title: microRNA-seq from left cerebral cortex (ENCLB606DMX)

description:
https://www.encodeproject.org/experiments/ENCSR020XUQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND14 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR020XUQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB606DMX
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (14 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND14 3x Males 03 left cerebral cortex for Wold biobank

value: male

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS993UDC at ENCODE; https://www.encodeproject.org/ENCBS993UDC/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from heart (ENCLB455AUP)

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/ENCSR523CTA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR523CTA
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB455AUP
size range: <30

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain 5xFAD/CAST male adult (8-10 months) heart tissue

value: heart

tag: biosample encode accession

tag: organism

value: Mus musculus

tag: Sex

tag: dev stage

value: adult

tag: age

value: 8-10 month

tag: lab

tag: source

tag: link

value: ENCBS391BLT at ENCODE; https://www.encodeproject.org/ENCBS391BLT/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: CRISPR RNA-seq from HepG2 (ENCLB766WPP)

description:
https://www.encodeproject.org/experiments/ENCSR256UIA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DBNL. (DBNL-BGHcLV29)
experiment encode accession: ENCSR256UIA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB766WPP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

organism: Homo sapiens

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a58e14cf-8f51-4f88-9a32-c8f1b3df3f2d/@@download/attachment/L-DBNL-BGHcLV29-59.pdf

tag: antibody

value: DBNL

tag: line

value: cell line

tag: description

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DBNL. (DBNL-BGHcLV29-59)

value: Homo sapiens

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS811ACC at ENCODE; https://www.encodeproject.org/ENCBS811ACC/

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


title: total RNA-seq from K562 (ENCLB232LKY)

description:
https://www.encodeproject.org/experiments/ENCSR689NPY/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with AR-42 for 24 hours
experiment encode accession: ENCSR689NPY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB232LKY
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 uM AR-42 for 24 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

tag: treatments

value: treatment_term_name:AR-42; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS096ZMQ at ENCODE; https://www.encodeproject.org/ENCBS096ZMQ/

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


title: microRNA-seq from left cerebral cortex (ENCLB927FOO)

description:
https://www.encodeproject.org/experiments/ENCSR020XUQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND14 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR020XUQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB927FOO
size range: <30

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND14 3x Males 04 left cerebral cortex for Wold biobank

value: male

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS233WUB at ENCODE; https://www.encodeproject.org/ENCBS233WUB/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from left cerebral cortex (ENCLB659CSH)

description:
https://www.encodeproject.org/experiments/ENCSR013XSN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR013XSN
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB659CSH
size range: <30

source_name: Mus musculus strain 5xFAD/CAST male adult (8-10 months) left cerebral cortex tissue

value: Mus musculus

value: adult

value: 8-10 month

value: ENCBS264WGP at ENCODE; https://www.encodeproject.org/ENCBS264WGP/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: total RNA-seq from K562 (ENCLB882VMI)

description:
https://www.encodeproject.org/experiments/ENCSR689NPY/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with AR-42 for 24 hours
experiment encode accession: ENCSR689NPY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB882VMI
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:AR-42; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS005GZJ at ENCODE; https://www.encodeproject.org/ENCBS005GZJ/


title: CRISPR RNA-seq from K562 (ENCLB747WRZ)

description:
https://www.encodeproject.org/experiments/ENCSR262ZBE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RIOK2. (RIOK2-BGKcLV30)
experiment encode accession: ENCSR262ZBE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB747WRZ
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 RIOK2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b1fa8e76-1166-4e8e-ac7f-b36faa74ed45/@@download/attachment/L-RIOK2-BGKcLV30-35.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RIOK2. (RIOK2-BGKcLV30-35)

value: Brenton Graveley, UConn

value: ENCBS262WNW at ENCODE; https://www.encodeproject.org/ENCBS262WNW/

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


title: microRNA-seq from left cerebral cortex (ENCLB066MSD)

description:
https://www.encodeproject.org/experiments/ENCSR013XSN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR013XSN
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB066MSD
size range: <30

value: left cerebral cortex

value: tissue

value: Mus musculus

value: male

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS328ZHX at ENCODE; https://www.encodeproject.org/ENCBS328ZHX/


title: microRNA-seq from F121-9 (ENCLB696JRY)

description:
https://www.encodeproject.org/experiments/ENCSR012KGU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation Cast ES cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR012KGU
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB696JRY
size range: <30

source_name: Mus musculus F121-9 cell line

value: cell line

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

value: not collected

value: unknown

value: David Gilbert

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

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


title: CRISPR RNA-seq from K562 (ENCLB637YEK)

description:
https://www.encodeproject.org/experiments/ENCSR688ZJS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT2. (CCT2-BGKcLV28)
experiment encode accession: ENCSR688ZJS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB637YEK
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 CCT2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5cd922ae-4cca-49f7-b991-acd949045a6f/@@download/attachment/L-CCT2-BGKcLV28-4.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT2. (CCT2-BGKcLV28-4)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS663RQN at ENCODE; https://www.encodeproject.org/ENCBS663RQN/

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


title: CRISPR RNA-seq from HepG2 (ENCLB886XUK)

description:
https://www.encodeproject.org/experiments/ENCSR251SXS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACO2. (ACO2-BGHcLV25)
experiment encode accession: ENCSR251SXS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB886XUK
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 ACO2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f8d7fc33-56d4-45e0-970d-4e6bc0a04d5c/@@download/attachment/L-ACO2-BGHcLV25-3.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACO2. (ACO2-BGHcLV25-3)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS720JSN at ENCODE; https://www.encodeproject.org/ENCBS720JSN/

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


title: CRISPR RNA-seq from K562 (ENCLB656CKD)

description:
https://www.encodeproject.org/experiments/ENCSR251LKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CSNK1E. (CSNK1E-BGKcLV28)
experiment encode accession: ENCSR251LKQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB656CKD
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 CSNK1E

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/06239ce6-52d2-404d-b584-624b892f7df0/@@download/attachment/L-CSNK1E-BGKcLV28-46.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CSNK1E. (CSNK1E-BGKcLV28-46)

value: adult

value: ENCBS394PBH at ENCODE; https://www.encodeproject.org/ENCBS394PBH/


title: microRNA-seq from middle frontal area 46 (ENCLB008ACT)

description:
https://www.encodeproject.org/experiments/ENCSR719PHY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR719PHY
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB008ACT
size range: <30

source_name: Homo sapiens female adult (82 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: 82 year

value: Barbara Wold, Caltech

value: Rush University

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 (ENCLB668VDO)

description:
https://www.encodeproject.org/experiments/ENCSR251LKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CSNK1E. (CSNK1E-BGKcLV28)
experiment encode accession: ENCSR251LKQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB668VDO
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/a8d09a11-a25e-4cfd-a573-94d1e9efea91/@@download/attachment/L-CSNK1E-BGKcLV28-45.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CSNK1E. (CSNK1E-BGKcLV28-45)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS140SWH at ENCODE; https://www.encodeproject.org/ENCBS140SWH/

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


title: microRNA-seq from heart (ENCLB886GHT)

description:
https://www.encodeproject.org/experiments/ENCSR523CTA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR523CTA
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB886GHT
size range: <30

value: heart

value: Mus musculus

value: male

value: adult

value: 8-10 month

value: The Jackson Laboratory

value: ENCBS657KFM at ENCODE; https://www.encodeproject.org/ENCBS657KFM/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: BruChase-seq from mammary epithelial cell (ENCLB290JZM)

description:
https://www.encodeproject.org/experiments/ENCSR677JOI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR677JOI
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR419IWZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB290JZM
size range: 400-500

source_name: Homo sapiens female adult (19 years) mammary epithelial primary cell, subjected to a 2 hour pulse-chase

value: mammary epithelial cell

value: primary cell

value: Homo sapiens

value: female

value: 19 year

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS634GPK at ENCODE; https://www.encodeproject.org/ENCBS634GPK/

value: Derived from ENCODE donor ENCDO955XOD; https://www.encodeproject.org/ENCDO955XOD/


title: BruChase-seq from mammary epithelial cell (ENCLB458IAB)

description:
https://www.encodeproject.org/experiments/ENCSR677JOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR677JOI
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR419IWZ
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB458IAB
size range: 400-500

value: ENCBS508PAK at ENCODE; https://www.encodeproject.org/ENCBS508PAK/


title: CRISPR RNA-seq from HepG2 (ENCLB201PIV)

description:
https://www.encodeproject.org/experiments/ENCSR251SXS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACO2. (ACO2-BGHcLV25)
experiment encode accession: ENCSR251SXS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB201PIV
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/a7afb364-87ba-4a4c-a678-8583ff013018/@@download/attachment/L-ACO2-BGHcLV25-4.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACO2. (ACO2-BGHcLV25-4)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS478QMB at ENCODE; https://www.encodeproject.org/ENCBS478QMB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB908SOL)

description:
https://www.encodeproject.org/experiments/ENCSR250QFO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF1. (ARHGEF1-BGHcLV27)
experiment encode accession: ENCSR250QFO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB908SOL
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 ARHGEF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/31671bbf-fd80-4d0d-83eb-e33bf4ac9ed4/@@download/attachment/L-ARHGEF1-BGHcLV27-13.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF1. (ARHGEF1-BGHcLV27-13)

value: Homo sapiens

value: male

value: ENCBS841VVB at ENCODE; https://www.encodeproject.org/ENCBS841VVB/


title: CRISPR RNA-seq from HepG2 (ENCLB104ZKE)

description:
https://www.encodeproject.org/experiments/ENCSR250QFO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF1. (ARHGEF1-BGHcLV27)
experiment encode accession: ENCSR250QFO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB104ZKE
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/2ed52e90-4080-47f9-a0c9-89ca7644ff29/@@download/attachment/L-ARHGEF1-BGHcLV27-14.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF1. (ARHGEF1-BGHcLV27-14)

value: ENCBS368CDS at ENCODE; https://www.encodeproject.org/ENCBS368CDS/


title: total RNA-seq from middle frontal area 46 (ENCLB454AKI)

description:
https://www.encodeproject.org/experiments/ENCSR292TYT/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_6341028_BS46_ENC4_cDNA656
experiment encode accession: ENCSR292TYT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB454AKI
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: female

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS660AUE at ENCODE; https://www.encodeproject.org/ENCBS660AUE/

value: Derived from ENCODE donor ENCDO223NTQ; https://www.encodeproject.org/ENCDO223NTQ/


title: CRISPR RNA-seq from HepG2 (ENCLB816QOS)

description:
https://www.encodeproject.org/experiments/ENCSR248WTR/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV29-B)
experiment encode accession: ENCSR248WTR
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB816QOS
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e0566724-fe00-40e0-92a5-f5df965e0920/@@download/attachment/L-NT-BGHcLV29-2B.pdf

value: cell line

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV29-2)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS692PXQ at ENCODE; https://www.encodeproject.org/ENCBS692PXQ/


title: microRNA-seq from WTC11 (ENCLB224ZCN)

description:
https://www.encodeproject.org/experiments/ENCSR291HNO/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation human WTC11 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR291HNO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB224ZCN
size range: <30

source_name: Homo sapiens WTC11 cell line

value: Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal

value: male

value: 30 year

value: Yiing Lin, MD, PhD

tag: passage number

value: ENCBS474NOC at ENCODE; https://www.encodeproject.org/ENCBS474NOC/

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


title: microRNA-seq from WTC11 (ENCLB403RVN)

description:
https://www.encodeproject.org/experiments/ENCSR291HNO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human WTC11 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR291HNO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB403RVN
size range: <30

value: adult

value: Barbara Wold, Caltech

value: ENCBS944CBA at ENCODE; https://www.encodeproject.org/ENCBS944CBA/


title: microRNA-seq from WTC11 (ENCLB072PYO)

description:
https://www.encodeproject.org/experiments/ENCSR291HNO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human WTC11 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR291HNO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB072PYO
size range: <30

value: cell line

value: ENCBS593PKA at ENCODE; https://www.encodeproject.org/ENCBS593PKA/


title: CRISPR RNA-seq from HepG2 (ENCLB997LJN)

description:
https://www.encodeproject.org/experiments/ENCSR248WTR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV29-B)
experiment encode accession: ENCSR248WTR
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB997LJN
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/0b5cb811-13bf-4f78-b755-1b07e042e3fe/@@download/attachment/L-NT-BGHcLV29-1B.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV29-1)

value: Homo sapiens

value: hepatocellular carcinoma

value: ENCBS125VHW at ENCODE; https://www.encodeproject.org/ENCBS125VHW/

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


title: total RNA-seq from middle frontal area 46 (ENCLB569VCZ)

description:
https://www.encodeproject.org/experiments/ENCSR290IHM/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_5194210_BS19_ENC4_cDNA654
experiment encode accession: ENCSR290IHM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB569VCZ
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 (79 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 79 year

value: Rush University

value: ENCBS411JUI at ENCODE; https://www.encodeproject.org/ENCBS411JUI/

value: Derived from ENCODE donor ENCDO609ZOG; https://www.encodeproject.org/ENCDO609ZOG/


title: microRNA-seq from middle frontal area 46 (ENCLB289IXL)

description:
https://www.encodeproject.org/experiments/ENCSR277ECT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR277ECT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB289IXL
size range: <30

source_name: Homo sapiens female adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: adult

value: 90 or above year

value: ENCBS997UQN at ENCODE; https://www.encodeproject.org/ENCBS997UQN/

value: Derived from ENCODE donor ENCDO746DTM; https://www.encodeproject.org/ENCDO746DTM/


title: CRISPR RNA-seq from K562 (ENCLB274BFN)

description:
https://www.encodeproject.org/experiments/ENCSR688ZJS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT2. (CCT2-BGKcLV28)
experiment encode accession: ENCSR688ZJS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB274BFN
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/5b866a9d-970b-4ab4-807b-a91f465aeebe/@@download/attachment/L-CCT2-BGKcLV28-3.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT2. (CCT2-BGKcLV28-3)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS492BTH at ENCODE; https://www.encodeproject.org/ENCBS492BTH/

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


title: BruChase-seq from Caco-2 (ENCLB148RYM)

description:
https://www.encodeproject.org/experiments/ENCSR245MXB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR245MXB
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR892NYB
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB148RYM
size range: 400-500

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

value: Homo sapiens

value: male

value: colorectal adenocarcinoma

value: 72 year

value: Mats Ljungman, UMichigan

value: ENCBS530WHW at ENCODE; https://www.encodeproject.org/ENCBS530WHW/

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


title: BruChase-seq from Caco-2 (ENCLB882VET)

description:
https://www.encodeproject.org/experiments/ENCSR245MXB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR245MXB
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR892NYB
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB882VET
size range: 400-500

value: adult

value: ENCBS590OGF at ENCODE; https://www.encodeproject.org/ENCBS590OGF/


title: microRNA-seq from middle frontal area 46 (ENCLB708YFK)

description:
https://www.encodeproject.org/experiments/ENCSR988ILZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR988ILZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB708YFK
size range: <30

value: middle frontal area 46

value: tissue

value: female

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 K562 (ENCLB774MRQ)

description:
https://www.encodeproject.org/experiments/ENCSR672NDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Chaetocin for 12 hours
experiment encode accession: ENCSR672NDZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB774MRQ
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 nM Chaetocin for 12 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:Chaetocin; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS323KDI at ENCODE; https://www.encodeproject.org/ENCBS323KDI/

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


title: CRISPR RNA-seq from HepG2 (ENCLB127EOR)

description:
https://www.encodeproject.org/experiments/ENCSR244OOV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CMTR1. (CMTR1-BGHcLV29)
experiment encode accession: ENCSR244OOV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB127EOR
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 CMTR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5dcb83df-7bbc-4529-8307-64f4b0dfc8f2/@@download/attachment/L-CMTR1-BGHcLV29-25.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CMTR1. (CMTR1-BGHcLV29-25)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS662RQC at ENCODE; https://www.encodeproject.org/ENCBS662RQC/

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


title: total RNA-seq from middle frontal area 46 (ENCLB601RDI)

description:
https://www.encodeproject.org/experiments/ENCSR275JSL/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_1764669_BS90_ENC4_cDNA667
experiment encode accession: ENCSR275JSL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB601RDI
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 (73 years) with Alzheimer's disease, Cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: adult

value: 73 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS542OFI at ENCODE; https://www.encodeproject.org/ENCBS542OFI/

value: Derived from ENCODE donor ENCDO059BOC; https://www.encodeproject.org/ENCDO059BOC/


title: microRNA-seq from A673 (ENCLB718YND)

description:
https://www.encodeproject.org/experiments/ENCSR982DED/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human A673 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR982DED
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB718YND
size range: <30

source_name: Homo sapiens A673 cell line

value: cell line

value: female

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS119CST at ENCODE; https://www.encodeproject.org/ENCBS119CST/

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


title: microRNA-seq from middle frontal area 46 (ENCLB192LZI)

description:
https://www.encodeproject.org/experiments/ENCSR975PQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR975PQJ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB192LZI
size range: <30

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

value: Homo sapiens

value: 83 year

value: ENCBS168FVU at ENCODE; https://www.encodeproject.org/ENCBS168FVU/

value: Derived from ENCODE donor ENCDO448ZXP; https://www.encodeproject.org/ENCDO448ZXP/


title: microRNA-seq from A673 (ENCLB579RKV)

description:
https://www.encodeproject.org/experiments/ENCSR982DED/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human A673 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR982DED
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB579RKV
size range: <30

value: child

value: 15 year

value: ENCBS060KJN at ENCODE; https://www.encodeproject.org/ENCBS060KJN/


title: CRISPR RNA-seq from HepG2 (ENCLB604IRA)

description:
https://www.encodeproject.org/experiments/ENCSR244OOV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CMTR1. (CMTR1-BGHcLV29)
experiment encode accession: ENCSR244OOV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB604IRA
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/30c3932b-0367-4332-88c5-b78885fb2b1f/@@download/attachment/L-CMTR1-BGHcLV29-26.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CMTR1. (CMTR1-BGHcLV29-26)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS154QKL at ENCODE; https://www.encodeproject.org/ENCBS154QKL/

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


title: microRNA-seq from Calu3 (ENCLB847MHO)

description:
https://www.encodeproject.org/experiments/ENCSR934NMC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human Calu-3 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR934NMC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB847MHO
size range: <30

source_name: Homo sapiens Calu3 cell line

value: cell line

value: Lung adenocarcinoma

value: adult

value: 25 year

value: Mats Ljungman, UMichigan

value: ENCBS806IYJ at ENCODE; https://www.encodeproject.org/ENCBS806IYJ/

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


title: total RNA-seq from middle frontal area 46 (ENCLB354WVS)

description:
https://www.encodeproject.org/experiments/ENCSR949UTT/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_8282759_BS106_ENC4_cDNA660
experiment encode accession: ENCSR949UTT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB354WVS
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 (83 years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: 83 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS431HLD at ENCODE; https://www.encodeproject.org/ENCBS431HLD/

value: Derived from ENCODE donor ENCDO832DBZ; https://www.encodeproject.org/ENCDO832DBZ/


title: BruChase-seq from Caco-2 (ENCLB725XYY)

description:
https://www.encodeproject.org/experiments/ENCSR672HUM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR672HUM
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR892NYB
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB725XYY
size range: 400-500

source_name: Homo sapiens Caco-2 cell line, subjected to a 6 hour pulse-chase

value: male

value: colorectal adenocarcinoma

value: 72 year

value: ATCC

value: ENCBS705JBM at ENCODE; https://www.encodeproject.org/ENCBS705JBM/

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


title: microRNA-seq from Calu3 (ENCLB794ESJ)

description:
https://www.encodeproject.org/experiments/ENCSR934NMC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Calu-3 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR934NMC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB794ESJ
size range: <30

value: cell line

value: Lung adenocarcinoma

value: adult

value: 25 year

value: Mats Ljungman, UMichigan

value: ENCBS961BBX at ENCODE; https://www.encodeproject.org/ENCBS961BBX/


title: CRISPR RNA-seq from HepG2 (ENCLB584JCE)

description:
https://www.encodeproject.org/experiments/ENCSR671FDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV24)
experiment encode accession: ENCSR671FDZ
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB584JCE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/abd80227-b47c-47ea-ad0e-0eece24fd9b8/@@download/attachment/L-NT-BGHcLV24-1.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV24-1)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS044WRF at ENCODE; https://www.encodeproject.org/ENCBS044WRF/

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


title: BruChase-seq from Caco-2 (ENCLB951UEO)

description:
https://www.encodeproject.org/experiments/ENCSR672HUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR672HUM
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR892NYB
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB951UEO
size range: 400-500

value: male

value: colorectal adenocarcinoma

value: 72 year

value: ATCC

value: ENCBS112LRL at ENCODE; https://www.encodeproject.org/ENCBS112LRL/


title: total RNA-seq from K562 (ENCLB673PEP)

description:
https://www.encodeproject.org/experiments/ENCSR672NDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Chaetocin for 12 hours
experiment encode accession: ENCSR672NDZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB673PEP
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

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

value: ENCBS759VCT at ENCODE; https://www.encodeproject.org/ENCBS759VCT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB543YEF)

description:
https://www.encodeproject.org/experiments/ENCSR671FDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV24)
experiment encode accession: ENCSR671FDZ
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB543YEF
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/b9b41ad4-8554-4bbc-b1ed-4fc9df810111/@@download/attachment/L-NT-BGHcLV24-2.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV24-2)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS835XBG at ENCODE; https://www.encodeproject.org/ENCBS835XBG/


title: CRISPR RNA-seq from HepG2 (ENCLB034HDS)

description:
https://www.encodeproject.org/experiments/ENCSR235JSA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGHcLV31)
experiment encode accession: ENCSR235JSA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB034HDS
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 RPUSD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2d1218e5-2df1-4f3c-b79c-cf94e63fcf7b/@@download/attachment/L-RPUSD2-BGHcLV31-14.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGHcLV31-14)

value: male

value: ATCC

value: ENCBS711EJM at ENCODE; https://www.encodeproject.org/ENCBS711EJM/

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


title: CRISPR RNA-seq from HepG2 (ENCLB529HTX)

description:
https://www.encodeproject.org/experiments/ENCSR235JSA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGHcLV31)
experiment encode accession: ENCSR235JSA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB529HTX
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/13bcee06-0779-4cbe-bbc8-28c998602be7/@@download/attachment/L-RPUSD2-BGHcLV31-13.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGHcLV31-13)

value: ENCBS417HWB at ENCODE; https://www.encodeproject.org/ENCBS417HWB/


title: microRNA-seq from middle frontal area 46 (ENCLB113QWC)

description:
https://www.encodeproject.org/experiments/ENCSR895MKD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR895MKD
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB113QWC
size range: <30

source_name: Homo sapiens male adult (87 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: adult

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS666KAY at ENCODE; https://www.encodeproject.org/ENCBS666KAY/

value: Derived from ENCODE donor ENCDO203ASI; https://www.encodeproject.org/ENCDO203ASI/


title: total RNA-seq from A549 (ENCLB172MPH)

description:
https://www.encodeproject.org/experiments/ENCSR234WEZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR234WEZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB172MPH
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM Mapracorat (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: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:177650; treatment_term_name:Mapracorat; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS151HDI at ENCODE; https://www.encodeproject.org/ENCBS151HDI/

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


title: microRNA-seq from middle frontal area 46 (ENCLB842DQA)

description:
https://www.encodeproject.org/experiments/ENCSR461TSM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR461TSM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB842DQA
size range: <30

value: female

value: 79 year

value: ENCBS411JUI at ENCODE; https://www.encodeproject.org/ENCBS411JUI/

value: Derived from ENCODE donor ENCDO609ZOG; https://www.encodeproject.org/ENCDO609ZOG/


title: microRNA-seq from middle frontal area 46 (ENCLB516WGP)

description:
https://www.encodeproject.org/experiments/ENCSR897QAH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR897QAH
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB516WGP
size range: <30

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: ENCBS308QTA at ENCODE; https://www.encodeproject.org/ENCBS308QTA/

value: Derived from ENCODE donor ENCDO651VQQ; https://www.encodeproject.org/ENCDO651VQQ/


title: microRNA-seq from middle frontal area 46 (ENCLB147CUI)

description:
https://www.encodeproject.org/experiments/ENCSR918HAI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR918HAI
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB147CUI
size range: <30

value: adult

value: 83 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS431HLD at ENCODE; https://www.encodeproject.org/ENCBS431HLD/

value: Derived from ENCODE donor ENCDO832DBZ; https://www.encodeproject.org/ENCDO832DBZ/


title: total RNA-seq from A549 (ENCLB459HSX)

description:
https://www.encodeproject.org/experiments/ENCSR234WEZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR234WEZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB459HSX
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:177650; treatment_term_name:Mapracorat; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS115RPO at ENCODE; https://www.encodeproject.org/ENCBS115RPO/


title: total RNA-seq from A549 (ENCLB393VDF)

description:
https://www.encodeproject.org/experiments/ENCSR234WEZ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR234WEZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB393VDF
size range: 200-300

value: ENCBS563NAX at ENCODE; https://www.encodeproject.org/ENCBS563NAX/

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


title: total RNA-seq from middle frontal area 46 (ENCLB945FYX)

description:
https://www.encodeproject.org/experiments/ENCSR875MVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_4368365_BS62_ENC4_cDNA651
experiment encode accession: ENCSR875MVZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB945FYX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: ENCBS644WSW at ENCODE; https://www.encodeproject.org/ENCBS644WSW/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: total RNA-seq from A549 (ENCLB319OFO)

description:
https://www.encodeproject.org/experiments/ENCSR234WEZ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR234WEZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB319OFO
size range: 200-300

value: adult

value: ENCBS525YTW at ENCODE; https://www.encodeproject.org/ENCBS525YTW/


title: microRNA-seq from middle frontal area 46 (ENCLB587YKV)

description:
https://www.encodeproject.org/experiments/ENCSR854EBO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR854EBO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB587YKV
size range: <30

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: female

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS819UHF at ENCODE; https://www.encodeproject.org/ENCBS819UHF/

value: Derived from ENCODE donor ENCDO250PFZ; https://www.encodeproject.org/ENCDO250PFZ/


title: microRNA-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB028QOH)

description:
https://www.encodeproject.org/experiments/ENCSR965INY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human memory CD8+ T cell (activated day 7) microRNA-seq from Mortazavi
experiment encode accession: ENCSR965INY
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB028QOH
size range: <30

source_name: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell

value: primary cell

value: Memory CD8+ cell, activated Day 7

value: male

value: 30 year

value: AllCells

value: ENCBS015SJV at ENCODE; https://www.encodeproject.org/ENCBS015SJV/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: microRNA-seq from middle frontal area 46 (ENCLB392UQT)

description:
https://www.encodeproject.org/experiments/ENCSR428BYN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR428BYN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB392UQT
size range: <30

source_name: Homo sapiens female adult (85 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 85 year

value: ENCBS166GKO at ENCODE; https://www.encodeproject.org/ENCBS166GKO/

value: Derived from ENCODE donor ENCDO741DAO; https://www.encodeproject.org/ENCDO741DAO/


title: CRISPR RNA-seq from K562 (ENCLB528YBR)

description:
https://www.encodeproject.org/experiments/ENCSR667JRK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CAT. (CAT-BGKcLV26)
experiment encode accession: ENCSR667JRK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB528YBR
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 CAT

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/994de923-08c1-46cf-97fe-d55f19b73842/@@download/attachment/L-CAT-BGKcLV26-61.pdf

value: CAT

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CAT. (CAT-BGKcLV26-61)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS137FIF at ENCODE; https://www.encodeproject.org/ENCBS137FIF/

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


title: microRNA-seq from middle frontal area 46 (ENCLB448FLF)

description:
https://www.encodeproject.org/experiments/ENCSR456UAR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR456UAR
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB448FLF
size range: <30

source_name: Homo sapiens female adult (89 years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: 89 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS675FWG at ENCODE; https://www.encodeproject.org/ENCBS675FWG/

value: Derived from ENCODE donor ENCDO843TIL; https://www.encodeproject.org/ENCDO843TIL/


title: microRNA-seq from middle frontal area 46 (ENCLB989GXR)

description:
https://www.encodeproject.org/experiments/ENCSR424JNK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR424JNK
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB989GXR
size range: <30

source_name: Homo sapiens male adult (85 years) middle frontal area 46 tissue

value: tissue

value: Homo sapiens

value: male

value: 85 year

value: ENCBS634VGA at ENCODE; https://www.encodeproject.org/ENCBS634VGA/

value: Derived from ENCODE donor ENCDO953KHI; https://www.encodeproject.org/ENCDO953KHI/


title: microRNA-seq from activated CD8-positive, alpha-beta T cell (ENCLB550LYG)

description:
https://www.encodeproject.org/experiments/ENCSR828OKX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human CD8+ T cells (activated day 2) microRNA-seq from Mortazavi
experiment encode accession: ENCSR828OKX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB550LYG
size range: <30

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS520WQB at ENCODE; https://www.encodeproject.org/ENCBS520WQB/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: CRISPR RNA-seq from K562 (ENCLB825DEN)

description:
https://www.encodeproject.org/experiments/ENCSR667JRK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CAT. (CAT-BGKcLV26)
experiment encode accession: ENCSR667JRK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB825DEN
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/c5ad3c76-8be7-48f0-ae85-c9496d2e2328/@@download/attachment/L-CAT-BGKcLV26-62.pdf

value: CAT

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CAT. (CAT-BGKcLV26-62)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS456UIQ at ENCODE; https://www.encodeproject.org/ENCBS456UIQ/

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


title: Bru-seq from HCT116 (ENCLB407OIH)

description:
https://www.encodeproject.org/experiments/ENCSR664LAL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR664LAL
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB407OIH
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 CTCF

value: Homo sapiens

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS014WRU at ENCODE; https://www.encodeproject.org/ENCBS014WRU/

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


title: microRNA-seq from activated CD8-positive, alpha-beta T cell (ENCLB384XBZ)

description:
https://www.encodeproject.org/experiments/ENCSR828OKX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human CD8+ T cells (activated day 2) microRNA-seq from Mortazavi
experiment encode accession: ENCSR828OKX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB384XBZ
size range: <30

value: primary cell

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS223BQO at ENCODE; https://www.encodeproject.org/ENCBS223BQO/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: CRISPR RNA-seq from HepG2 (ENCLB528CKU)

description:
https://www.encodeproject.org/experiments/ENCSR234UAM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGHcLV29-B)
experiment encode accession: ENCSR234UAM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR248WTR
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB528CKU
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 ATXN2L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2e515d5c-157b-475a-92bb-eb0bfe671cba/@@download/attachment/L-ATXN2L-BGHcLV29-12B.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGHcLV29-12B)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS238XWI at ENCODE; https://www.encodeproject.org/ENCBS238XWI/

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


title: microRNA-seq from middle frontal area 46 (ENCLB857NXR)

description:
https://www.encodeproject.org/experiments/ENCSR411PXI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR411PXI
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB857NXR
size range: <30

source_name: Homo sapiens male adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: male

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

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

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


title: total RNA-seq from middle frontal area 46 (ENCLB465PLC)

description:
https://www.encodeproject.org/experiments/ENCSR395DKP/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_7204277_BS116_ENC4_cDNA666
experiment encode accession: ENCSR395DKP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB465PLC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: 87 year

value: ENCBS709FQH at ENCODE; https://www.encodeproject.org/ENCBS709FQH/

value: Derived from ENCODE donor ENCDO203ASI; https://www.encodeproject.org/ENCDO203ASI/


title: total RNA-seq from middle frontal area 46 (ENCLB567VCK)

description:
https://www.encodeproject.org/experiments/ENCSR863VFU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_5115600_BS16_ENC4_cDNA653
experiment encode accession: ENCSR863VFU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB567VCK
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) middle frontal area 46 tissue

value: female

value: 88 year

value: ENCBS105DDE at ENCODE; https://www.encodeproject.org/ENCBS105DDE/

value: Derived from ENCODE donor ENCDO669IVL; https://www.encodeproject.org/ENCDO669IVL/


title: total RNA-seq from middle frontal area 46 (ENCLB104LSA)

description:
https://www.encodeproject.org/experiments/ENCSR394ZSF/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_7204277_BS105_ENC4_cDNA659
experiment encode accession: ENCSR394ZSF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB104LSA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: ENCBS666KAY at ENCODE; https://www.encodeproject.org/ENCBS666KAY/


title: total RNA-seq from A549 (ENCLB926FOA)

description:
https://www.encodeproject.org/experiments/ENCSR234WEZ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR234WEZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB926FOA
size range: 200-300

value: cell line

value: Homo sapiens

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:177650; treatment_term_name:Mapracorat; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS927GRP at ENCODE; https://www.encodeproject.org/ENCBS927GRP/

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


title: CRISPR RNA-seq from K562 (ENCLB611BNQ)

description:
https://www.encodeproject.org/experiments/ENCSR233MJI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGKcLV26)
experiment encode accession: ENCSR233MJI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB611BNQ
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 ARHGEF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6d4f58dc-bb15-48de-bda3-3d1876e17838/@@download/attachment/L-ARHGEF2-BGKcLV26-32.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGKcLV26-32)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS098LQT at ENCODE; https://www.encodeproject.org/ENCBS098LQT/

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


title: microRNA-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB635QAK)

description:
https://www.encodeproject.org/experiments/ENCSR384ONW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human memory CD4+ T cells (activated day 2) microRNA-seq from Mortazavi
experiment encode accession: ENCSR384ONW
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB635QAK
size range: <30

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell

value: primary cell

value: Memory CD4+ T cell, activated Day 2

value: male

value: 43 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS655INE at ENCODE; https://www.encodeproject.org/ENCBS655INE/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: CRISPR RNA-seq from HepG2 (ENCLB053HTH)

description:
https://www.encodeproject.org/experiments/ENCSR234UAM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGHcLV29-B)
experiment encode accession: ENCSR234UAM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR248WTR
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB053HTH
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/52354c74-e70c-4194-b34e-2ac6611be4dc/@@download/attachment/L-ATXN2L-BGHcLV29-11B.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGHcLV29-11B)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS917JIO at ENCODE; https://www.encodeproject.org/ENCBS917JIO/

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


title: microRNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB911IJZ)

description:
https://www.encodeproject.org/experiments/ENCSR389QNT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human naive CD4+ T cell microRNA-seq from Mortazavi
experiment encode accession: ENCSR389QNT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB911IJZ
size range: <30

source_name: Homo sapiens male adult (43 years) CD4-positive naive resting alpha-beta T primary cell

value: primary cell

value: naïve CD4+ T cell(CD45RO- RA+CCR7+)

value: adult

value: ENCBS054ELI at ENCODE; https://www.encodeproject.org/ENCBS054ELI/


title: microRNA-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB689QSE)

description:
https://www.encodeproject.org/experiments/ENCSR384ONW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human memory CD4+ T cells (activated day 2) microRNA-seq from Mortazavi
experiment encode accession: ENCSR384ONW
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB689QSE
size range: <30

value: Memory CD4+ T cell, activated Day 2

value: male

value: 43 year

value: Barbara Wold, Caltech

value: ENCBS714OYB at ENCODE; https://www.encodeproject.org/ENCBS714OYB/


title: CRISPR RNA-seq from K562 (ENCLB377HZR)

description:
https://www.encodeproject.org/experiments/ENCSR233MJI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGKcLV26)
experiment encode accession: ENCSR233MJI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB377HZR
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/b064cd08-aaa2-45b1-a303-6fac6c7c8716/@@download/attachment/L-ARHGEF2-BGKcLV26-31.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGKcLV26-31)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS158GLY at ENCODE; https://www.encodeproject.org/ENCBS158GLY/

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


title: microRNA-seq from middle frontal area 46 (ENCLB815ZRV)

description:
https://www.encodeproject.org/experiments/ENCSR382EIX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR382EIX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB815ZRV
size range: <30

source_name: Homo sapiens male adult (71 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 71 year

value: Rush University

value: ENCBS310NAE at ENCODE; https://www.encodeproject.org/ENCBS310NAE/

value: Derived from ENCODE donor ENCDO570AKP; https://www.encodeproject.org/ENCDO570AKP/


title: microRNA-seq from middle frontal area 46 (ENCLB255YDF)

description:
https://www.encodeproject.org/experiments/ENCSR379NYN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR379NYN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB255YDF
size range: <30

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: ENCBS742MVD at ENCODE; https://www.encodeproject.org/ENCBS742MVD/

value: Derived from ENCODE donor ENCDO250PFZ; https://www.encodeproject.org/ENCDO250PFZ/


title: microRNA-seq from middle frontal area 46 (ENCLB219YXA)

description:
https://www.encodeproject.org/experiments/ENCSR378JSK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR378JSK
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB219YXA
size range: <30

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

value: male

value: 83 year

value: ENCBS545PYF at ENCODE; https://www.encodeproject.org/ENCBS545PYF/

value: Derived from ENCODE donor ENCDO592ZWW; https://www.encodeproject.org/ENCDO592ZWW/


title: CRISPR RNA-seq from HepG2 (ENCLB518OWP)

description:
https://www.encodeproject.org/experiments/ENCSR232ERY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32)
experiment encode accession: ENCSR232ERY
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB518OWP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e2e857eb-2952-4847-b79e-58ca44a9eb32/@@download/attachment/L-NT-BGHcLV32-1.pdf

value: cell line

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32-1)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS907MRZ at ENCODE; https://www.encodeproject.org/ENCBS907MRZ/

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


title: microRNA-seq from middle frontal area 46 (ENCLB540NPF)

description:
https://www.encodeproject.org/experiments/ENCSR426AVN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR426AVN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB540NPF
size range: <30

source_name: Homo sapiens female adult (74 years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: adult

value: 74 year

value: Rush University

value: ENCBS177AWD at ENCODE; https://www.encodeproject.org/ENCBS177AWD/

value: Derived from ENCODE donor ENCDO907CMO; https://www.encodeproject.org/ENCDO907CMO/


title: microRNA-seq from middle frontal area 46 (ENCLB247JIT)

description:
https://www.encodeproject.org/experiments/ENCSR367JOT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR367JOT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB247JIT
size range: <30

source_name: Homo sapiens female adult (86 years) with Alzheimer's disease; middle frontal area 46 tissue

value: 86 year

value: Barbara Wold, Caltech

value: ENCBS048EXC at ENCODE; https://www.encodeproject.org/ENCBS048EXC/

value: Derived from ENCODE donor ENCDO997SGX; https://www.encodeproject.org/ENCDO997SGX/


title: CRISPR RNA-seq from HepG2 (ENCLB881WRB)

description:
https://www.encodeproject.org/experiments/ENCSR232ERY/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32)
experiment encode accession: ENCSR232ERY
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB881WRB
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/d79b5dda-8a75-4150-884e-e161b95e1bf1/@@download/attachment/L-NT-BGHcLV32-2.pdf

value: cell line

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32-2)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS969BWM at ENCODE; https://www.encodeproject.org/ENCBS969BWM/


title: BruChase-seq from endothelial cell of umbilical vein (ENCLB707XFZ)

description:
https://www.encodeproject.org/experiments/ENCSR656QKV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR656QKV
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR849FAX
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB707XFZ
size range: 400-500

source_name: Homo sapiens male newborn endothelial of umbilical vein primary cell, subjected to a 6 hour pulse-chase

value: endothelial cell of umbilical vein

value: primary cell

value: Homo sapiens

value: newborn

value: unknown

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS704YXU at ENCODE; https://www.encodeproject.org/ENCBS704YXU/

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


title: total RNA-seq from middle frontal area 46 (ENCLB096BRA)

description:
https://www.encodeproject.org/experiments/ENCSR795GYH/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_2705751_BS113_ENC4_cDNA663
experiment encode accession: ENCSR795GYH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB096BRA
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 (85 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: adult

value: 85 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS179KFU at ENCODE; https://www.encodeproject.org/ENCBS179KFU/

value: Derived from ENCODE donor ENCDO982NCL; https://www.encodeproject.org/ENCDO982NCL/


title: Bru-seq from HCT116 (ENCLB163XFV)

description:
https://www.encodeproject.org/experiments/ENCSR664LAL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR664LAL
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB163XFV
size range: 400-500

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS826WOF at ENCODE; https://www.encodeproject.org/ENCBS826WOF/

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


title: total RNA-seq from middle frontal area 46 (ENCLB320NDJ)

description:
https://www.encodeproject.org/experiments/ENCSR366LFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_2518687_BS93_ENC4_cDNA670
experiment encode accession: ENCSR366LFQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB320NDJ
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: Homo sapiens

value: 88 year

value: ENCBS928RYN at ENCODE; https://www.encodeproject.org/ENCBS928RYN/

value: Derived from ENCODE donor ENCDO801BII; https://www.encodeproject.org/ENCDO801BII/


title: CRISPR RNA-seq from HepG2 (ENCLB851YYJ)

description:
https://www.encodeproject.org/experiments/ENCSR340ZLQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATP5A1. (ATP5A1-BGHcLV29)
experiment encode accession: ENCSR340ZLQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB851YYJ
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 ATP5F1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/90634a31-4f44-477c-9fa4-f3e3e488e845/@@download/attachment/L-ATP5A1-BGHcLV29-9.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATP5A1. (ATP5A1-BGHcLV29-9)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS822FZF at ENCODE; https://www.encodeproject.org/ENCBS822FZF/

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


title: microRNA-seq from PC-9 (ENCLB792AQP)

description:
https://www.encodeproject.org/experiments/ENCSR349RCY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human PC-9 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR349RCY
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB792AQP
size range: <30

source_name: Homo sapiens PC-9 cell line

value: cell line

value: not collected

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS021NLC at ENCODE; https://www.encodeproject.org/ENCBS021NLC/

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


title: microRNA-seq from PC-9 (ENCLB833ASS)

description:
https://www.encodeproject.org/experiments/ENCSR349RCY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human PC-9 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR349RCY
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB833ASS
size range: <30

value: ENCBS511ZVG at ENCODE; https://www.encodeproject.org/ENCBS511ZVG/


title: BruChase-seq from endothelial cell of umbilical vein (ENCLB494UNH)

description:
https://www.encodeproject.org/experiments/ENCSR656QKV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR656QKV
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR849FAX
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB494UNH
size range: 400-500

value: endothelial cell of umbilical vein

value: primary cell

value: Homo sapiens

value: male

value: newborn

value: Lonza

value: ENCBS750CKY at ENCODE; https://www.encodeproject.org/ENCBS750CKY/

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


title: microRNA-seq from mesothelial cell of epicardium (ENCLB165WAR)

description:
https://www.encodeproject.org/experiments/ENCSR341PLF/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation WA09-derived epicardium microRNA-seq from Mortazavi
experiment encode accession: ENCSR341PLF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB165WAR
size range: <30

source_name: Homo sapiens female embryo (5 days) mesothelial of epicardium in vitro differentiated cells

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

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

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


title: total RNA-seq from middle frontal area 46 (ENCLB386AZN)

description:
https://www.encodeproject.org/experiments/ENCSR365ARV/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_3453103_BS49_ENC4_cDNA649
experiment encode accession: ENCSR365ARV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB386AZN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS075IEY at ENCODE; https://www.encodeproject.org/ENCBS075IEY/

value: Derived from ENCODE donor ENCDO006DAA; https://www.encodeproject.org/ENCDO006DAA/


title: CRISPR RNA-seq from HepG2 (ENCLB035XKP)

description:
https://www.encodeproject.org/experiments/ENCSR224XSS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGHcLV29)
experiment encode accession: ENCSR224XSS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB035XKP
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 CPSF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/459c84c2-be5d-4afa-8db0-e351043dcdd4/@@download/attachment/L-CPSF2-BGHcLV29-34.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGHcLV29-34)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS253TGN at ENCODE; https://www.encodeproject.org/ENCBS253TGN/

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


title: microRNA-seq from mesothelial cell of epicardium (ENCLB063NUQ)

description:
https://www.encodeproject.org/experiments/ENCSR341PLF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation WA09-derived epicardium microRNA-seq from Mortazavi
experiment encode accession: ENCSR341PLF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB063NUQ
size range: <30

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

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

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


title: microRNA-seq from middle frontal area 46 (ENCLB716HEC)

description:
https://www.encodeproject.org/experiments/ENCSR258RLB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR258RLB
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB716HEC
size range: <30

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS377PCM at ENCODE; https://www.encodeproject.org/ENCBS377PCM/

value: Derived from ENCODE donor ENCDO081AHA; https://www.encodeproject.org/ENCDO081AHA/


title: CRISPR RNA-seq from K562 (ENCLB927MKA)

description:
https://www.encodeproject.org/experiments/ENCSR654SOD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGKcLV26)
experiment encode accession: ENCSR654SOD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB927MKA
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 AGFG1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6fb998a8-52c6-4f6b-aab4-711ecd27e9ec/@@download/attachment/L-AGFG1-BGKcLV26-16.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGKcLV26-16)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS063IQR at ENCODE; https://www.encodeproject.org/ENCBS063IQR/

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


title: microRNA-seq from middle frontal area 46 (ENCLB917OHH)

description:
https://www.encodeproject.org/experiments/ENCSR308AGV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR308AGV
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB917OHH
size range: <30

value: middle frontal area 46

value: tissue

value: 85 year

value: ENCBS179KFU at ENCODE; https://www.encodeproject.org/ENCBS179KFU/

value: Derived from ENCODE donor ENCDO982NCL; https://www.encodeproject.org/ENCDO982NCL/


title: CRISPR RNA-seq from HepG2 (ENCLB936RIK)

description:
https://www.encodeproject.org/experiments/ENCSR224XSS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGHcLV29)
experiment encode accession: ENCSR224XSS
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB936RIK
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/cabff9cf-77da-490a-a5dc-87495dcae00e/@@download/attachment/L-CPSF2-BGHcLV29-33.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGHcLV29-33)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS174HKA at ENCODE; https://www.encodeproject.org/ENCBS174HKA/

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


title: microRNA-seq from middle frontal area 46 (ENCLB263LAA)

description:
https://www.encodeproject.org/experiments/ENCSR769VPS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR769VPS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB263LAA
size range: <30

source_name: Homo sapiens male adult (87 years) middle frontal area 46 tissue

value: adult

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS709FQH at ENCODE; https://www.encodeproject.org/ENCBS709FQH/

value: Derived from ENCODE donor ENCDO203ASI; https://www.encodeproject.org/ENCDO203ASI/


title: total RNA-seq from K562 (ENCLB876GNN)

description:
https://www.encodeproject.org/experiments/ENCSR223DWL/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Bortezomib for 48 hours
experiment encode accession: ENCSR223DWL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB876GNN
size range: 300-600

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

value: cell line

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_id:CHEBI:52717; treatment_term_name:Bortezomib; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS536HUT at ENCODE; https://www.encodeproject.org/ENCBS536HUT/

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