title: CRISPR RNA-seq from HepG2 (ENCLB580AXP)

description:
https://www.encodeproject.org/experiments/ENCSR330VES/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SCAF8. (SCAF8-BGHcLV31)
experiment encode accession: ENCSR330VES
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB580AXP
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 SCAF8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/762f3af9-c565-4222-a614-ea9c617bfbfa/@@download/attachment/L-SCAF8-BGHcLV31-29.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SCAF8. (SCAF8-BGHcLV31-29)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS320ZIE at ENCODE; https://www.encodeproject.org/ENCBS320ZIE/

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


title: microRNA-seq from heart (ENCLB703WWV)

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/ENCSR846QZK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND25 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR846QZK
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB703WWV
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 B6CASTF1/J female (25 days) heart tissue

value: heart

value: tissue

tag: description

value: B6Cast F1 PND25 Female 03 heart for Wold biobank

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: unknown

tag: age

value: 25 day

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS395IFQ at ENCODE; https://www.encodeproject.org/ENCBS395IFQ/

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


title: total RNA-seq from K562 (ENCLB325UKP)

description:
https://www.encodeproject.org/experiments/ENCSR758BAT/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with C646 for 4 hours
experiment encode accession: ENCSR758BAT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB325UKP
size range: 300-600

organism: Homo sapiens

source_name: Homo sapiens K562 cell line treated with 50 uM C646 for 4 hours, preserved by flash-freezing

tag: line

value: cell line

value: RNA-seq on human cell line K562

tag: organism

value: Homo sapiens

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

tag: treatments

value: treatment_term_name:C646; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS959KXI at ENCODE; https://www.encodeproject.org/ENCBS959KXI/

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


title: microRNA-seq from heart (ENCLB908LGQ)

description:
https://www.encodeproject.org/experiments/ENCSR846QZK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND25 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR846QZK
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB908LGQ
size range: <30

value: heart

value: tissue

value: B6Cast F1 PND25 Female 04 heart for Wold biobank

value: female

value: unknown

value: ENCBS130WUG at ENCODE; https://www.encodeproject.org/ENCBS130WUG/


title: microRNA-seq from heart (ENCLB665GEZ)

description:
https://www.encodeproject.org/experiments/ENCSR840QPN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND36 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR840QPN
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB665GEZ
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (36 days) heart tissue

value: B6Cast F1 PND36 Male 04 heart for Wold biobank

value: male

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS378WXL at ENCODE; https://www.encodeproject.org/ENCBS378WXL/

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


title: CRISPR RNA-seq from HepG2 (ENCLB080DMV)

description:
https://www.encodeproject.org/experiments/ENCSR330VES/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SCAF8. (SCAF8-BGHcLV31)
experiment encode accession: ENCSR330VES
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB080DMV
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/6b5e83ac-5a1c-47ad-b891-f74d765f8d97/@@download/attachment/L-SCAF8-BGHcLV31-30.pdf

tag: antibody

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SCAF8. (SCAF8-BGHcLV31-30)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS320KXQ at ENCODE; https://www.encodeproject.org/ENCBS320KXQ/

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


title: microRNA-seq from heart (ENCLB170ARB)

description:
https://www.encodeproject.org/experiments/ENCSR840QPN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND36 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR840QPN
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB170ARB
size range: <30

value: heart

value: tissue

value: B6Cast F1 PND36 Male 03 heart for Wold biobank

value: unknown

value: ENCBS001UUS at ENCODE; https://www.encodeproject.org/ENCBS001UUS/


title: microRNA-seq from left cerebral cortex (ENCLB351XSN)

description:
https://www.encodeproject.org/experiments/ENCSR429KRO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND14 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR429KRO
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB351XSN
size range: <30

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

value: left cerebral cortex

value: B6Cast F1 PND14 Female 04 left cerebral cortex for Wold biobank

value: female

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS120AVS at ENCODE; https://www.encodeproject.org/ENCBS120AVS/


title: CRISPR RNA-seq from K562 (ENCLB123ZJK)

description:
https://www.encodeproject.org/experiments/ENCSR329UEC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SCAF8. (SCAF8-BGKcLV33)
experiment encode accession: ENCSR329UEC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB123ZJK
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 SEC62

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b646f88a-b476-45dc-a7e2-539f37c8a550/@@download/attachment/L-SCAF8-BGKcLV33-33.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SCAF8. (SCAF8-BGKcLV33-33)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS504VVD at ENCODE; https://www.encodeproject.org/ENCBS504VVD/

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


title: CRISPR RNA-seq from K562 (ENCLB708XMB)

description:
https://www.encodeproject.org/experiments/ENCSR328DHD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ATP5A1. (ATP5A1-BGKcLV26)
experiment encode accession: ENCSR328DHD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB708XMB
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 ATP5F1A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6e61834d-3be6-4b13-9122-2d9da5cc9fc3/@@download/attachment/L-ATP5A1-BGKcLV26-37.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ATP5A1. (ATP5A1-BGKcLV26-37)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS311PCG at ENCODE; https://www.encodeproject.org/ENCBS311PCG/


title: microRNA-seq from left cerebral cortex (ENCLB859LYY)

description:
https://www.encodeproject.org/experiments/ENCSR429KRO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND14 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR429KRO
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB859LYY
size range: <30

value: left cerebral cortex

value: tissue

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

value: female

value: unknown

value: ENCBS374ENP at ENCODE; https://www.encodeproject.org/ENCBS374ENP/

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


title: microRNA-seq from left cerebral cortex (ENCLB489FLJ)

description:
https://www.encodeproject.org/experiments/ENCSR419RHJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND4 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR419RHJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB489FLJ
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (4 days) left cerebral cortex tissue

value: B6Cast F1 PND4 Male 04 left cerebral cortex for Wold biobank

value: male

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS178USG at ENCODE; https://www.encodeproject.org/ENCBS178USG/


title: microRNA-seq from heart (ENCLB232ILJ)

description:
https://www.encodeproject.org/experiments/ENCSR911AIY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND10 female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR911AIY
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB232ILJ
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (10 days) heart tissue

value: heart

value: B6Cast F1 PND10 Female 03 heart for Wold biobank

value: 10 day

value: ENCBS661GMI at ENCODE; https://www.encodeproject.org/ENCBS661GMI/


title: microRNA-seq from gastrocnemius (ENCLB920ALV)

description:
https://www.encodeproject.org/experiments/ENCSR418QXY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR418QXY
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB920ALV
size range: <30

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

value: gastrocnemius

value: Mus musculus

value: adult

value: 8-10 month

value: ENCBS480BER at ENCODE; https://www.encodeproject.org/ENCBS480BER/

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


title: microRNA-seq from left cerebral cortex (ENCLB766VHU)

description:
https://www.encodeproject.org/experiments/ENCSR419RHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND4 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR419RHJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB766VHU
size range: <30

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND4 Male 03 left cerebral cortex for Wold biobank

value: unknown

value: ENCBS398MXZ at ENCODE; https://www.encodeproject.org/ENCBS398MXZ/

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


title: microRNA-seq from gastrocnemius (ENCLB783PST)

description:
https://www.encodeproject.org/experiments/ENCSR418QXY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR418QXY
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB783PST
size range: <30

value: male

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS197MJZ at ENCODE; https://www.encodeproject.org/ENCBS197MJZ/


title: microRNA-seq from adrenal gland (ENCLB964PYG)

description:
https://www.encodeproject.org/experiments/ENCSR820VUG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female adrenal microRNA-seq from Mortazavi
experiment encode accession: ENCSR820VUG
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB964PYG
size range: <30

source_name: Mus musculus strain 5xFAD/CAST female adult (8-10 months) adrenal gland tissue

value: adrenal gland

value: female

value: ENCBS375TMX at ENCODE; https://www.encodeproject.org/ENCBS375TMX/


title: CRISPR RNA-seq from HepG2 (ENCLB718SSA)

description:
https://www.encodeproject.org/experiments/ENCSR747MHD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPRD1B. (RPRD1B-BGHcLV32)
experiment encode accession: ENCSR747MHD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB718SSA
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 RPRD1B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d835a1cf-6663-48b1-9815-f08383e43cec/@@download/attachment/L-RPRD1B-BGHcLV32-58.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPRD1B. (RPRD1B-BGHcLV32-58)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS634TDN at ENCODE; https://www.encodeproject.org/ENCBS634TDN/

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


title: CRISPR RNA-seq from HepG2 (ENCLB134BFX)

description:
https://www.encodeproject.org/experiments/ENCSR740WAG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF4. (CPSF4-BGHcLV24)
experiment encode accession: ENCSR740WAG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB134BFX
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 CPSF4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/47e71065-7398-41c0-b21d-bf73f208c0f3/@@download/attachment/L-CPSF4-BGHcLV24-23.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF4. (CPSF4-BGHcLV24-23)

value: male

value: ENCBS458UWG at ENCODE; https://www.encodeproject.org/ENCBS458UWG/


title: CRISPR RNA-seq from HepG2 (ENCLB872BZK)

description:
https://www.encodeproject.org/experiments/ENCSR745KNE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC23IP. (SEC23IP-BGHcLV31)
experiment encode accession: ENCSR745KNE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB872BZK
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 SEC23IP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/faa181a8-ee30-4b0e-a5ac-5fdbf3c9af63/@@download/attachment/L-SEC23IP-BGHcLV31-32.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC23IP. (SEC23IP-BGHcLV31-32)

value: ENCBS547LXE at ENCODE; https://www.encodeproject.org/ENCBS547LXE/


title: CRISPR RNA-seq from HepG2 (ENCLB873RFS)

description:
https://www.encodeproject.org/experiments/ENCSR745KNE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC23IP. (SEC23IP-BGHcLV31)
experiment encode accession: ENCSR745KNE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB873RFS
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/491e5842-9623-48aa-9d96-ac4c9efc363a/@@download/attachment/L-SEC23IP-BGHcLV31-31.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC23IP. (SEC23IP-BGHcLV31-31)

value: ENCBS023BGM at ENCODE; https://www.encodeproject.org/ENCBS023BGM/


title: total RNA-seq from K562 (ENCLB624JUQ)

description:
https://www.encodeproject.org/experiments/ENCSR325BJP/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Galeterone for 48 hours
experiment encode accession: ENCSR325BJP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB624JUQ
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 25 uM Galeterone 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: adult

value: 53 year

value: Will Greenleaf, Stanford

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

value: ENCBS426DQB at ENCODE; https://www.encodeproject.org/ENCBS426DQB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB192ZWS)

description:
https://www.encodeproject.org/experiments/ENCSR747MHD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPRD1B. (RPRD1B-BGHcLV32)
experiment encode accession: ENCSR747MHD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB192ZWS
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/f019d536-c473-4965-9788-8efa3f002846/@@download/attachment/L-RPRD1B-BGHcLV32-57.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPRD1B. (RPRD1B-BGHcLV32-57)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS060LCH at ENCODE; https://www.encodeproject.org/ENCBS060LCH/

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


title: microRNA-seq from left cerebral cortex (ENCLB987USS)

description:
https://www.encodeproject.org/experiments/ENCSR401RSJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND36 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR401RSJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-21
lab: Ali Mortazavi, UCI
library encode accession: ENCLB987USS
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (36 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND36 Male 04 left cerebral cortex for Wold biobank

value: male

value: unknown

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS452FVI at ENCODE; https://www.encodeproject.org/ENCBS452FVI/

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


title: microRNA-seq from adrenal gland (ENCLB377DRF)

description:
https://www.encodeproject.org/experiments/ENCSR820VUG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female adrenal microRNA-seq from Mortazavi
experiment encode accession: ENCSR820VUG
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB377DRF
size range: <30

value: adrenal gland

value: Mus musculus

value: female

value: adult

value: 8-10 month

value: ENCBS206LPG at ENCODE; https://www.encodeproject.org/ENCBS206LPG/

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


title: CRISPR RNA-seq from HepG2 (ENCLB910KLA)

description:
https://www.encodeproject.org/experiments/ENCSR740WAG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF4. (CPSF4-BGHcLV24)
experiment encode accession: ENCSR740WAG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB910KLA
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/60814d51-7fcb-4736-9463-f37aa26888c9/@@download/attachment/L-CPSF4-BGHcLV24-24.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF4. (CPSF4-BGHcLV24-24)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS137YOG at ENCODE; https://www.encodeproject.org/ENCBS137YOG/

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


title: total RNA-seq from K562 (ENCLB763GZK)

description:
https://www.encodeproject.org/experiments/ENCSR325BJP/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Galeterone for 48 hours
experiment encode accession: ENCSR325BJP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB763GZK
size range: 300-600

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

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

value: ENCBS580XHX at ENCODE; https://www.encodeproject.org/ENCBS580XHX/

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


title: microRNA-seq from gastrocnemius (ENCLB999ORQ)

description:
https://www.encodeproject.org/experiments/ENCSR815DQP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND4 male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR815DQP
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB999ORQ
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (4 days) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: B6Cast F1 PND4 Male 04 gastrocnemius for Wold core

value: male

value: unknown

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS659ATN at ENCODE; https://www.encodeproject.org/ENCBS659ATN/

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


title: CRISPR RNA-seq from K562 (ENCLB713HZE)

description:
https://www.encodeproject.org/experiments/ENCSR323SDL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGKcLV28)
experiment encode accession: ENCSR323SDL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB713HZE
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 CD3EAP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/babf1372-ea3e-4cec-9dc0-3778610e7ad6/@@download/attachment/L-CD3EAP-BGKcLV28-10.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGKcLV28-9)

value: Homo sapiens

value: female

value: adult

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS598YTE at ENCODE; https://www.encodeproject.org/ENCBS598YTE/


title: microRNA-seq from gastrocnemius (ENCLB140KPQ)

description:
https://www.encodeproject.org/experiments/ENCSR815DQP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND4 male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR815DQP
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB140KPQ
size range: <30

value: gastrocnemius

value: tissue

value: B6Cast F1 PND4 Male 03 gastrocnemius for Wold core

value: ENCBS895ZIH at ENCODE; https://www.encodeproject.org/ENCBS895ZIH/


title: CRISPR RNA-seq from K562 (ENCLB244JAM)

description:
https://www.encodeproject.org/experiments/ENCSR328DHD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ATP5A1. (ATP5A1-BGKcLV26)
experiment encode accession: ENCSR328DHD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB244JAM
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/ed95f18b-5127-4650-b247-34461229af8c/@@download/attachment/L-ATP5A1-BGKcLV26-38.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ATP5A1. (ATP5A1-BGKcLV26-38)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS492EVY at ENCODE; https://www.encodeproject.org/ENCBS492EVY/

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


title: CRISPR RNA-seq from K562 (ENCLB172XDC)

description:
https://www.encodeproject.org/experiments/ENCSR329UEC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SCAF8. (SCAF8-BGKcLV33)
experiment encode accession: ENCSR329UEC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB172XDC
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/e9c5fcb6-5fcb-4454-b75b-e934a7889b25/@@download/attachment/L-SCAF8-BGKcLV33-34.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SCAF8. (SCAF8-BGKcLV33-34)

value: ENCBS462NYH at ENCODE; https://www.encodeproject.org/ENCBS462NYH/


title: CRISPR RNA-seq from HepG2 (ENCLB043NCV)

description:
https://www.encodeproject.org/experiments/ENCSR739ZMF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGHcLV32)
experiment encode accession: ENCSR739ZMF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB043NCV
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 RBM25

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/62852d14-c327-4dfc-a639-e5dc6f949bbc/@@download/attachment/L-RBM25-BGHcLV32-10.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGHcLV32-9)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS652ECV at ENCODE; https://www.encodeproject.org/ENCBS652ECV/

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


title: microRNA-seq from left cerebral cortex (ENCLB890YOS)

description:
https://www.encodeproject.org/experiments/ENCSR367RBT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR367RBT
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB890YOS
size range: <30

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

value: left cerebral cortex

value: tissue

value: Mus musculus

value: female

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS869WPR at ENCODE; https://www.encodeproject.org/ENCBS869WPR/

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


title: CRISPR RNA-seq from K562 (ENCLB625HZR)

description:
https://www.encodeproject.org/experiments/ENCSR323RFB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC42EP4. (CDC42EP4-BGKcLV33)
experiment encode accession: ENCSR323RFB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB625HZR
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 RPS9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3ba4f734-4cb9-40bf-bd71-c7d990943f08/@@download/attachment/L-CDC42EP4-BGKcLV33-7.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC42EP4. (CDC42EP4-BGKcLV33-7)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS665FPO at ENCODE; https://www.encodeproject.org/ENCBS665FPO/

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


title: CRISPR RNA-seq from HepG2 (ENCLB076UGB)

description:
https://www.encodeproject.org/experiments/ENCSR739ZMF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGHcLV32)
experiment encode accession: ENCSR739ZMF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB076UGB
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/28bd6dd1-2189-4ff1-a2c1-35495061c8e2/@@download/attachment/L-RBM25-BGHcLV32-9.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGHcLV32-10)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS876WAS at ENCODE; https://www.encodeproject.org/ENCBS876WAS/

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


title: microRNA-seq from heart (ENCLB418LFZ)

description:
https://www.encodeproject.org/experiments/ENCSR794QRE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR794QRE
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB418LFZ
size range: <30

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

value: heart

value: tissue

value: Mus musculus

value: female

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS734MAN at ENCODE; https://www.encodeproject.org/ENCBS734MAN/

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


title: microRNA-seq from heart (ENCLB026ZOR)

description:
https://www.encodeproject.org/experiments/ENCSR794QRE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR794QRE
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB026ZOR
size range: <30

value: ENCBS669PYZ at ENCODE; https://www.encodeproject.org/ENCBS669PYZ/


title: CRISPR RNA-seq from K562 (ENCLB102QFO)

description:
https://www.encodeproject.org/experiments/ENCSR323RFB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC42EP4. (CDC42EP4-BGKcLV33)
experiment encode accession: ENCSR323RFB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB102QFO
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/949ca0fc-872b-4750-ae62-705351eab3dc/@@download/attachment/L-CDC42EP4-BGKcLV33-8.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CDC42EP4. (CDC42EP4-BGKcLV33-8)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS098OWP at ENCODE; https://www.encodeproject.org/ENCBS098OWP/

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


title: microRNA-seq from left cerebral cortex (ENCLB953RRJ)

description:
https://www.encodeproject.org/experiments/ENCSR367RBT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR367RBT
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB953RRJ
size range: <30

value: left cerebral cortex

value: tissue

value: Mus musculus

value: female

value: ENCBS505BIQ at ENCODE; https://www.encodeproject.org/ENCBS505BIQ/


title: microRNA-seq from left cerebral cortex (ENCLB599FYO)

description:
https://www.encodeproject.org/experiments/ENCSR332HPA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND10 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR332HPA
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB599FYO
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (10 days) left cerebral cortex tissue

value: B6Cast F1 PND10 Female 03 left cerebral cortex for Wold biobank

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS056HYO at ENCODE; https://www.encodeproject.org/ENCBS056HYO/

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


title: microRNA-seq from left cerebral cortex (ENCLB352FZK)

description:
https://www.encodeproject.org/experiments/ENCSR401RSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND36 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR401RSJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-21
lab: Ali Mortazavi, UCI
library encode accession: ENCLB352FZK
size range: <30

value: B6Cast F1 PND36 Male 03 left cerebral cortex for Wold biobank

value: male

value: 36 day

value: ENCBS994YKJ at ENCODE; https://www.encodeproject.org/ENCBS994YKJ/


title: total RNA-seq from K562 (ENCLB657JJE)

description:
https://www.encodeproject.org/experiments/ENCSR738ZHN/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Crizotinib for 12 hours
experiment encode accession: ENCSR738ZHN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB657JJE
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 uM Crizotinib 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: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS812VEL at ENCODE; https://www.encodeproject.org/ENCBS812VEL/

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


title: microRNA-seq from left cerebral cortex (ENCLB046CST)

description:
https://www.encodeproject.org/experiments/ENCSR332HPA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND10 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR332HPA
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB046CST
size range: <30

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND10 Female 04 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS716XOP at ENCODE; https://www.encodeproject.org/ENCBS716XOP/


title: CRISPR RNA-seq from K562 (ENCLB290PZH)

description:
https://www.encodeproject.org/experiments/ENCSR323SDL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGKcLV28)
experiment encode accession: ENCSR323SDL
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB290PZH
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/55d0ab15-bade-477e-972b-984443c86a88/@@download/attachment/L-CD3EAP-BGKcLV28-9.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CD3EAP. (CD3EAP-BGKcLV28-10)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS099LSY at ENCODE; https://www.encodeproject.org/ENCBS099LSY/


title: total RNA-seq from motor neuron (ENCLB382SRT)

description:
https://www.encodeproject.org/experiments/ENCSR319GRO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR319GRO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB382SRT
size range: 300-600

source_name: Homo sapiens male adult (55 years) motor neuron in vitro differentiated cells, preserved by flash-freezing

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: male

value: Healthy donor

value: adult

value: 55 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS909TQU at ENCODE; https://www.encodeproject.org/ENCBS909TQU/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: total RNA-seq from motor neuron (ENCLB071BMY)

description:
https://www.encodeproject.org/experiments/ENCSR319GRO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR319GRO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB071BMY
size range: 300-600

value: ENCBS718ILE at ENCODE; https://www.encodeproject.org/ENCBS718ILE/


title: microRNA-seq from left cerebral cortex (ENCLB887WDN)

description:
https://www.encodeproject.org/experiments/ENCSR326SPS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND25 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR326SPS
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB887WDN
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (25 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND25 Female 03 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS532TZI at ENCODE; https://www.encodeproject.org/ENCBS532TZI/

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


title: CRISPR RNA-seq from HepG2 (ENCLB888EKF)

description:
https://www.encodeproject.org/experiments/ENCSR735FXX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGHcLV27)
experiment encode accession: ENCSR735FXX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB888EKF
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 ALDOA

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e2f56079-ecfb-4c06-b31c-c84379687044/@@download/attachment/L-ALDOA-BGHcLV27-7.pdf

value: ALDOA

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGHcLV27-7)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS651VNU at ENCODE; https://www.encodeproject.org/ENCBS651VNU/

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


title: microRNA-seq from left cerebral cortex (ENCLB076HGS)

description:
https://www.encodeproject.org/experiments/ENCSR326SPS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND25 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR326SPS
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB076HGS
size range: <30

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND25 Female 04 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 25 day

value: ENCBS168HOX at ENCODE; https://www.encodeproject.org/ENCBS168HOX/


title: microRNA-seq from left cerebral cortex (ENCLB132AFN)

description:
https://www.encodeproject.org/experiments/ENCSR305JTG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND36 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR305JTG
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB132AFN
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (36 days) left cerebral cortex tissue

value: B6Cast F1 PND36 Female 04 left cerebral cortex for Wold biobank

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS888DCZ at ENCODE; https://www.encodeproject.org/ENCBS888DCZ/

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


title: microRNA-seq from left cerebral cortex (ENCLB375OLS)

description:
https://www.encodeproject.org/experiments/ENCSR305JTG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND36 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR305JTG
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB375OLS
size range: <30

value: B6Cast F1 PND36 Female 03 left cerebral cortex for Wold biobank

value: ENCBS527XPI at ENCODE; https://www.encodeproject.org/ENCBS527XPI/


title: CRISPR RNA-seq from HepG2 (ENCLB265NKA)

description:
https://www.encodeproject.org/experiments/ENCSR735FXX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGHcLV27)
experiment encode accession: ENCSR735FXX
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB265NKA
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/8e1994bd-5c90-4e99-9622-2918f34a7af8/@@download/attachment/L-ALDOA-BGHcLV27-8.pdf

value: ALDOA

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGHcLV27-8)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS084MWU at ENCODE; https://www.encodeproject.org/ENCBS084MWU/


title: microRNA-seq from left cerebral cortex (ENCLB445PQG)

description:
https://www.encodeproject.org/experiments/ENCSR268MII/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND10 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR268MII
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB445PQG
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (10 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND10 Male 03 left cerebral cortex for Wold biobank

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: ENCBS941MMJ at ENCODE; https://www.encodeproject.org/ENCBS941MMJ/


title: CRISPR RNA-seq from K562 (ENCLB715YSX)

description:
https://www.encodeproject.org/experiments/ENCSR737OPD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPRD1B. (RPRD1B-BGKcLV30)
experiment encode accession: ENCSR737OPD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB715YSX
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 RPRD1B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e13b031c-ff4f-4ab2-8c5c-d34335d997b4/@@download/attachment/L-RPRD1B-BGKcLV30-60.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPRD1B. (RPRD1B-BGKcLV30-60)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS174IZH at ENCODE; https://www.encodeproject.org/ENCBS174IZH/

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


title: total RNA-seq from K562 (ENCLB844XUY)

description:
https://www.encodeproject.org/experiments/ENCSR733QST/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Panobinostat for 24 hours
experiment encode accession: ENCSR733QST
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB844XUY
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 7.5 nM Panobinostat for 24 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: Homo sapiens

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS477EBR at ENCODE; https://www.encodeproject.org/ENCBS477EBR/


title: microRNA-seq from heart (ENCLB853WWP)

description:
https://www.encodeproject.org/experiments/ENCSR303XYS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR303XYS
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB853WWP
size range: <30

source_name: Mus musculus strain B6CASTF1/J female adult (18-20 months) heart tissue

value: heart

value: tissue

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS281CBG at ENCODE; https://www.encodeproject.org/ENCBS281CBG/

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


title: total RNA-seq from K562 (ENCLB329AJY)

description:
https://www.encodeproject.org/experiments/ENCSR733QST/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Panobinostat for 24 hours
experiment encode accession: ENCSR733QST
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB329AJY
size range: 300-600

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS816PFE at ENCODE; https://www.encodeproject.org/ENCBS816PFE/


title: microRNA-seq from heart (ENCLB231LKS)

description:
https://www.encodeproject.org/experiments/ENCSR303XYS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR303XYS
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB231LKS
size range: <30

value: Barbara Wold, Caltech

value: ENCBS007ZPS at ENCODE; https://www.encodeproject.org/ENCBS007ZPS/


title: total RNA-seq from A549 (ENCLB632AKP)

description:
https://www.encodeproject.org/experiments/ENCSR307PVU/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR307PVU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB632AKP
size range: 200-300

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

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

value: Homo sapiens

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

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

value: ENCBS452OHN at ENCODE; https://www.encodeproject.org/ENCBS452OHN/

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


title: total RNA-seq from A549 (ENCLB300AZX)

description:
https://www.encodeproject.org/experiments/ENCSR307PVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307PVU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB300AZX
size range: 200-300

value: ENCBS556EEU at ENCODE; https://www.encodeproject.org/ENCBS556EEU/


title: microRNA-seq from left cerebral cortex (ENCLB260ZAK)

description:
https://www.encodeproject.org/experiments/ENCSR268MII/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND10 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR268MII
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB260ZAK
size range: <30

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND10 Male 04 left cerebral cortex for Wold biobank

value: unknown

value: 10 day

value: The Jackson Laboratory

value: ENCBS919NNU at ENCODE; https://www.encodeproject.org/ENCBS919NNU/

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


title: total RNA-seq from A549 (ENCLB389CLS)

description:
https://www.encodeproject.org/experiments/ENCSR307PVU/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR307PVU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB389CLS
size range: 200-300

value: cell line

value: Homo sapiens

value: adult

value: ENCBS298JFY at ENCODE; https://www.encodeproject.org/ENCBS298JFY/


title: total RNA-seq from A549 (ENCLB054RSJ)

description:
https://www.encodeproject.org/experiments/ENCSR307PVU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR307PVU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB054RSJ
size range: 200-300

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS076KCC at ENCODE; https://www.encodeproject.org/ENCBS076KCC/


title: CRISPR RNA-seq from K562 (ENCLB247HXV)

description:
https://www.encodeproject.org/experiments/ENCSR727WPW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGKcLV33)
experiment encode accession: ENCSR727WPW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB247HXV
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 SF3B2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4bd7e365-d44c-431d-a384-a48c87955f07/@@download/attachment/L-SEPT11-BGKcLV33-46.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGKcLV33-46)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS347VSX at ENCODE; https://www.encodeproject.org/ENCBS347VSX/

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


title: CRISPR RNA-seq from K562 (ENCLB325FES)

description:
https://www.encodeproject.org/experiments/ENCSR737OPD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPRD1B. (RPRD1B-BGKcLV30)
experiment encode accession: ENCSR737OPD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB325FES
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/dd480a95-0463-4dcb-bd36-2cbd80601344/@@download/attachment/L-RPRD1B-BGKcLV30-59.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPRD1B. (RPRD1B-BGKcLV30-59)

value: ENCBS633IOB at ENCODE; https://www.encodeproject.org/ENCBS633IOB/


title: microRNA-seq from heart (ENCLB829AIC)

description:
https://www.encodeproject.org/experiments/ENCSR673ZSX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND25 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR673ZSX
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB829AIC
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (25 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND25 Male 04 heart for Wold biobank

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS857DKA at ENCODE; https://www.encodeproject.org/ENCBS857DKA/

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


title: microRNA-seq from heart (ENCLB125SON)

description:
https://www.encodeproject.org/experiments/ENCSR673ZSX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND25 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR673ZSX
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB125SON
size range: <30

value: B6Cast F1 PND25 Male 03 heart for Wold biobank

value: male

value: ENCBS139NCJ at ENCODE; https://www.encodeproject.org/ENCBS139NCJ/


title: total RNA-seq from A549 (ENCLB338IYV)

description:
https://www.encodeproject.org/experiments/ENCSR307PVU/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR307PVU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB338IYV
size range: 200-300

value: cell line

value: Homo sapiens

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

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

value: ENCBS410LGD at ENCODE; https://www.encodeproject.org/ENCBS410LGD/

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


title: microRNA-seq from layer of hippocampus (ENCLB635LYK)

description:
https://www.encodeproject.org/experiments/ENCSR234WVC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR234WVC
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB635LYK
size range: <30

source_name: Mus musculus strain 5xFAD/CAST female adult (8-10 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: Mus musculus

value: female

value: 8-10 month

value: ENCBS125BDZ at ENCODE; https://www.encodeproject.org/ENCBS125BDZ/

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


title: microRNA-seq from layer of hippocampus (ENCLB490TUL)

description:
https://www.encodeproject.org/experiments/ENCSR234WVC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR234WVC
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB490TUL
size range: <30

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS900NRB at ENCODE; https://www.encodeproject.org/ENCBS900NRB/


title: total RNA-seq from K562 (ENCLB088YLM)

description:
https://www.encodeproject.org/experiments/ENCSR738ZHN/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Crizotinib for 12 hours
experiment encode accession: ENCSR738ZHN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB088YLM
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

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

value: ENCBS777YEV at ENCODE; https://www.encodeproject.org/ENCBS777YEV/

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


title: CRISPR RNA-seq from K562 (ENCLB252HGZ)

description:
https://www.encodeproject.org/experiments/ENCSR727WPW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGKcLV33)
experiment encode accession: ENCSR727WPW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB252HGZ
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/3838c834-751a-4166-b900-2b11d8a61acd/@@download/attachment/L-SEPT11-BGKcLV33-45.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGKcLV33-45)

value: female

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS765CBQ at ENCODE; https://www.encodeproject.org/ENCBS765CBQ/


title: microRNA-seq from left cerebral cortex (ENCLB905WBY)

description:
https://www.encodeproject.org/experiments/ENCSR640XEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND25 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR640XEJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB905WBY
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (25 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND25 Male 04 left cerebral cortex for Wold biobank

value: male

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS964RWE at ENCODE; https://www.encodeproject.org/ENCBS964RWE/

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


title: microRNA-seq from left cerebral cortex (ENCLB885XNK)

description:
https://www.encodeproject.org/experiments/ENCSR640XEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND25 male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR640XEJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB885XNK
size range: <30

value: B6Cast F1 PND25 Male 03 left cerebral cortex for Wold biobank

value: ENCBS770ANB at ENCODE; https://www.encodeproject.org/ENCBS770ANB/


title: microRNA-seq from heart (ENCLB995SLA)

description:
https://www.encodeproject.org/experiments/ENCSR173OTH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND36 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR173OTH
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB995SLA
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (36 days) heart tissue

value: heart

value: B6Cast F1 PND36 Female 03 heart for Wold biobank

value: 36 day

value: ENCBS170UDX at ENCODE; https://www.encodeproject.org/ENCBS170UDX/


title: CRISPR RNA-seq from K562 (ENCLB736RXW)

description:
https://www.encodeproject.org/experiments/ENCSR307GHU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGKcLV28)
experiment encode accession: ENCSR307GHU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB736RXW
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 CHCHD3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/84cb85e5-7801-46a5-a227-48287bf08a52/@@download/attachment/L-CHCHD3-BGKcLV28-17.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGKcLV28-17)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS129MBJ at ENCODE; https://www.encodeproject.org/ENCBS129MBJ/

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


title: microRNA-seq from adrenal gland (ENCLB149XTM)

description:
https://www.encodeproject.org/experiments/ENCSR178KAF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male adrenal microRNA-seq from Mortazavi
experiment encode accession: ENCSR178KAF
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB149XTM
size range: <30

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

value: adrenal gland

value: tissue

value: Mus musculus

value: male

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS515VBP at ENCODE; https://www.encodeproject.org/ENCBS515VBP/

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


title: CRISPR RNA-seq from K562 (ENCLB260VRJ)

description:
https://www.encodeproject.org/experiments/ENCSR307GHU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGKcLV28)
experiment encode accession: ENCSR307GHU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB260VRJ
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/1a64d424-e6b6-4a4d-a5e1-613c17a90d45/@@download/attachment/L-CHCHD3-BGKcLV28-18.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGKcLV28-18)

value: Homo sapiens

value: female

value: ENCBS249NVQ at ENCODE; https://www.encodeproject.org/ENCBS249NVQ/


title: microRNA-seq from adrenal gland (ENCLB736HUL)

description:
https://www.encodeproject.org/experiments/ENCSR178KAF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male adrenal microRNA-seq from Mortazavi
experiment encode accession: ENCSR178KAF
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB736HUL
size range: <30

value: adult

value: ENCBS943GNI at ENCODE; https://www.encodeproject.org/ENCBS943GNI/


title: CRISPR RNA-seq from HepG2 (ENCLB182CTD)

description:
https://www.encodeproject.org/experiments/ENCSR726RTM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RTCB. (RTCB-BGHcLV31)
experiment encode accession: ENCSR726RTM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB182CTD
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 RTCB

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/95baa86a-4fa9-45f9-815a-c2af56451a5e/@@download/attachment/L-RTCB-BGHcLV31-17.pdf

value: RTCB

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RTCB. (RTCB-BGHcLV31-17)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS550JRC at ENCODE; https://www.encodeproject.org/ENCBS550JRC/

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


title: CRISPR RNA-seq from K562 (ENCLB076SAH)

description:
https://www.encodeproject.org/experiments/ENCSR697NDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CMTR1. (CMTR1-BGKcLV28)
experiment encode accession: ENCSR697NDQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB076SAH
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 CMTR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ba5041bb-d786-4eb4-a8bc-2aa5ca2ca6af/@@download/attachment/L-CMTR1-BGKcLV28-25.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CMTR1. (CMTR1-BGKcLV28-25)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS050NNR at ENCODE; https://www.encodeproject.org/ENCBS050NNR/

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


title: microRNA-seq from heart (ENCLB087VZX)

description:
https://www.encodeproject.org/experiments/ENCSR173OTH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND36 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR173OTH
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB087VZX
size range: <30

value: heart

value: tissue

value: B6Cast F1 PND36 Female 04 heart for Wold biobank

value: female

value: unknown

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS578XBR at ENCODE; https://www.encodeproject.org/ENCBS578XBR/

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


title: CRISPR RNA-seq from HepG2 (ENCLB126CBQ)

description:
https://www.encodeproject.org/experiments/ENCSR726RTM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RTCB. (RTCB-BGHcLV31)
experiment encode accession: ENCSR726RTM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB126CBQ
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/1f6df06e-51c7-4fbb-9ff1-980d27dd743f/@@download/attachment/L-RTCB-BGHcLV31-18.pdf

value: RTCB

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RTCB. (RTCB-BGHcLV31-18)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS156HXW at ENCODE; https://www.encodeproject.org/ENCBS156HXW/


title: CRISPR RNA-seq from K562 (ENCLB868OQW)

description:
https://www.encodeproject.org/experiments/ENCSR697NDQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CMTR1. (CMTR1-BGKcLV28)
experiment encode accession: ENCSR697NDQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB868OQW
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/3a37cd46-f68c-4c86-a21c-d7507ad7b787/@@download/attachment/L-CMTR1-BGKcLV28-26.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CMTR1. (CMTR1-BGKcLV28-26)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS170BGM at ENCODE; https://www.encodeproject.org/ENCBS170BGM/

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


title: CRISPR RNA-seq from K562 (ENCLB810LAP)

description:
https://www.encodeproject.org/experiments/ENCSR267SUE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CARS. (CARS-BGKcLV26)
experiment encode accession: ENCSR267SUE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB810LAP
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 CARS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6a0e3bac-9851-4908-aaee-c781c2d5361e/@@download/attachment/L-CARS-BGKcLV26-57.pdf

value: CARS

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CARS. (CARS-BGKcLV26-57)

value: ENCBS328HQA at ENCODE; https://www.encodeproject.org/ENCBS328HQA/


title: microRNA-seq from layer of hippocampus (ENCLB905QPH)

description:
https://www.encodeproject.org/experiments/ENCSR625RML/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND25 female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR625RML
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB905QPH
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (25 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS690ORU at ENCODE; https://www.encodeproject.org/ENCBS690ORU/

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


title: CRISPR RNA-seq from K562 (ENCLB843NIU)

description:
https://www.encodeproject.org/experiments/ENCSR267SUE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CARS. (CARS-BGKcLV26)
experiment encode accession: ENCSR267SUE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB843NIU
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/0fe3ab5a-7b50-47ae-ae95-21a90202a876/@@download/attachment/L-CARS-BGKcLV26-58.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CARS. (CARS-BGKcLV26-58)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS870SOW at ENCODE; https://www.encodeproject.org/ENCBS870SOW/


title: microRNA-seq from heart (ENCLB628CGY)

description:
https://www.encodeproject.org/experiments/ENCSR108XJW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR108XJW
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB628CGY
size range: <30

source_name: Mus musculus strain B6CASTF1/J male adult (18-20 months) heart tissue

value: heart

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: ENCBS897MIA at ENCODE; https://www.encodeproject.org/ENCBS897MIA/


title: microRNA-seq from heart (ENCLB547YJA)

description:
https://www.encodeproject.org/experiments/ENCSR108XJW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR108XJW
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB547YJA
size range: <30

value: tissue

value: Barbara Wold, Caltech

value: ENCBS540JOT at ENCODE; https://www.encodeproject.org/ENCBS540JOT/


title: microRNA-seq from layer of hippocampus (ENCLB155YNH)

description:
https://www.encodeproject.org/experiments/ENCSR076IZU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR076IZU
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB155YNH
size range: <30

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

value: layer of hippocampus

value: Mus musculus

value: 8-10 month

value: The Jackson Laboratory

value: ENCBS116ERU at ENCODE; https://www.encodeproject.org/ENCBS116ERU/

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


title: total RNA-seq from K562 (ENCLB764BWN)

description:
https://www.encodeproject.org/experiments/ENCSR264IXQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with AR-42 for 4 hours
experiment encode accession: ENCSR264IXQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB764BWN
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 uM AR-42 for 4 hours, preserved by flash-freezing

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:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS273QOE at ENCODE; https://www.encodeproject.org/ENCBS273QOE/

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


title: total RNA-seq from K562 (ENCLB084JOX)

description:
https://www.encodeproject.org/experiments/ENCSR264IXQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with AR-42 for 4 hours
experiment encode accession: ENCSR264IXQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB084JOX
size range: 300-600

value: adult

value: ENCBS747ITB at ENCODE; https://www.encodeproject.org/ENCBS747ITB/


title: microRNA-seq from heart (ENCLB642SKU)

description:
https://www.encodeproject.org/experiments/ENCSR576VFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND14 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR576VFQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB642SKU
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (14 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND14 3x Males 04 heart for Wold biobank

value: male

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS306HAS at ENCODE; https://www.encodeproject.org/ENCBS306HAS/

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


title: microRNA-seq from left cerebral cortex (ENCLB027PRS)

description:
https://www.encodeproject.org/experiments/ENCSR560FAG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND4 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR560FAG
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB027PRS
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (4 days) left cerebral cortex tissue

value: left cerebral cortex

value: B6Cast F1 PND4 Female 03 left cerebral cortex for Wold biobank

value: female

value: 4 day

value: The Jackson Laboratory

value: ENCBS151XIY at ENCODE; https://www.encodeproject.org/ENCBS151XIY/


title: microRNA-seq from layer of hippocampus (ENCLB317RSR)

description:
https://www.encodeproject.org/experiments/ENCSR076IZU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation 5xFAD/Cast mouse male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR076IZU
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB317RSR
size range: <30

value: layer of hippocampus

value: Mus musculus

value: adult

value: 8-10 month

value: ENCBS830OUL at ENCODE; https://www.encodeproject.org/ENCBS830OUL/

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


title: CRISPR RNA-seq from K562 (ENCLB369KFL)

description:
https://www.encodeproject.org/experiments/ENCSR262ZBE/
***************
biological replicate number: 2
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: ENCLB369KFL
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/c810998b-da7c-4b21-b8c4-c2050fbb6b66/@@download/attachment/L-RIOK2-BGKcLV30-36.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RIOK2. (RIOK2-BGKcLV30-36)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS255XED at ENCODE; https://www.encodeproject.org/ENCBS255XED/

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


title: microRNA-seq from layer of hippocampus (ENCLB390SCS)

description:
https://www.encodeproject.org/experiments/ENCSR625RML/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND25 female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR625RML
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB390SCS
size range: <30

value: tissue

value: female

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS369QTC at ENCODE; https://www.encodeproject.org/ENCBS369QTC/

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


title: total RNA-seq from K562 (ENCLB974PDS)

description:
https://www.encodeproject.org/experiments/ENCSR693JOK/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with GSK J4 for 24 hours
experiment encode accession: ENCSR693JOK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB974PDS
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 100 nM GSK J4 for 24 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: adult

value: Will Greenleaf, Stanford

value: treatment_term_name:GSK J4; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS190GEP at ENCODE; https://www.encodeproject.org/ENCBS190GEP/


title: total RNA-seq from K562 (ENCLB826PKS)

description:
https://www.encodeproject.org/experiments/ENCSR693JOK/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with GSK J4 for 24 hours
experiment encode accession: ENCSR693JOK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB826PKS
size range: 300-600

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS491OPF at ENCODE; https://www.encodeproject.org/ENCBS491OPF/


title: microRNA-seq from gastrocnemius (ENCLB143ZWD)

description:
https://www.encodeproject.org/experiments/ENCSR549CLV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR549CLV
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB143ZWD
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (2 months) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: B6Cast F1 PND 2 months Male 04 gastrocnemius for Wold core

value: male

value: unknown

value: 2 month

value: ENCBS689CSE at ENCODE; https://www.encodeproject.org/ENCBS689CSE/


title: PRO-cap from HCT116 (ENCLB673JCC)

description:
https://www.encodeproject.org/experiments/ENCSR261OWE/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CTCF_T.
experiment encode accession: ENCSR261OWE
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB673JCC
spikeins used: The drosophila spike-in reference used for alignment

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

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS637VLU at ENCODE; https://www.encodeproject.org/ENCBS637VLU/

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


title: microRNA-seq from left cerebral cortex (ENCLB010ADV)

description:
https://www.encodeproject.org/experiments/ENCSR560FAG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND4 female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR560FAG
assay title: microRNA-seq
assembly: mm10
encode release date: 2022-01-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB010ADV
size range: <30

value: left cerebral cortex

value: B6Cast F1 PND4 Female 04 left cerebral cortex for Wold biobank

value: female

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS567ZSA at ENCODE; https://www.encodeproject.org/ENCBS567ZSA/

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


title: microRNA-seq from gastrocnemius (ENCLB761GUO)

description:
https://www.encodeproject.org/experiments/ENCSR549CLV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR549CLV
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB761GUO
size range: <30

value: gastrocnemius

value: tissue

value: B6Cast F1 PND 2 months Male 03 gastrocnemius for Wold core

value: male

value: unknown

value: 2 month

value: ENCBS258UBR at ENCODE; https://www.encodeproject.org/ENCBS258UBR/


title: PRO-cap from HCT116 (ENCLB041FKF)

description:
https://www.encodeproject.org/experiments/ENCSR261OWE/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CTCF_T.
experiment encode accession: ENCSR261OWE
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB041FKF
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: Homo sapiens

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS304XWN at ENCODE; https://www.encodeproject.org/ENCBS304XWN/


title: CRISPR RNA-seq from HepG2 (ENCLB922HEC)

description:
https://www.encodeproject.org/experiments/ENCSR256UIA/
***************
biological replicate number: 2
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: ENCLB922HEC
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 DBNL

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/efbd2dc7-9790-4595-8a93-0dfa86443798/@@download/attachment/L-DBNL-BGHcLV29-60.pdf

value: DBNL

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DBNL. (DBNL-BGHcLV29-60)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS839YIC at ENCODE; https://www.encodeproject.org/ENCBS839YIC/

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