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB587LXJ
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: middle frontal area 46

value: tissue

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS801JBH at ENCODE; https://www.encodeproject.org/ENCBS801JBH/

value: Derived from ENCODE donor ENCDO020MJV; https://www.encodeproject.org/ENCDO020MJV/


title: total RNA-seq from A549 (ENCLB854CYG)

description:
https://www.encodeproject.org/experiments/ENCSR048LHL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR048LHL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB854CYG
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM RU486 (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

value: cell line

value: Homo sapiens

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:50692; treatment_term_name:RU486; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS652MTO at ENCODE; https://www.encodeproject.org/ENCBS652MTO/

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


title: CRISPR RNA-seq from K562 (ENCLB164VBO)

description:
https://www.encodeproject.org/experiments/ENCSR558XPA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SETD1A. (SETD1A-BGKcLV33)
experiment encode accession: ENCSR558XPA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB164VBO
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 MTREX

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dfbb4ce8-6b1f-469d-a45e-2c5e7841c36c/@@download/attachment/L-SETD1A-BGKcLV33-49.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SETD1A. (SETD1A-BGKcLV33-49)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS202NAP at ENCODE; https://www.encodeproject.org/ENCBS202NAP/

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


title: total RNA-seq from A549 (ENCLB376XTA)

description:
https://www.encodeproject.org/experiments/ENCSR048LHL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR048LHL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB376XTA
size range: 200-300

value: cell line

value: ENCBS911ZFS at ENCODE; https://www.encodeproject.org/ENCBS911ZFS/


title: total RNA-seq from middle frontal area 46 (ENCLB649HEY)

description:
https://www.encodeproject.org/experiments/ENCSR012UFU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8969200_BS188_ENC4_cDNA742
experiment encode accession: ENCSR012UFU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB649HEY
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: middle frontal area 46

value: tissue

value: Homo sapiens

value: male

value: 86 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS612UJI at ENCODE; https://www.encodeproject.org/ENCBS612UJI/

value: Derived from ENCODE donor ENCDO022VWV; https://www.encodeproject.org/ENCDO022VWV/


title: total RNA-seq from A549 (ENCLB459QTH)

description:
https://www.encodeproject.org/experiments/ENCSR048LHL/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR048LHL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB459QTH
size range: 200-300

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:50692; treatment_term_name:RU486; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS486RRL at ENCODE; https://www.encodeproject.org/ENCBS486RRL/

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


title: CRISPR RNA-seq from HepG2 (ENCLB188QWO)

description:
https://www.encodeproject.org/experiments/ENCSR558DZW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADD3. (ADD3-BGHcLV25)
experiment encode accession: ENCSR558DZW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB188QWO
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 ADD3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4ffa010d-e734-41e3-85fc-5a82bd988707/@@download/attachment/L-ADD3-BGHcLV25-14.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADD3. (ADD3-BGHcLV25-14)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS605JYS at ENCODE; https://www.encodeproject.org/ENCBS605JYS/

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


title: PRO-seq from HCT116 (ENCLB251UYW)

description:
https://www.encodeproject.org/experiments/ENCSR019RWT/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in MED14_U
experiment encode accession: ENCSR019RWT
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB251UYW
spikeins used: The drosophila spike-in reference used for alignment

value: Homo sapiens

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS007ZIG at ENCODE; https://www.encodeproject.org/ENCBS007ZIG/

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


title: total RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB107GPH)

description:
https://www.encodeproject.org/experiments/ENCSR011VQI/
***************
biological replicate number: 1
technical replicate number: 2
description: h.CD4.Naive_DONOR 5: 0 hour no activation
experiment encode accession: ENCSR011VQI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB107GPH
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) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS593WOX at ENCODE; https://www.encodeproject.org/ENCBS593WOX/

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


title: total RNA-seq from placenta (ENCLB095TZI)

description:
https://www.encodeproject.org/experiments/ENCSR010HIU/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11004 (redo)
experiment encode accession: ENCSR010HIU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB095TZI
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 embryo placenta tissue

value: placenta

value: tissue

value: embryonic

value: unknown

value: John Stamatoyannopoulos

value: ENCBS992IKC at ENCODE; https://www.encodeproject.org/ENCBS992IKC/

value: Derived from ENCODE donor ENCDO824PZQ; https://www.encodeproject.org/ENCDO824PZQ/


title: total RNA-seq from A549 (ENCLB382BGR)

description:
https://www.encodeproject.org/experiments/ENCSR048LHL/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR048LHL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB382BGR
size range: 200-300

value: cell line

value: Homo sapiens

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:50692; treatment_term_name:RU486; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS732EAU at ENCODE; https://www.encodeproject.org/ENCBS732EAU/

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


title: PRO-seq from HCT116 (ENCLB680AIH)

description:
https://www.encodeproject.org/experiments/ENCSR516VKD/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in SUPT16H_T
experiment encode accession: ENCSR516VKD
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB680AIH
spikeins used: The drosophila spike-in reference used for alignment

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: ENCBS093CJI at ENCODE; https://www.encodeproject.org/ENCBS093CJI/

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


title: total RNA-seq from middle frontal area 46 (ENCLB013KRE)

description:
https://www.encodeproject.org/experiments/ENCSR515MED/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6735279_BS207_ENC4_cDNA762
experiment encode accession: ENCSR515MED
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB013KRE
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: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS327PNC at ENCODE; https://www.encodeproject.org/ENCBS327PNC/

value: Derived from ENCODE donor ENCDO859HCD; https://www.encodeproject.org/ENCDO859HCD/


title: total RNA-seq from A549 (ENCLB061ZZG)

description:
https://www.encodeproject.org/experiments/ENCSR048LHL/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR048LHL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB061ZZG
size range: 200-300

value: cell line

value: Homo sapiens

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:50692; treatment_term_name:RU486; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS555RZQ at ENCODE; https://www.encodeproject.org/ENCBS555RZQ/


title: total RNA-seq from middle frontal area 46 (ENCLB018KVT)

description:
https://www.encodeproject.org/experiments/ENCSR013HWB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8325260_BS168_ENC4_cDNA718
experiment encode accession: ENCSR013HWB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB018KVT
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 Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: 88 year

value: ENCBS046CJD at ENCODE; https://www.encodeproject.org/ENCBS046CJD/

value: Derived from ENCODE donor ENCDO070VNS; https://www.encodeproject.org/ENCDO070VNS/


title: total RNA-seq from middle frontal area 46 (ENCLB652GYY)

description:
https://www.encodeproject.org/experiments/ENCSR007SVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1121653_BS119_ENC4_cDNA681
experiment encode accession: ENCSR007SVQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB652GYY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens female adult (86 years) middle frontal area 46 tissue

value: tissue

value: female

value: 86 year

value: Barbara Wold, Caltech

value: ENCBS875BBD at ENCODE; https://www.encodeproject.org/ENCBS875BBD/

value: Derived from ENCODE donor ENCDO888KBY; https://www.encodeproject.org/ENCDO888KBY/


title: CRISPR RNA-seq from HepG2 (ENCLB991QAF)

description:
https://www.encodeproject.org/experiments/ENCSR044GQU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF3. (CSTF3-BGHcLV29)
experiment encode accession: ENCSR044GQU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB991QAF
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 CSTF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f593e88c-53a5-4a80-971c-38dcb0b240d9/@@download/attachment/L-CSTF3-BGHcLV29-48.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF3. (CSTF3-BGHcLV29-48)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS986CSI at ENCODE; https://www.encodeproject.org/ENCBS986CSI/

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


title: CRISPR RNA-seq from K562 (ENCLB230KGJ)

description:
https://www.encodeproject.org/experiments/ENCSR041IXV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV30)
experiment encode accession: ENCSR041IXV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB230KGJ
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 RBM25

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ce3a9f11-3d2a-4ac3-87c8-b3c1c89d9b43/@@download/attachment/L-RBM25-BGKcLV30-11.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV30-11)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS873CAZ at ENCODE; https://www.encodeproject.org/ENCBS873CAZ/

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


title: DNase-seq from suppressor macrophage (ENCLB151JAW)

description:
https://www.encodeproject.org/experiments/ENCSR367FKP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR367FKP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB151JAW
instrument models: Illumina HiSeq 2000,Illumina HiSeq 4000

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens male adult (24 years) suppressor macrophage primary cell

value: suppressor macrophage

value: primary cell

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS117SZU at ENCODE; https://www.encodeproject.org/ENCBS117SZU/

value: Derived from ENCODE donor ENCDO488BDS; https://www.encodeproject.org/ENCDO488BDS/


title: total RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB943CTN)

description:
https://www.encodeproject.org/experiments/ENCSR011VQI/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Naive_DONOR 5: 0 hour no activation
experiment encode accession: ENCSR011VQI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB943CTN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: Homo sapiens

value: male

value: 48 year

value: StemExpress

value: ENCBS593WOX at ENCODE; https://www.encodeproject.org/ENCBS593WOX/

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


title: CRISPR RNA-seq from K562 (ENCLB426GTV)

description:
https://www.encodeproject.org/experiments/ENCSR036ZTN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGKcLV30)
experiment encode accession: ENCSR036ZTN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB426GTV
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 RPL29

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1692107d-b65c-486d-adc4-df3ec7c9629d/@@download/attachment/L-RPL29-BGKcLV30-48.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGKcLV30-48)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS919IEY at ENCODE; https://www.encodeproject.org/ENCBS919IEY/


title: total RNA-seq from middle frontal area 46 (ENCLB047JLP)

description:
https://www.encodeproject.org/experiments/ENCSR001QSI/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2504543_BS178_ENC4_cDNA732
experiment encode accession: ENCSR001QSI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB047JLP
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 (80 years) with Cognitive impairment, Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 80 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS120DQN at ENCODE; https://www.encodeproject.org/ENCBS120DQN/

value: Derived from ENCODE donor ENCDO920NSS; https://www.encodeproject.org/ENCDO920NSS/


title: total RNA-seq from middle frontal area 46 (ENCLB489NSS)

description:
https://www.encodeproject.org/experiments/ENCSR539OQU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5605087_BS124_ENC4_cDNA686
experiment encode accession: ENCSR539OQU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB489NSS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

value: Homo sapiens

value: 90 or above year

value: ENCBS787ZKP at ENCODE; https://www.encodeproject.org/ENCBS787ZKP/

value: Derived from ENCODE donor ENCDO865EMM; https://www.encodeproject.org/ENCDO865EMM/


title: total RNA-seq from middle frontal area 46 (ENCLB354TVO)

description:
https://www.encodeproject.org/experiments/ENCSR501XXE/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3439501_BS153_ENC4_cDNA703
experiment encode accession: ENCSR501XXE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB354TVO
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: female

value: ENCBS540BVM at ENCODE; https://www.encodeproject.org/ENCBS540BVM/

value: Derived from ENCODE donor ENCDO921LXT; https://www.encodeproject.org/ENCDO921LXT/


title: CRISPR RNA-seq from HepG2 (ENCLB049DGV)

description:
https://www.encodeproject.org/experiments/ENCSR558DZW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADD3. (ADD3-BGHcLV25)
experiment encode accession: ENCSR558DZW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB049DGV
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/c93a33df-c6d5-444a-b081-a32fbb105c0a/@@download/attachment/L-ADD3-BGHcLV25-13.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADD3. (ADD3-BGHcLV25-13)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS914PTZ at ENCODE; https://www.encodeproject.org/ENCBS914PTZ/

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


title: CRISPR RNA-seq from K562 (ENCLB368KUX)

description:
https://www.encodeproject.org/experiments/ENCSR046XQE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BRD2. (BRD2-BGKcLV26)
experiment encode accession: ENCSR046XQE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB368KUX
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 BRD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1799f029-c2ad-4501-b20d-cac9fdca34ab/@@download/attachment/L-BRD2-BGKcLV26-41.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BRD2. (BRD2-BGKcLV26-41)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS706ZAQ at ENCODE; https://www.encodeproject.org/ENCBS706ZAQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB656ZWO)

description:
https://www.encodeproject.org/experiments/ENCSR036HUB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGHcLV31)
experiment encode accession: ENCSR036HUB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB656ZWO
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 SEPT11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b9fdc3d2-9480-48d4-8656-4d2dcc0a8c41/@@download/attachment/L-SEPT11-BGHcLV31-41.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGHcLV31-41)

value: Homo sapiens

value: ENCBS024CFI at ENCODE; https://www.encodeproject.org/ENCBS024CFI/


title: CRISPR RNA-seq from K562 (ENCLB160MQI)

description:
https://www.encodeproject.org/experiments/ENCSR046XQE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BRD2. (BRD2-BGKcLV26)
experiment encode accession: ENCSR046XQE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB160MQI
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/d5edf187-5089-48cb-8647-b33386bc65b2/@@download/attachment/L-BRD2-BGKcLV26-42.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BRD2. (BRD2-BGKcLV26-42)

value: female

value: ENCBS816PZZ at ENCODE; https://www.encodeproject.org/ENCBS816PZZ/


title: CRISPR RNA-seq from K562 (ENCLB985NHG)

description:
https://www.encodeproject.org/experiments/ENCSR558XPA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SETD1A. (SETD1A-BGKcLV33)
experiment encode accession: ENCSR558XPA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB985NHG
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/decbeedc-8473-4e69-b1b9-ee6ae4124720/@@download/attachment/L-SETD1A-BGKcLV33-50.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SETD1A. (SETD1A-BGKcLV33-50)

value: ATCC

value: ENCBS754IVU at ENCODE; https://www.encodeproject.org/ENCBS754IVU/


title: CRISPR RNA-seq from K562 (ENCLB821TNP)

description:
https://www.encodeproject.org/experiments/ENCSR035MKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CCNT1. (CCNT1-BGKcLV26)
experiment encode accession: ENCSR035MKJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB821TNP
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 CCNT1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/13fbe4a0-9f67-44e1-bd96-25fe1524913b/@@download/attachment/L-CCNT1-BGKcLV26-66.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CCNT1. (CCNT1-BGKcLV26-66)

value: ENCBS999TYZ at ENCODE; https://www.encodeproject.org/ENCBS999TYZ/


title: total RNA-seq from middle frontal area 46 (ENCLB646NTS)

description:
https://www.encodeproject.org/experiments/ENCSR497KUU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3666162_BS197_ENC4_cDNA752
experiment encode accession: ENCSR497KUU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB646NTS
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 (86 years) with Cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: adult

value: 86 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS068FIA at ENCODE; https://www.encodeproject.org/ENCBS068FIA/

value: Derived from ENCODE donor ENCDO845GYA; https://www.encodeproject.org/ENCDO845GYA/


title: CRISPR RNA-seq from HepG2 (ENCLB839ZVL)

description:
https://www.encodeproject.org/experiments/ENCSR044GQU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF3. (CSTF3-BGHcLV29)
experiment encode accession: ENCSR044GQU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB839ZVL
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/e61a4a99-4537-48f4-8501-45b76b8013da/@@download/attachment/L-CSTF3-BGHcLV29-47.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF3. (CSTF3-BGHcLV29-47)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS197FRN at ENCODE; https://www.encodeproject.org/ENCBS197FRN/

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


title: CRISPR RNA-seq from HepG2 (ENCLB934XDP)

description:
https://www.encodeproject.org/experiments/ENCSR034VEC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ROCK2. (ROCK2-BGHcLV32)
experiment encode accession: ENCSR034VEC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB934XDP
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 ROCK2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/55bb54a0-87b3-4d35-93a9-f48abefa3a66/@@download/attachment/L-ROCK2-BGHcLV32-41.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ROCK2. (ROCK2-BGHcLV32-41)

value: ATCC

value: ENCBS712HXB at ENCODE; https://www.encodeproject.org/ENCBS712HXB/


title: CRISPR RNA-seq from K562 (ENCLB886YKI)

description:
https://www.encodeproject.org/experiments/ENCSR041IXV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV30)
experiment encode accession: ENCSR041IXV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB886YKI
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/6e4a1c80-9e5c-45f1-aa53-5b535a1a66e8/@@download/attachment/L-RBM25-BGKcLV30-12.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV30-12)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS824XKV at ENCODE; https://www.encodeproject.org/ENCBS824XKV/

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


title: CRISPR RNA-seq from K562 (ENCLB923DGL)

description:
https://www.encodeproject.org/experiments/ENCSR034FLW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B3. (SF3B3-BGKcLV33)
experiment encode accession: ENCSR034FLW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB923DGL
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 SMG7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e90f9d15-eb2a-4b09-b46e-896fe5f31f17/@@download/attachment/L-SF3B3-BGKcLV33-54.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B3. (SF3B3-BGKcLV33-54)

value: Homo sapiens

value: ENCBS612ZRN at ENCODE; https://www.encodeproject.org/ENCBS612ZRN/


title: CRISPR RNA-seq from K562 (ENCLB153BJX)

description:
https://www.encodeproject.org/experiments/ENCSR034FLW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B3. (SF3B3-BGKcLV33)
experiment encode accession: ENCSR034FLW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB153BJX
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/423b9c10-8f7e-46dd-96b5-fc0874fd8b60/@@download/attachment/L-SF3B3-BGKcLV33-53.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B3. (SF3B3-BGKcLV33-53)

value: Brenton Graveley, UConn

value: ENCBS586NYG at ENCODE; https://www.encodeproject.org/ENCBS586NYG/


title: CRISPR RNA-seq from K562 (ENCLB041BKJ)

description:
https://www.encodeproject.org/experiments/ENCSR036ZTN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGKcLV30)
experiment encode accession: ENCSR036ZTN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB041BKJ
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/6c4af9ad-690a-463c-92ff-8bbb679bcb1f/@@download/attachment/L-RPL29-BGKcLV30-47.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGKcLV30-47)

value: ENCBS540NPH at ENCODE; https://www.encodeproject.org/ENCBS540NPH/


title: total RNA-seq from K562 (ENCLB114HWF)

description:
https://www.encodeproject.org/experiments/ENCSR534TGM/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with JQ1 for 48 hours
experiment encode accession: ENCSR534TGM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB114HWF
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM JQ1 for 48 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:JQ1; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS089TXQ at ENCODE; https://www.encodeproject.org/ENCBS089TXQ/


title: CRISPR RNA-seq from K562 (ENCLB102SLL)

description:
https://www.encodeproject.org/experiments/ENCSR544ZMX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC5L. (CDC5L-BGKcLV28)
experiment encode accession: ENCSR544ZMX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB102SLL
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 CDC5L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/38f71fe2-7cd1-40f5-8e7e-d2dfa283e9af/@@download/attachment/L-CDC5L-BGKcLV28-12.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC5L. (CDC5L-BGKcLV28-12)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS607GSW at ENCODE; https://www.encodeproject.org/ENCBS607GSW/


title: CRISPR RNA-seq from K562 (ENCLB195GQV)

description:
https://www.encodeproject.org/experiments/ENCSR544ZMX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC5L. (CDC5L-BGKcLV28)
experiment encode accession: ENCSR544ZMX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB195GQV
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/d78adee4-361d-4ccd-b84f-c212aa969172/@@download/attachment/L-CDC5L-BGKcLV28-11.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC5L. (CDC5L-BGKcLV28-11)

value: Homo sapiens

value: ENCBS183DAH at ENCODE; https://www.encodeproject.org/ENCBS183DAH/

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


title: CRISPR RNA-seq from K562 (ENCLB535ZXW)

description:
https://www.encodeproject.org/experiments/ENCSR033MIV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRA1. (SRA1-BGKcLV33)
experiment encode accession: ENCSR033MIV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB535ZXW
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 SRA1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9ebdcf13-8398-48ff-98a2-00ba94c50b40/@@download/attachment/L-SRA1-BGKcLV33-73.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRA1. (SRA1-BGKcLV33-73)

value: Brenton Graveley, UConn

value: ENCBS234IIM at ENCODE; https://www.encodeproject.org/ENCBS234IIM/


title: CRISPR RNA-seq from HepG2 (ENCLB185LWB)

description:
https://www.encodeproject.org/experiments/ENCSR029LLJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACTN4. (ACTN4-BGHcLV25)
experiment encode accession: ENCSR029LLJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB185LWB
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 ACTN4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3f31e821-c56e-42cf-b981-3fddd435baf5/@@download/attachment/L-ACTN4-BGHcLV25-6.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACTN4. (ACTN4-BGHcLV25-6)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS887WYP at ENCODE; https://www.encodeproject.org/ENCBS887WYP/

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


title: CRISPR RNA-seq from K562 (ENCLB008HEL)

description:
https://www.encodeproject.org/experiments/ENCSR528OVC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGKcLV26)
experiment encode accession: ENCSR528OVC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB008HEL
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 BZW2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b3bea863-85a5-417e-9e72-b02d79e41490/@@download/attachment/L-BZW2-BGKcLV26-45.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGKcLV26-45)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS972LHO at ENCODE; https://www.encodeproject.org/ENCBS972LHO/


title: CRISPR RNA-seq from HepG2 (ENCLB401CQK)

description:
https://www.encodeproject.org/experiments/ENCSR036HUB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGHcLV31)
experiment encode accession: ENCSR036HUB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB401CQK
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/9c933f8c-1c5f-4c0f-a6a5-e00b8e16cfad/@@download/attachment/L-SEPT11-BGHcLV31-42.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGHcLV31-42)

value: Homo sapiens

value: ENCBS236PDD at ENCODE; https://www.encodeproject.org/ENCBS236PDD/


title: CRISPR RNA-seq from K562 (ENCLB651VVC)

description:
https://www.encodeproject.org/experiments/ENCSR528OVC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGKcLV26)
experiment encode accession: ENCSR528OVC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB651VVC
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/eb79b96d-d680-45d2-93e0-7cc9e73612e8/@@download/attachment/L-BZW2-BGKcLV26-46.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGKcLV26-46)

value: Brenton Graveley, UConn

value: ENCBS652IYM at ENCODE; https://www.encodeproject.org/ENCBS652IYM/

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


title: CRISPR RNA-seq from K562 (ENCLB478PHH)

description:
https://www.encodeproject.org/experiments/ENCSR033MIV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRA1. (SRA1-BGKcLV33)
experiment encode accession: ENCSR033MIV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB478PHH
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/6c4fa8fd-751e-406e-b7d9-6c1c352a78e1/@@download/attachment/L-SRA1-BGKcLV33-74.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRA1. (SRA1-BGKcLV33-74)

value: ATCC

value: ENCBS885CJQ at ENCODE; https://www.encodeproject.org/ENCBS885CJQ/


title: CRISPR RNA-seq from K562 (ENCLB264ENU)

description:
https://www.encodeproject.org/experiments/ENCSR535TPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SPATS2. (SPATS2-BGKcLV33)
experiment encode accession: ENCSR535TPQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB264ENU
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/d6bdd931-b53b-4911-9bfe-0bac6515fb13/@@download/attachment/L-SPATS2-BGKcLV33-69.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SPATS2. (SPATS2-BGKcLV33-69)

value: ENCBS228HSK at ENCODE; https://www.encodeproject.org/ENCBS228HSK/


title: total RNA-seq from K562 (ENCLB025NEJ)

description:
https://www.encodeproject.org/experiments/ENCSR534TGM/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with JQ1 for 48 hours
experiment encode accession: ENCSR534TGM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB025NEJ
size range: 300-600

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: Will Greenleaf, Stanford

value: treatment_term_name:JQ1; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS094KCL at ENCODE; https://www.encodeproject.org/ENCBS094KCL/


title: CRISPR RNA-seq from HepG2 (ENCLB354VMJ)

description:
https://www.encodeproject.org/experiments/ENCSR034VEC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ROCK2. (ROCK2-BGHcLV32)
experiment encode accession: ENCSR034VEC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB354VMJ
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/05740b04-9baf-4dc9-942b-b12d327e4fc8/@@download/attachment/L-ROCK2-BGHcLV32-42.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ROCK2. (ROCK2-BGHcLV32-42)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS925GYT at ENCODE; https://www.encodeproject.org/ENCBS925GYT/

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


title: Bru-seq from HCT116 (ENCLB495VFP)

description:
https://www.encodeproject.org/experiments/ENCSR025QKI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR025QKI
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR877LIZ
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB495VFP
size range: 400-500

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: colorectal carcinoma

value: adult

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: ENCBS769NMQ at ENCODE; https://www.encodeproject.org/ENCBS769NMQ/

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


title: CRISPR RNA-seq from K562 (ENCLB389NKG)

description:
https://www.encodeproject.org/experiments/ENCSR535TPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SPATS2. (SPATS2-BGKcLV33)
experiment encode accession: ENCSR535TPQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB389NKG
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/aec45580-fc87-41a3-acb3-c189e1848f87/@@download/attachment/L-SPATS2-BGKcLV33-70.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SPATS2. (SPATS2-BGKcLV33-70)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS312MQH at ENCODE; https://www.encodeproject.org/ENCBS312MQH/

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


title: CRISPR RNA-seq from K562 (ENCLB968GDN)

description:
https://www.encodeproject.org/experiments/ENCSR035MKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CCNT1. (CCNT1-BGKcLV26)
experiment encode accession: ENCSR035MKJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB968GDN
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/d3f62a99-c337-4f68-9053-ed98500c9bfe/@@download/attachment/L-CCNT1-BGKcLV26-65.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CCNT1. (CCNT1-BGKcLV26-65)

value: Homo sapiens

value: ENCBS773ARL at ENCODE; https://www.encodeproject.org/ENCBS773ARL/


title: PRO-cap from Calu3 (ENCLB715UPC)

description:
https://www.encodeproject.org/experiments/ENCSR935RNW/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CALU3.
experiment encode accession: ENCSR935RNW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB715UPC
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens Calu3 cell line

value: male

value: Lung adenocarcinoma

value: adult

value: 25 year

value: Mats Ljungman, UMichigan

value: ENCBS842EEJ at ENCODE; https://www.encodeproject.org/ENCBS842EEJ/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: CRISPR RNA-seq from HepG2 (ENCLB584ULM)

description:
https://www.encodeproject.org/experiments/ENCSR029LLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACTN4. (ACTN4-BGHcLV25)
experiment encode accession: ENCSR029LLJ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB584ULM
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/6390b3a0-d8e0-4459-b82c-97a0c48dc724/@@download/attachment/L-ACTN4-BGHcLV25-5.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACTN4. (ACTN4-BGHcLV25-5)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS395IEJ at ENCODE; https://www.encodeproject.org/ENCBS395IEJ/

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


title: PRO-cap from Calu3 (ENCLB785FAS)

description:
https://www.encodeproject.org/experiments/ENCSR935RNW/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CALU3.
experiment encode accession: ENCSR935RNW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB785FAS
spikeins used: The drosophila spike-in reference used for alignment

value: ATCC

value: ENCBS974LON at ENCODE; https://www.encodeproject.org/ENCBS974LON/


title: PRO-cap from Caco-2 (ENCLB419WCW)

description:
https://www.encodeproject.org/experiments/ENCSR100LIJ/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CACO2.
experiment encode accession: ENCSR100LIJ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB419WCW
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens Caco-2 cell line

value: Homo sapiens

value: colorectal adenocarcinoma

value: 72 year

value: ENCBS344ACZ at ENCODE; https://www.encodeproject.org/ENCBS344ACZ/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: PRO-cap from MCF 10A (ENCLB999OBL)

description:
https://www.encodeproject.org/experiments/ENCSR799DGV/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in MCF10A.
experiment encode accession: ENCSR799DGV
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB999OBL
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: female

value: fibrocystic disease

value: adult

value: 36 year

value: Mats Ljungman, UMichigan

value: ENCBS296FKB at ENCODE; https://www.encodeproject.org/ENCBS296FKB/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: Bru-seq from HCT116 (ENCLB277HHT)

description:
https://www.encodeproject.org/experiments/ENCSR025QKI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR025QKI
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR877LIZ
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB277HHT
size range: 400-500

value: cell line

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: ENCBS309JWT at ENCODE; https://www.encodeproject.org/ENCBS309JWT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB202NGF)

description:
https://www.encodeproject.org/experiments/ENCSR524NOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGHcLV29)
experiment encode accession: ENCSR524NOZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB202NGF
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 DCPS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/95ca3dcd-315e-4bf3-9833-b877a09425d5/@@download/attachment/L-DCPS-BGHcLV29-63.pdf

value: DCPS

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGHcLV29-63)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS330HJH at ENCODE; https://www.encodeproject.org/ENCBS330HJH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB468DVU)

description:
https://www.encodeproject.org/experiments/ENCSR524NOZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGHcLV29)
experiment encode accession: ENCSR524NOZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB468DVU
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/ad0cefcf-b9d7-4148-9f7a-167be2b4f23a/@@download/attachment/L-DCPS-BGHcLV29-64.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGHcLV29-64)

value: male

value: ENCBS055NUJ at ENCODE; https://www.encodeproject.org/ENCBS055NUJ/


title: PRO-cap from Caco-2 (ENCLB590KEW)

description:
https://www.encodeproject.org/experiments/ENCSR100LIJ/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CACO2.
experiment encode accession: ENCSR100LIJ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB590KEW
spikeins used: The drosophila spike-in reference used for alignment

value: colorectal adenocarcinoma

value: adult

value: 72 year

value: Mats Ljungman, UMichigan

value: ENCBS568BYI at ENCODE; https://www.encodeproject.org/ENCBS568BYI/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: Bru-seq from Calu3 (ENCLB012LKG)

description:
https://www.encodeproject.org/experiments/ENCSR025EUU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR025EUU
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR692DCF
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB012LKG
size range: 400-500

source_name: Homo sapiens Calu3 cell line treated with 500 rad irradiation

value: Homo sapiens

value: Lung adenocarcinoma

value: 25 year

value: ENCBS933DZT at ENCODE; https://www.encodeproject.org/ENCBS933DZT/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: CRISPR RNA-seq from K562 (ENCLB799XBG)

description:
https://www.encodeproject.org/experiments/ENCSR527XZI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGKcLV26)
experiment encode accession: ENCSR527XZI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB799XBG
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 CAND1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/70a8d48c-f3ab-4cfd-ac2f-6d6ea0d6fbd3/@@download/attachment/L-CAND1-BGKcLV26-52.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGKcLV26-52)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS338UWS at ENCODE; https://www.encodeproject.org/ENCBS338UWS/

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


title: CRISPR RNA-seq from K562 (ENCLB373SXC)

description:
https://www.encodeproject.org/experiments/ENCSR527XZI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGKcLV26)
experiment encode accession: ENCSR527XZI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB373SXC
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/c7e4c2ae-1848-463d-8892-a156dfc20255/@@download/attachment/L-CAND1-BGKcLV26-51.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGKcLV26-51)

value: adult

value: ENCBS010UIL at ENCODE; https://www.encodeproject.org/ENCBS010UIL/


title: PRO-cap from endothelial cell of umbilical vein (ENCLB985JUV)

description:
https://www.encodeproject.org/experiments/ENCSR098LLB/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in HUVEC.
experiment encode accession: ENCSR098LLB
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB985JUV
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens male newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: primary cell

value: Homo sapiens

value: male

value: newborn

value: unknown

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS161BVI at ENCODE; https://www.encodeproject.org/ENCBS161BVI/

value: Derived from ENCODE donor ENCDO628LXZ; https://www.encodeproject.org/ENCDO628LXZ/


title: Bru-seq from Calu3 (ENCLB395TXY)

description:
https://www.encodeproject.org/experiments/ENCSR025EUU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR025EUU
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR692DCF
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB395TXY
size range: 400-500

value: Lung adenocarcinoma

value: 25 year

value: ATCC

value: ENCBS071BUY at ENCODE; https://www.encodeproject.org/ENCBS071BUY/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: PRO-cap from A673 (ENCLB616FNA)

description:
https://www.encodeproject.org/experiments/ENCSR046BCI/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in A673.
experiment encode accession: ENCSR046BCI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB616FNA
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens A673 cell line

value: cell line

value: female

value: child

value: 15 year

value: ENCBS975LBZ at ENCODE; https://www.encodeproject.org/ENCBS975LBZ/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: total RNA-seq from A549 (ENCLB849TUJ)

description:
https://www.encodeproject.org/experiments/ENCSR522CJR/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR522CJR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB849TUJ
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM Hydrocortisone (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

value: Homo sapiens

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:17650; treatment_term_name:Hydrocortisone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS122JGP at ENCODE; https://www.encodeproject.org/ENCBS122JGP/

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


title: PRO-cap from A673 (ENCLB986UCY)

description:
https://www.encodeproject.org/experiments/ENCSR046BCI/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in A673.
experiment encode accession: ENCSR046BCI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB986UCY
spikeins used: The drosophila spike-in reference used for alignment

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS841YGY at ENCODE; https://www.encodeproject.org/ENCBS841YGY/


title: total RNA-seq from A549 (ENCLB168ZFK)

description:
https://www.encodeproject.org/experiments/ENCSR522CJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR522CJR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB168ZFK
size range: 200-300

value: cell line

value: ENCBS594GCK at ENCODE; https://www.encodeproject.org/ENCBS594GCK/


title: total RNA-seq from A549 (ENCLB337EGN)

description:
https://www.encodeproject.org/experiments/ENCSR522CJR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR522CJR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB337EGN
size range: 200-300

value: ENCBS746ATL at ENCODE; https://www.encodeproject.org/ENCBS746ATL/


title: polyA plus RNA-seq from layer of hippocampus (ENCLB591DUT)

description:
https://www.encodeproject.org/experiments/ENCSR898LNL/
***************
biological replicate number: 1
technical replicate number: 1
description: Hippocampus from 6 mo C57BL/6 male
experiment encode accession: ENCSR898LNL
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2021-11-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB591DUT
fragmentation methods: chemical (Nextera tagmentation)
size range: <200
nucleic acid starting quantity: 20
nucleic acid starting quantity units: ng

organism: Mus musculus

source_name: Mus musculus strain B6NCrl adult (6 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: Hippocampus from 6 mo C57BL/6 male

value: Mus musculus

value: not collected

value: 6 month

value: Ali Mortazavi, UCI

value: Andrea Tenner

value: ENCBS486VZJ at ENCODE; https://www.encodeproject.org/ENCBS486VZJ/

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


title: PRO-cap from MCF 10A (ENCLB817CDN)

description:
https://www.encodeproject.org/experiments/ENCSR799DGV/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in MCF10A.
experiment encode accession: ENCSR799DGV
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB817CDN
spikeins used: The drosophila spike-in reference used for alignment

value: MCF 10A

value: Homo sapiens

value: female

value: fibrocystic disease

value: adult

value: 36 year

value: ENCBS834CIE at ENCODE; https://www.encodeproject.org/ENCBS834CIE/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: PAS-seq from left cerebral cortex (ENCLB469YPD)

description:
https://www.encodeproject.org/experiments/ENCSR432LIX/
***************
biological replicate number: 1
technical replicate number: 1
description: Mouse cortex QuantSeq
experiment encode accession: ENCSR432LIX
assay title: PAS-seq
assembly: mm10
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB469YPD

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

value: left cerebral cortex

value: tissue

value: Cortex from 6 mo C57BL/6 male

value: MODEL-AD

value: ENCBS913WLS at ENCODE; https://www.encodeproject.org/ENCBS913WLS/


title: total RNA-seq from A549 (ENCLB652QLY)

description:
https://www.encodeproject.org/experiments/ENCSR018YHY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR018YHY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB652QLY
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM CORT108297 (agonist) for 4 hours

value: cell line

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_name:CORT108297; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS679VZQ at ENCODE; https://www.encodeproject.org/ENCBS679VZQ/

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


title: polyA plus RNA-seq from layer of hippocampus (ENCLB626JBH)

description:
https://www.encodeproject.org/experiments/ENCSR898LNL/
***************
biological replicate number: 2
technical replicate number: 1
description: Hippocampus from 6 mo C57BL/6 male
experiment encode accession: ENCSR898LNL
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2021-11-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB626JBH
fragmentation methods: chemical (Nextera tagmentation)
size range: <200
nucleic acid starting quantity: 20
nucleic acid starting quantity units: ng

value: layer of hippocampus

value: Hippocampus from 6 mo C57BL/6 male

value: Mus musculus

value: not collected

value: adult

value: 6 month

value: Ali Mortazavi, UCI

value: Andrea Tenner

value: ENCBS864FVU at ENCODE; https://www.encodeproject.org/ENCBS864FVU/

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


title: microRNA-seq from myotube (ENCLB122WRU)

description:
https://www.encodeproject.org/experiments/ENCSR312YTR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation C2C12 differentiated for 72 hours microRNA-seq from Mortazavi
experiment encode accession: ENCSR312YTR
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB122WRU
size range: <30

source_name: Mus musculus myotube in vitro differentiated cells

value: myotube

value: in vitro differentiated cells

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury; differentiated from C2C12 cells for 72 hours

value: unknown

value: ENCBS102KBH at ENCODE; https://www.encodeproject.org/ENCBS102KBH/

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


title: total RNA-seq from A549 (ENCLB763OPY)

description:
https://www.encodeproject.org/experiments/ENCSR522CJR/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR522CJR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB763OPY
size range: 200-300

value: cell line

value: Homo sapiens

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:17650; treatment_term_name:Hydrocortisone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS773MQM at ENCODE; https://www.encodeproject.org/ENCBS773MQM/

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


title: total RNA-seq from A549 (ENCLB814KSU)

description:
https://www.encodeproject.org/experiments/ENCSR018YHY/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR018YHY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB814KSU
size range: 200-300

value: adult

value: treatment_term_name:CORT108297; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS695AYB at ENCODE; https://www.encodeproject.org/ENCBS695AYB/


title: total RNA-seq from A549 (ENCLB146XWJ)

description:
https://www.encodeproject.org/experiments/ENCSR522CJR/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR522CJR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB146XWJ
size range: 200-300

value: ENCBS111RUU at ENCODE; https://www.encodeproject.org/ENCBS111RUU/


title: total RNA-seq from A549 (ENCLB824WXP)

description:
https://www.encodeproject.org/experiments/ENCSR018YHY/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR018YHY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB824WXP
size range: 200-300

value: ENCBS114TMY at ENCODE; https://www.encodeproject.org/ENCBS114TMY/


title: microRNA-seq from myotube (ENCLB891UHM)

description:
https://www.encodeproject.org/experiments/ENCSR312YTR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation C2C12 differentiated for 72 hours microRNA-seq from Mortazavi
experiment encode accession: ENCSR312YTR
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB891UHM
size range: <30

value: myotube

value: in vitro differentiated cells

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury; differentiated from C2C12 cells for 72 hours

value: Mus musculus

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ENCBS249UFI at ENCODE; https://www.encodeproject.org/ENCBS249UFI/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB093XCH)

description:
https://www.encodeproject.org/experiments/ENCSR941MHZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR941MHZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB093XCH

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interferon alpha-2 for 1 hour

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: 39 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P01563; treatment_term_name:Interferon alpha-2; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS110WWY at ENCODE; https://www.encodeproject.org/ENCBS110WWY/

value: Derived from ENCODE donor ENCDO222BBW; https://www.encodeproject.org/ENCDO222BBW/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB485NUZ)

description:
https://www.encodeproject.org/experiments/ENCSR566XSD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR566XSD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB485NUZ

source_name: Homo sapiens female adult (26 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-1 beta for 1 hour

value: adult

value: 26 year

value: treatment_term_id:UniProtKB:P01584; treatment_term_name:Interleukin-1 beta; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS777VKG at ENCODE; https://www.encodeproject.org/ENCBS777VKG/

value: Derived from ENCODE donor ENCDO134JGU; https://www.encodeproject.org/ENCDO134JGU/


title: CRISPR RNA-seq from K562 (ENCLB903PYV)

description:
https://www.encodeproject.org/experiments/ENCSR519LZD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM28. (RBM28-BGKcLV30)
experiment encode accession: ENCSR519LZD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB903PYV
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 RBM28

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e7e69eea-8bd1-4477-b84f-4fc442e40bae/@@download/attachment/L-RBM28-BGKcLV30-17.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM28. (RBM28-BGKcLV30-17)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS539OCN at ENCODE; https://www.encodeproject.org/ENCBS539OCN/

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


title: total RNA-seq from A549 (ENCLB671EFF)

description:
https://www.encodeproject.org/experiments/ENCSR018YHY/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR018YHY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB671EFF
size range: 200-300

value: male

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_name:CORT108297; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS680RXP at ENCODE; https://www.encodeproject.org/ENCBS680RXP/

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB589TWJ)

description:
https://www.encodeproject.org/experiments/ENCSR483PGP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR483PGP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB589TWJ

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-4 for 1 hour

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 39 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS718CKJ at ENCODE; https://www.encodeproject.org/ENCBS718CKJ/

value: Derived from ENCODE donor ENCDO222BBW; https://www.encodeproject.org/ENCDO222BBW/


title: total RNA-seq from K562 (ENCLB691UWQ)

description:
https://www.encodeproject.org/experiments/ENCSR015SAT/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Crizotinib for 48 hours
experiment encode accession: ENCSR015SAT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB691UWQ
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 uM Crizotinib for 48 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:Crizotinib; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS427YHC at ENCODE; https://www.encodeproject.org/ENCBS427YHC/

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