title: microRNA-seq from middle frontal area 46 (ENCLB027ZAV)

description:
https://www.encodeproject.org/experiments/ENCSR757ALD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR757ALD
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB027ZAV
size range: <30

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 90 or above year

value: ENCBS253LWF at ENCODE; https://www.encodeproject.org/ENCBS253LWF/

value: Derived from ENCODE donor ENCDO242JQO; https://www.encodeproject.org/ENCDO242JQO/


title: total RNA-seq from middle frontal area 46 (ENCLB210MRR)

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/ENCSR693KOP/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_2842953_BS95_ENC4_cDNA672
experiment encode accession: ENCSR693KOP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB210MRR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

tag: description

tag: biosample encode accession

tag: organism

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: 86 year

tag: lab

value: Barbara Wold, Caltech

tag: source

value: Rush University

tag: link

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

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


title: microRNA-seq from activated naive CD8-positive, alpha-beta T cell (ENCLB516WVY)

description:
https://www.encodeproject.org/experiments/ENCSR235AGT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human naive CD8+ T cell (activated day 7) microRNA-seq from Mortazavi
experiment encode accession: ENCSR235AGT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB516WVY
size range: <30

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

value: primary cell

value: naive CD8+ cell, activated Day 7

value: male

value: 30 year

value: AllCells

value: ENCBS900CSN at ENCODE; https://www.encodeproject.org/ENCBS900CSN/

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


title: microRNA-seq from middle frontal area 46 (ENCLB516VKB)

description:
https://www.encodeproject.org/experiments/ENCSR211KOS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR211KOS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB516VKB
size range: <30

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

value: middle frontal area 46

value: tissue

value: human_brain_Rush ID_E3348003_BS71

value: Homo sapiens

value: 90 or above year

value: ENCBS127CGY at ENCODE; https://www.encodeproject.org/ENCBS127CGY/

value: Derived from ENCODE donor ENCDO730UYW; https://www.encodeproject.org/ENCDO730UYW/


title: microRNA-seq from middle frontal area 46 (ENCLB334UTQ)

description:
https://www.encodeproject.org/experiments/ENCSR795ARM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR795ARM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB334UTQ
size range: <30

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

value: adult

value: 83 year

value: Barbara Wold, Caltech

value: Rush University

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

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


title: total RNA-seq from middle frontal area 46 (ENCLB004MEV)

description:
https://www.encodeproject.org/experiments/ENCSR339NMQ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_8074960_BS43_ENC4_cDNA658
experiment encode accession: ENCSR339NMQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB004MEV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: female

value: 89 year

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

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


title: microRNA-seq from middle frontal area 46 (ENCLB053ICS)

description:
https://www.encodeproject.org/experiments/ENCSR650DHI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR650DHI
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB053ICS
size range: <30

value: middle frontal area 46

value: ENCBS960KGD at ENCODE; https://www.encodeproject.org/ENCBS960KGD/

value: Derived from ENCODE donor ENCDO853VGZ; https://www.encodeproject.org/ENCDO853VGZ/


title: CRISPR RNA-seq from K562 (ENCLB274FLM)

description:
https://www.encodeproject.org/experiments/ENCSR654SOD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGKcLV26)
experiment encode accession: ENCSR654SOD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB274FLM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens AGFG1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b5e8b05f-cb5a-4a4f-9870-19fc80b1e4ca/@@download/attachment/L-AGFG1-BGKcLV26-15.pdf

tag: antibody

tag: line

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGKcLV26-15)

value: Homo sapiens

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS035SQW at ENCODE; https://www.encodeproject.org/ENCBS035SQW/

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


title: total RNA-seq from middle frontal area 46 (ENCLB623NJE)

description:
https://www.encodeproject.org/experiments/ENCSR648JOK/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_4933693_BS56_ENC4_cDNA652
experiment encode accession: ENCSR648JOK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB623NJE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS436WHA at ENCODE; https://www.encodeproject.org/ENCBS436WHA/

value: Derived from ENCODE donor ENCDO258GJF; https://www.encodeproject.org/ENCDO258GJF/


title: Bru-seq from HCT116 (ENCLB131XKM)

description:
https://www.encodeproject.org/experiments/ENCSR651PJF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR651PJF
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR810EZV
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB131XKM
size range: 400-500

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

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

value: ENCBS156BEM at ENCODE; https://www.encodeproject.org/ENCBS156BEM/

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


title: Bru-seq from HCT116 (ENCLB859EPD)

description:
https://www.encodeproject.org/experiments/ENCSR651PJF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR651PJF
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR810EZV
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB859EPD
size range: 400-500

value: cell line

value: Homo sapiens

value: ENCBS488HJZ at ENCODE; https://www.encodeproject.org/ENCBS488HJZ/


title: microRNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB983NUU)

description:
https://www.encodeproject.org/experiments/ENCSR641JYN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human naive CD8+ T cell microRNA-seq from Mortazavi
experiment encode accession: ENCSR641JYN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB983NUU
size range: <30

source_name: Homo sapiens male adult (30 years) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: naïve CD8+ T cell(CD45RO-CCR7+)

value: adult

value: 30 year

value: AllCells

value: ENCBS048QUB at ENCODE; https://www.encodeproject.org/ENCBS048QUB/

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


title: microRNA-seq from Caco-2 (ENCLB693HZV)

description:
https://www.encodeproject.org/experiments/ENCSR638OIX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human Caco-2 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR638OIX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB693HZV
size range: <30

source_name: Homo sapiens Caco-2 cell line

value: male

value: colorectal adenocarcinoma

value: 72 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS020DQC at ENCODE; https://www.encodeproject.org/ENCBS020DQC/

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


title: CRISPR RNA-seq from K562 (ENCLB253YLV)

description:
https://www.encodeproject.org/experiments/ENCSR220DTX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV28)
experiment encode accession: ENCSR220DTX
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB253YLV
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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/101fd91d-998f-4382-8920-8610c1c2621d/@@download/attachment/L-NT-BGKcLV28-1.pdf

value: cell line

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV28-1)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS735BVV at ENCODE; https://www.encodeproject.org/ENCBS735BVV/

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


title: microRNA-seq from Caco-2 (ENCLB535WFH)

description:
https://www.encodeproject.org/experiments/ENCSR638OIX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Caco-2 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR638OIX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB535WFH
size range: <30

value: Homo sapiens

value: adult

value: ENCBS075YII at ENCODE; https://www.encodeproject.org/ENCBS075YII/


title: total RNA-seq from middle frontal area 46 (ENCLB972TKV)

description:
https://www.encodeproject.org/experiments/ENCSR634JQK/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_9867116_BS108_ENC4_cDNA662
experiment encode accession: ENCSR634JQK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB972TKV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS253LWF at ENCODE; https://www.encodeproject.org/ENCBS253LWF/

value: Derived from ENCODE donor ENCDO242JQO; https://www.encodeproject.org/ENCDO242JQO/


title: microRNA-seq from middle frontal area 46 (ENCLB179WJW)

description:
https://www.encodeproject.org/experiments/ENCSR256YPC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR256YPC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB179WJW
size range: <30

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

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

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


title: CRISPR RNA-seq from K562 (ENCLB911CEZ)

description:
https://www.encodeproject.org/experiments/ENCSR220DTX/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV28)
experiment encode accession: ENCSR220DTX
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB911CEZ
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/4fb0af7f-8185-41f9-8354-600f65c459e0/@@download/attachment/L-NT-BGKcLV28-2.pdf

value: cell line

value: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV28-2)

value: female

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS225NCG at ENCODE; https://www.encodeproject.org/ENCBS225NCG/


title: microRNA-seq from MCF 10A (ENCLB282NGB)

description:
https://www.encodeproject.org/experiments/ENCSR165HDP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human MCF10A cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR165HDP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB282NGB
size range: <30

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: Homo sapiens

value: fibrocystic disease

value: adult

value: 36 year

value: Mats Ljungman, UMichigan

value: ENCBS863SFU at ENCODE; https://www.encodeproject.org/ENCBS863SFU/

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


title: microRNA-seq from MCF 10A (ENCLB286VNX)

description:
https://www.encodeproject.org/experiments/ENCSR165HDP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human MCF10A cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR165HDP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB286VNX
size range: <30

value: ENCBS534SPQ at ENCODE; https://www.encodeproject.org/ENCBS534SPQ/


title: long read RNA-seq from myotube (ENCLB959RPY)

description:
https://www.encodeproject.org/experiments/ENCSR907NKV/
***************
biological replicate number: 1
technical replicate number: 1
description: C2C12 myotube
experiment encode accession: ENCSR907NKV
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB959RPY
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 0
nucleic acid starting quantity units: µg

organism: Mus musculus

source_name: Mus musculus myotube in vitro differentiated cells

value: myotube

value: in vitro differentiated cells

value: C2C12-derived myotube

value: Mus musculus

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ENCBS373BHL at ENCODE; https://www.encodeproject.org/ENCBS373BHL/

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


title: CRISPR RNA-seq from K562 (ENCLB602NAY)

description:
https://www.encodeproject.org/experiments/ENCSR218ITU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC31A. (SEC31A-BGKcLV33)
experiment encode accession: ENCSR218ITU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB602NAY
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 SECISBP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/af5562f3-0cb0-4330-97a9-f55d43047e29/@@download/attachment/L-SEC31A-BGKcLV33-37.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC31A. (SEC31A-BGKcLV33-37)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS820TRC at ENCODE; https://www.encodeproject.org/ENCBS820TRC/

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


title: microRNA-seq from middle frontal area 46 (ENCLB411JKX)

description:
https://www.encodeproject.org/experiments/ENCSR160XES/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR160XES
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB411JKX
size range: <30

value: middle frontal area 46

value: tissue

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS958WOW at ENCODE; https://www.encodeproject.org/ENCBS958WOW/

value: Derived from ENCODE donor ENCDO394ZHU; https://www.encodeproject.org/ENCDO394ZHU/


title: microRNA-seq from middle frontal area 46 (ENCLB406TDP)

description:
https://www.encodeproject.org/experiments/ENCSR153PPA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR153PPA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB406TDP
size range: <30

value: ENCBS305EMK at ENCODE; https://www.encodeproject.org/ENCBS305EMK/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: microRNA-seq from middle frontal area 46 (ENCLB246CFA)

description:
https://www.encodeproject.org/experiments/ENCSR630MSF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR630MSF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB246CFA
size range: <30

value: Homo sapiens

value: female

value: ENCBS420NOS at ENCODE; https://www.encodeproject.org/ENCBS420NOS/

value: Derived from ENCODE donor ENCDO093CLS; https://www.encodeproject.org/ENCDO093CLS/


title: CRISPR RNA-seq from K562 (ENCLB714DBW)

description:
https://www.encodeproject.org/experiments/ENCSR218ITU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC31A. (SEC31A-BGKcLV33)
experiment encode accession: ENCSR218ITU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB714DBW
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/9455b9f4-eda3-4850-862c-564bf25b7827/@@download/attachment/L-SEC31A-BGKcLV33-38.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC31A. (SEC31A-BGKcLV33-38)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS258NMY at ENCODE; https://www.encodeproject.org/ENCBS258NMY/


title: CRISPR RNA-seq from HepG2 (ENCLB492RCN)

description:
https://www.encodeproject.org/experiments/ENCSR213ILK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against LARS. (LARS-BGHcLV24)
experiment encode accession: ENCSR213ILK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB492RCN
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 LARS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/310ff896-3f62-4768-887e-958104465fbc/@@download/attachment/L-LARS-BGHcLV24-36.pdf

value: LARS

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against LARS. (LARS-BGHcLV24-36)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS195ZYH at ENCODE; https://www.encodeproject.org/ENCBS195ZYH/

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


title: microRNA-seq from OCI-LY7 (ENCLB047FOU)

description:
https://www.encodeproject.org/experiments/ENCSR596ZXX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human OCI-LY7 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR596ZXX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB047FOU
size range: <30

source_name: Homo sapiens OCI-LY7 cell line

value: Homo sapiens

value: B cell lymphoma

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS869GJQ at ENCODE; https://www.encodeproject.org/ENCBS869GJQ/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: microRNA-seq from middle frontal area 46 (ENCLB152ZMP)

description:
https://www.encodeproject.org/experiments/ENCSR142LHL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR142LHL
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB152ZMP
size range: <30

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

value: middle frontal area 46

value: tissue

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS506TDA at ENCODE; https://www.encodeproject.org/ENCBS506TDA/

value: Derived from ENCODE donor ENCDO123QRW; https://www.encodeproject.org/ENCDO123QRW/


title: long read RNA-seq from myotube (ENCLB627KIH)

description:
https://www.encodeproject.org/experiments/ENCSR907NKV/
***************
biological replicate number: 2
technical replicate number: 1
description: C2C12 myotube
experiment encode accession: ENCSR907NKV
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB627KIH
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 0
nucleic acid starting quantity units: µg

value: myotube

value: in vitro differentiated cells

value: C2C12-derived myotube

value: Mus musculus

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ATCC

value: ENCBS606QKU at ENCODE; https://www.encodeproject.org/ENCBS606QKU/

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


title: total RNA-seq from middle frontal area 46 (ENCLB854WVF)

description:
https://www.encodeproject.org/experiments/ENCSR198QAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_3002106_BS114_ENC4_cDNA664
experiment encode accession: ENCSR198QAJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB854WVF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: Homo sapiens

value: female

value: adult

value: 90 or above year

value: ENCBS833CJR at ENCODE; https://www.encodeproject.org/ENCBS833CJR/

value: Derived from ENCODE donor ENCDO101GPB; https://www.encodeproject.org/ENCDO101GPB/


title: total RNA-seq from middle frontal area 46 (ENCLB877LCI)

description:
https://www.encodeproject.org/experiments/ENCSR596KAH/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_6207143_BS26_ENC4_cDNA655
experiment encode accession: ENCSR596KAH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB877LCI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS481WHG at ENCODE; https://www.encodeproject.org/ENCBS481WHG/

value: Derived from ENCODE donor ENCDO597SRH; https://www.encodeproject.org/ENCDO597SRH/


title: microRNA-seq from middle frontal area 46 (ENCLB220DBG)

description:
https://www.encodeproject.org/experiments/ENCSR158OEV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR158OEV
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB220DBG
size range: <30

value: ENCBS436WHA at ENCODE; https://www.encodeproject.org/ENCBS436WHA/

value: Derived from ENCODE donor ENCDO258GJF; https://www.encodeproject.org/ENCDO258GJF/


title: microRNA-seq from middle frontal area 46 (ENCLB555NDV)

description:
https://www.encodeproject.org/experiments/ENCSR134UWT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR134UWT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB555NDV
size range: <30

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

value: 87 year

value: ENCBS439FJF at ENCODE; https://www.encodeproject.org/ENCBS439FJF/

value: Derived from ENCODE donor ENCDO423GGP; https://www.encodeproject.org/ENCDO423GGP/


title: total RNA-seq from K562 (ENCLB101WAP)

description:
https://www.encodeproject.org/experiments/ENCSR223DWL/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Bortezomib for 48 hours
experiment encode accession: ENCSR223DWL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB101WAP
size range: 300-600

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

value: cell line

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS681WMY at ENCODE; https://www.encodeproject.org/ENCBS681WMY/

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


title: total RNA-seq from motor neuron (ENCLB423YFJ)

description:
https://www.encodeproject.org/experiments/ENCSR215KUO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR215KUO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB423YFJ
size range: 300-600

source_name: Homo sapiens male child (6 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: Homo sapiens

value: male

value: Healthy donor

value: child

value: 6 year

value: Michael Snyder, Stanford

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

value: ENCBS729GGJ at ENCODE; https://www.encodeproject.org/ENCBS729GGJ/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: microRNA-seq from middle frontal area 46 (ENCLB644MRA)

description:
https://www.encodeproject.org/experiments/ENCSR630RSK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR630RSK
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB644MRA
size range: <30

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

value: middle frontal area 46

value: tissue

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB147JVO)

description:
https://www.encodeproject.org/experiments/ENCSR213ILK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against LARS. (LARS-BGHcLV24)
experiment encode accession: ENCSR213ILK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB147JVO
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/9e28487f-ae00-47aa-aa8f-5a659b2603c4/@@download/attachment/L-LARS-BGHcLV24-35.pdf

value: LARS

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against LARS. (LARS-BGHcLV24-35)

value: Homo sapiens

value: hepatocellular carcinoma

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS428JUW at ENCODE; https://www.encodeproject.org/ENCBS428JUW/

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


title: Bru-seq from endothelial cell of umbilical vein (ENCLB131CLH)

description:
https://www.encodeproject.org/experiments/ENCSR651FWH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR651FWH
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR849FAX
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB131CLH
size range: 400-500

source_name: Homo sapiens male newborn endothelial of umbilical vein primary cell treated with 500 rad irradiation

value: endothelial cell of umbilical vein

value: primary cell

value: male

value: newborn

value: unknown

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS266RDY at ENCODE; https://www.encodeproject.org/ENCBS266RDY/

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


title: microRNA-seq from middle frontal area 46 (ENCLB971AYW)

description:
https://www.encodeproject.org/experiments/ENCSR153LFS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR153LFS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB971AYW
size range: <30

value: middle frontal area 46

value: tissue

value: human_brain_Rush ID_E7461192_BS73

value: female

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS086OWN at ENCODE; https://www.encodeproject.org/ENCBS086OWN/

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


title: total RNA-seq from motor neuron (ENCLB897BGM)

description:
https://www.encodeproject.org/experiments/ENCSR215KUO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR215KUO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB897BGM
size range: 300-600

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: Homo sapiens

value: male

value: Healthy donor

value: child

value: 6 year

value: Michael Snyder, Stanford

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

value: ENCBS127UZI at ENCODE; https://www.encodeproject.org/ENCBS127UZI/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: microRNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB737QCN)

description:
https://www.encodeproject.org/experiments/ENCSR077VTG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human naive CD4+ T cells (activated day 7) microRNA-seq from Mortazavi
experiment encode accession: ENCSR077VTG
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB737QCN
size range: <30

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

value: primary cell

value: Naïve CD4+ T cell, activated Day 7

value: adult

value: 43 year

value: AllCells

value: ENCBS917XRI at ENCODE; https://www.encodeproject.org/ENCBS917XRI/

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


title: microRNA-seq from middle frontal area 46 (ENCLB398YHM)

description:
https://www.encodeproject.org/experiments/ENCSR135RRX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR135RRX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB398YHM
size range: <30

source_name: Homo sapiens male adult (84 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 84 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS934BVK at ENCODE; https://www.encodeproject.org/ENCBS934BVK/

value: Derived from ENCODE donor ENCDO999WDR; https://www.encodeproject.org/ENCDO999WDR/


title: Bru-seq from endothelial cell of umbilical vein (ENCLB682IEH)

description:
https://www.encodeproject.org/experiments/ENCSR651FWH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR651FWH
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR849FAX
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB682IEH
size range: 400-500

value: endothelial cell of umbilical vein

value: Homo sapiens

value: male

value: newborn

value: unknown

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS347UZX at ENCODE; https://www.encodeproject.org/ENCBS347UZX/

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


title: DNase-seq from suppressor macrophage (ENCLB925CYY)

description:
https://www.encodeproject.org/experiments/ENCSR405FAK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR405FAK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB925CYY
instrument models: Illumina HiSeq 2500,Illumina HiSeq 4000

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens male adult (40 years) suppressor macrophage primary cell treated with lipopolysaccharide for 1 hour

value: suppressor macrophage

value: primary cell

value: adult

value: 40 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:1; duration_units:hour;

value: ENCBS857VYG at ENCODE; https://www.encodeproject.org/ENCBS857VYG/

value: Derived from ENCODE donor ENCDO661IWU; https://www.encodeproject.org/ENCDO661IWU/


title: DNase-seq from suppressor macrophage (ENCLB040XRV)

description:
https://www.encodeproject.org/experiments/ENCSR325GNM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR325GNM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB040XRV
instrument models: Illumina HiSeq 2500,Illumina HiSeq 4000,Illumina NextSeq 500

source_name: Homo sapiens male adult (21 years) suppressor macrophage primary cell

value: 21 year

value: ENCBS012PFZ at ENCODE; https://www.encodeproject.org/ENCBS012PFZ/

value: Derived from ENCODE donor ENCDO733YAB; https://www.encodeproject.org/ENCDO733YAB/


title: microRNA-seq from OCI-LY7 (ENCLB351HMI)

description:
https://www.encodeproject.org/experiments/ENCSR596ZXX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human OCI-LY7 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR596ZXX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB351HMI
size range: <30

value: cell line

value: Homo sapiens

value: male

value: B cell lymphoma

value: 48 year

value: DSMZ

value: ENCBS112SEO at ENCODE; https://www.encodeproject.org/ENCBS112SEO/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: microRNA-seq from middle frontal area 46 (ENCLB209VRB)

description:
https://www.encodeproject.org/experiments/ENCSR105ZCZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR105ZCZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB209VRB
size range: <30

source_name: Homo sapiens female adult (75 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: adult

value: 75 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS721KTA at ENCODE; https://www.encodeproject.org/ENCBS721KTA/

value: Derived from ENCODE donor ENCDO989QRD; https://www.encodeproject.org/ENCDO989QRD/


title: total RNA-seq from middle frontal area 46 (ENCLB090QPS)

description:
https://www.encodeproject.org/experiments/ENCSR296RWI/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8949399_BS187_ENC4_cDNA741
experiment encode accession: ENCSR296RWI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB090QPS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: 89 year

value: ENCBS395DLA at ENCODE; https://www.encodeproject.org/ENCBS395DLA/

value: Derived from ENCODE donor ENCDO830KFO; https://www.encodeproject.org/ENCDO830KFO/


title: CRISPR RNA-seq from HepG2 (ENCLB119ENP)

description:
https://www.encodeproject.org/experiments/ENCSR207GTU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGHcLV31)
experiment encode accession: ENCSR207GTU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB119ENP
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 SARNP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4392a0ed-f002-4a14-abb0-47ed07853951/@@download/attachment/L-SARNP-BGHcLV31-28.pdf

value: SARNP

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGHcLV31-28)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS227PHU at ENCODE; https://www.encodeproject.org/ENCBS227PHU/

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


title: CRISPR RNA-seq from HepG2 (ENCLB426TCI)

description:
https://www.encodeproject.org/experiments/ENCSR650TTU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV27)
experiment encode accession: ENCSR650TTU
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB426TCI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a0759517-6740-47df-8be4-127db5954065/@@download/attachment/L-NT-BGHcLV27-1.pdf

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV27-1)

value: ENCBS622KXD at ENCODE; https://www.encodeproject.org/ENCBS622KXD/


title: microRNA-seq from activated CD8-positive, alpha-beta T cell (ENCLB448FSZ)

description:
https://www.encodeproject.org/experiments/ENCSR092HEE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human CD8+ T cells (activated day 7) microRNA-seq from Mortazavi
experiment encode accession: ENCSR092HEE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB448FSZ
size range: <30

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS272IFK at ENCODE; https://www.encodeproject.org/ENCBS272IFK/

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


title: microRNA-seq from endothelial cell of umbilical vein (ENCLB075OZQ)

description:
https://www.encodeproject.org/experiments/ENCSR076EJO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human HUVEC primary cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR076EJO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB075OZQ
size range: <30

source_name: Homo sapiens newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: not collected

value: unknown

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS820SXP at ENCODE; https://www.encodeproject.org/ENCBS820SXP/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: total RNA-seq from middle frontal area 46 (ENCLB124MLY)

description:
https://www.encodeproject.org/experiments/ENCSR718YUW/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1097236_BS118_ENC4_cDNA680
experiment encode accession: ENCSR718YUW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB124MLY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens female adult (85 years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: 85 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS372KDQ at ENCODE; https://www.encodeproject.org/ENCBS372KDQ/

value: Derived from ENCODE donor ENCDO080EZF; https://www.encodeproject.org/ENCDO080EZF/


title: total RNA-seq from middle frontal area 46 (ENCLB144CQU)

description:
https://www.encodeproject.org/experiments/ENCSR706NYL/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2987202_BS122_ENC4_cDNA684
experiment encode accession: ENCSR706NYL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB144CQU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

value: male

value: adult

value: 90 or above year

value: ENCBS606ENA at ENCODE; https://www.encodeproject.org/ENCBS606ENA/

value: Derived from ENCODE donor ENCDO921RVK; https://www.encodeproject.org/ENCDO921RVK/


title: microRNA-seq from CD8-positive, alpha-beta T cell (ENCLB314RRC)

description:
https://www.encodeproject.org/experiments/ENCSR583BQO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human CD8+ T cell microRNA-seq from Mortazavi
experiment encode accession: ENCSR583BQO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB314RRC
size range: <30

source_name: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS222RFX at ENCODE; https://www.encodeproject.org/ENCBS222RFX/

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


title: PRO-seq from HCT116 (ENCLB327EMN)

description:
https://www.encodeproject.org/experiments/ENCSR703UYN/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in RAD21_U
experiment encode accession: ENCSR703UYN
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB327EMN
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 RAD21

value: cell line

value: Homo sapiens

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS858EAQ at ENCODE; https://www.encodeproject.org/ENCBS858EAQ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB036MLA)

description:
https://www.encodeproject.org/experiments/ENCSR207GTU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGHcLV31)
experiment encode accession: ENCSR207GTU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB036MLA
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/9b1a394b-2ea9-41a6-8a4c-c984ff57b37e/@@download/attachment/L-SARNP-BGHcLV31-27.pdf

value: SARNP

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGHcLV31-27)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS621TYJ at ENCODE; https://www.encodeproject.org/ENCBS621TYJ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB019FUI)

description:
https://www.encodeproject.org/experiments/ENCSR650TTU/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV27)
experiment encode accession: ENCSR650TTU
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB019FUI
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/0283f731-f743-4873-b91d-c79c03beea71/@@download/attachment/L-NT-BGHcLV27-2.pdf

value: cell line

value: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV27-2)

value: Homo sapiens

value: ENCBS462HZR at ENCODE; https://www.encodeproject.org/ENCBS462HZR/


title: PRO-seq from HCT116 (ENCLB344QZS)

description:
https://www.encodeproject.org/experiments/ENCSR703UYN/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in RAD21_U
experiment encode accession: ENCSR703UYN
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB344QZS
spikeins used: The drosophila spike-in reference used for alignment

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS645VXU at ENCODE; https://www.encodeproject.org/ENCBS645VXU/


title: microRNA-seq from middle frontal area 46 (ENCLB306UDA)

description:
https://www.encodeproject.org/experiments/ENCSR067CHU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR067CHU
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB306UDA
size range: <30

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

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS745ELX at ENCODE; https://www.encodeproject.org/ENCBS745ELX/

value: Derived from ENCODE donor ENCDO730UYW; https://www.encodeproject.org/ENCDO730UYW/


title: total RNA-seq from K562 (ENCLB498HGW)

description:
https://www.encodeproject.org/experiments/ENCSR206KFV/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Galeterone for 4 hours
experiment encode accession: ENCSR206KFV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB498HGW
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 25 uM Galeterone for 4 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS511LEK at ENCODE; https://www.encodeproject.org/ENCBS511LEK/

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


title: total RNA-seq from K562 (ENCLB277SMD)

description:
https://www.encodeproject.org/experiments/ENCSR206KFV/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Galeterone for 4 hours
experiment encode accession: ENCSR206KFV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB277SMD
size range: 300-600

value: Homo sapiens

value: adult

value: ENCBS849QLO at ENCODE; https://www.encodeproject.org/ENCBS849QLO/


title: total RNA-seq from middle frontal area 46 (ENCLB007CFV)

description:
https://www.encodeproject.org/experiments/ENCSR061HMO/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_4163791_BS53_ENC4_cDNA650
experiment encode accession: ENCSR061HMO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB007CFV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB773IQI)

description:
https://www.encodeproject.org/experiments/ENCSR206ICZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGHcLV29)
experiment encode accession: ENCSR206ICZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB773IQI
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 CHCHD3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/73f6373d-62e5-4d74-a6f8-31668355e932/@@download/attachment/L-CHCHD3-BGHcLV29-17.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGHcLV29-17)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS950SXM at ENCODE; https://www.encodeproject.org/ENCBS950SXM/

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


title: total RNA-seq from middle frontal area 46 (ENCLB734LZJ)

description:
https://www.encodeproject.org/experiments/ENCSR282UMY/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2962456_BS145_ENC4_cDNA695
experiment encode accession: ENCSR282UMY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB734LZJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

value: Homo sapiens

value: adult

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS305EMK at ENCODE; https://www.encodeproject.org/ENCBS305EMK/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: microRNA-seq from endothelial cell of umbilical vein (ENCLB501KHI)

description:
https://www.encodeproject.org/experiments/ENCSR076EJO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human HUVEC primary cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR076EJO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB501KHI
size range: <30

value: endothelial cell of umbilical vein

value: primary cell

value: not collected

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

value: unknown

value: ENCBS023JCN at ENCODE; https://www.encodeproject.org/ENCBS023JCN/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: total RNA-seq from middle frontal area 46 (ENCLB582TIL)

description:
https://www.encodeproject.org/experiments/ENCSR277QAN/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3348003_BS123_ENC4_cDNA685
experiment encode accession: ENCSR277QAN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB582TIL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: ENCBS745ELX at ENCODE; https://www.encodeproject.org/ENCBS745ELX/

value: Derived from ENCODE donor ENCDO730UYW; https://www.encodeproject.org/ENCDO730UYW/


title: total RNA-seq from middle frontal area 46 (ENCLB280NIG)

description:
https://www.encodeproject.org/experiments/ENCSR061RDC/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_2585111_BS94_ENC4_cDNA671
experiment encode accession: ENCSR061RDC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB280NIG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (87 years) with Alzheimer's disease, Cognitive impairment; middle frontal area 46 tissue

value: Homo sapiens

value: adult

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS839OMR at ENCODE; https://www.encodeproject.org/ENCBS839OMR/

value: Derived from ENCODE donor ENCDO940VNT; https://www.encodeproject.org/ENCDO940VNT/


title: total RNA-seq from middle frontal area 46 (ENCLB115HZP)

description:
https://www.encodeproject.org/experiments/ENCSR052LON/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_9158123_BS107_ENC4_cDNA661
experiment encode accession: ENCSR052LON
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB115HZP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: male

value: 71 year

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

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


title: CRISPR RNA-seq from K562 (ENCLB544CHY)

description:
https://www.encodeproject.org/experiments/ENCSR642RCV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ALDH18A1. (ALDH18A1-BGKcLV26)
experiment encode accession: ENCSR642RCV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB544CHY
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 ALDH18A1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c29b9405-e2ce-48d1-b010-5a56397e0b87/@@download/attachment/L-ALDH18A1-BGKcLV26-21.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ALDH18A1. (ALDH18A1-BGKcLV26-21)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS747IVW at ENCODE; https://www.encodeproject.org/ENCBS747IVW/

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


title: total RNA-seq from T-helper 17 cell (ENCLB359ITU)

description:
https://www.encodeproject.org/experiments/ENCSR276QGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Th17_DONOR 5: 0 hour no activation
experiment encode accession: ENCSR276QGJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB359ITU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (48 years) T-helper 17 primary cell

value: T-helper 17 cell

value: primary cell

value: Homo sapiens

value: adult

value: 48 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS765XDW at ENCODE; https://www.encodeproject.org/ENCBS765XDW/

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


title: total RNA-seq from middle frontal area 46 (ENCLB727THT)

description:
https://www.encodeproject.org/experiments/ENCSR562BUN/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_4163791_BS115_ENC4_cDNA665
experiment encode accession: ENCSR562BUN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB727THT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

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

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


title: CRISPR RNA-seq from K562 (ENCLB822RLA)

description:
https://www.encodeproject.org/experiments/ENCSR642RCV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ALDH18A1. (ALDH18A1-BGKcLV26)
experiment encode accession: ENCSR642RCV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB822RLA
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/0cf3cfb0-42d1-4792-b93a-bb05f4754344/@@download/attachment/L-ALDH18A1-BGKcLV26-22.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ALDH18A1. (ALDH18A1-BGKcLV26-22)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS138CBR at ENCODE; https://www.encodeproject.org/ENCBS138CBR/

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


title: microRNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB224PDN)

description:
https://www.encodeproject.org/experiments/ENCSR077VTG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human naive CD4+ T cells (activated day 7) microRNA-seq from Mortazavi
experiment encode accession: ENCSR077VTG
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB224PDN
size range: <30

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

value: primary cell

value: Naïve CD4+ T cell, activated Day 7

value: male

value: adult

value: 43 year

value: AllCells

value: ENCBS125FDB at ENCODE; https://www.encodeproject.org/ENCBS125FDB/

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


title: total RNA-seq from middle frontal area 46 (ENCLB068TJY)

description:
https://www.encodeproject.org/experiments/ENCSR997XXK/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1652886_BS174_ENC4_cDNA728
experiment encode accession: ENCSR997XXK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB068TJY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (86 years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: 86 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS492ELW at ENCODE; https://www.encodeproject.org/ENCBS492ELW/

value: Derived from ENCODE donor ENCDO943KXE; https://www.encodeproject.org/ENCDO943KXE/


title: microRNA-seq from middle frontal area 46 (ENCLB823TMQ)

description:
https://www.encodeproject.org/experiments/ENCSR027DKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR027DKQ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB823TMQ
size range: <30

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

value: 90 or above year

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

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


title: CRISPR RNA-seq from HepG2 (ENCLB509UKE)

description:
https://www.encodeproject.org/experiments/ENCSR199WMC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against REXO2. (REXO2-BGHcLV32)
experiment encode accession: ENCSR199WMC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB509UKE
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 REXO2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c3c3f9dc-e1ff-4165-836c-bce7b240369d/@@download/attachment/L-REXO2-BGHcLV32-30.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against REXO2. (REXO2-BGHcLV32-30)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS897RMB at ENCODE; https://www.encodeproject.org/ENCBS897RMB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB217NFR)

description:
https://www.encodeproject.org/experiments/ENCSR199WMC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against REXO2. (REXO2-BGHcLV32)
experiment encode accession: ENCSR199WMC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR232ERY
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB217NFR
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/d9353a82-60b6-4c98-94fe-9ee60d35626e/@@download/attachment/L-REXO2-BGHcLV32-29.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against REXO2. (REXO2-BGHcLV32-29)

value: Homo sapiens

value: ENCBS727HEC at ENCODE; https://www.encodeproject.org/ENCBS727HEC/


title: microRNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB329DLF)

description:
https://www.encodeproject.org/experiments/ENCSR522TYY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human naive CD4+ T cells (activated day 2) microRNA-seq from Mortazavi
experiment encode accession: ENCSR522TYY
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB329DLF
size range: <30

value: primary cell

value: Naïve CD4+ T cell, activated Day 2

value: adult

value: 43 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS545EHI at ENCODE; https://www.encodeproject.org/ENCBS545EHI/

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


title: CRISPR RNA-seq from HepG2 (ENCLB971MRZ)

description:
https://www.encodeproject.org/experiments/ENCSR206ICZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGHcLV29)
experiment encode accession: ENCSR206ICZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB971MRZ
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/9d52e6e2-302d-4b0b-b950-b8366950ceff/@@download/attachment/L-CHCHD3-BGHcLV29-18.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGHcLV29-18)

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS907ALU at ENCODE; https://www.encodeproject.org/ENCBS907ALU/


title: CRISPR RNA-seq from K562 (ENCLB042VFP)

description:
https://www.encodeproject.org/experiments/ENCSR642LZB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGKcLV33)
experiment encode accession: ENCSR642LZB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB042VFP
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 SPATS2L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/58638fdf-2caa-480d-97f4-16b187a835a2/@@download/attachment/L-SPAG9-BGKcLV33-67.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGKcLV33-67)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS885LGM at ENCODE; https://www.encodeproject.org/ENCBS885LGM/

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


title: total RNA-seq from middle frontal area 46 (ENCLB781GCN)

description:
https://www.encodeproject.org/experiments/ENCSR036SUN/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_1863332_BS91_ENC4_cDNA668
experiment encode accession: ENCSR036SUN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB781GCN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS958WOW at ENCODE; https://www.encodeproject.org/ENCBS958WOW/

value: Derived from ENCODE donor ENCDO394ZHU; https://www.encodeproject.org/ENCDO394ZHU/


title: total RNA-seq from activated T-cell (ENCLB357ADU)

description:
https://www.encodeproject.org/experiments/ENCSR995GRL/
***************
biological replicate number: 1
technical replicate number: 2
description: CD3+_DONOR 4: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR995GRL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB357ADU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (21 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: primary cell

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

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

value: ENCBS257FNC at ENCODE; https://www.encodeproject.org/ENCBS257FNC/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: microRNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB906YYU)

description:
https://www.encodeproject.org/experiments/ENCSR522TYY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human naive CD4+ T cells (activated day 2) microRNA-seq from Mortazavi
experiment encode accession: ENCSR522TYY
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB906YYU
size range: <30

value: Naïve CD4+ T cell, activated Day 2

value: male

value: 43 year

value: AllCells

value: ENCBS211PXT at ENCODE; https://www.encodeproject.org/ENCBS211PXT/

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


title: CRISPR RNA-seq from K562 (ENCLB769HXE)

description:
https://www.encodeproject.org/experiments/ENCSR642LZB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGKcLV33)
experiment encode accession: ENCSR642LZB
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB769HXE
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/be9b9030-8067-4892-8752-e852ca0d1b7b/@@download/attachment/L-SPAG9-BGKcLV33-68.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGKcLV33-68)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS390WRH at ENCODE; https://www.encodeproject.org/ENCBS390WRH/

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


title: microRNA-seq from mammary epithelial cell (ENCLB675PEB)

description:
https://www.encodeproject.org/experiments/ENCSR022IFZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human HMEC cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR022IFZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB675PEB
size range: <30

source_name: Homo sapiens female mammary epithelial primary cell

value: mammary epithelial cell

value: primary cell

value: unknown

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS996RLF at ENCODE; https://www.encodeproject.org/ENCBS996RLF/

value: Derived from ENCODE donor ENCDO343AAA; https://www.encodeproject.org/ENCDO343AAA/


title: PRO-cap from HCT116 (ENCLB926QHU)

description:
https://www.encodeproject.org/experiments/ENCSR197JLW/
***************
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 POLR2A_T.
experiment encode accession: ENCSR197JLW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB926QHU
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

treatment_protocol: E14.5 and E17.5 pancreata from either WT B6 or eFev-YFP transgenic mice were dissociated to single cells and subjected to FACS. WT pancreas was sorted for all live single cells, and Fev-YFP+ pancreas was further sorted for CD140a-/CD326+/YFP+ cells.

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS275ZVJ at ENCODE; https://www.encodeproject.org/ENCBS275ZVJ/

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


title: total RNA-seq from activated T-cell (ENCLB008GSE)

description:
https://www.encodeproject.org/experiments/ENCSR995GRL/
***************
biological replicate number: 1
technical replicate number: 1
description: CD3+_DONOR 4: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR995GRL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB008GSE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: activated T-cell

value: Homo sapiens

value: female

value: adult

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

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

value: ENCBS257FNC at ENCODE; https://www.encodeproject.org/ENCBS257FNC/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: total RNA-seq from middle frontal area 46 (ENCLB706XFB)

description:
https://www.encodeproject.org/experiments/ENCSR985WSV/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7431498_BS183_ENC4_cDNA737
experiment encode accession: ENCSR985WSV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB706XFB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (84 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 84 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS967WLC at ENCODE; https://www.encodeproject.org/ENCBS967WLC/

value: Derived from ENCODE donor ENCDO461DJY; https://www.encodeproject.org/ENCDO461DJY/


title: PRO-cap from HCT116 (ENCLB413GVQ)

description:
https://www.encodeproject.org/experiments/ENCSR197JLW/
***************
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 POLR2A_T.
experiment encode accession: ENCSR197JLW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB413GVQ
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS486IFU at ENCODE; https://www.encodeproject.org/ENCBS486IFU/

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


title: microRNA-seq from mammary epithelial cell (ENCLB621NSR)

description:
https://www.encodeproject.org/experiments/ENCSR022IFZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human HMEC cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR022IFZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-12-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB621NSR
size range: <30

value: mammary epithelial cell

value: primary cell

value: female

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS710VQU at ENCODE; https://www.encodeproject.org/ENCBS710VQU/

value: Derived from ENCODE donor ENCDO343AAA; https://www.encodeproject.org/ENCDO343AAA/


title: total RNA-seq from activated T-cell (ENCLB474RDC)

description:
https://www.encodeproject.org/experiments/ENCSR995GRL/
***************
biological replicate number: 1
technical replicate number: 3
description: CD3+_DONOR 4: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR995GRL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB474RDC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: activated T-cell

value: Homo sapiens

value: adult

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

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

value: ENCBS257FNC at ENCODE; https://www.encodeproject.org/ENCBS257FNC/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: total RNA-seq from middle frontal area 46 (ENCLB878WIT)

description:
https://www.encodeproject.org/experiments/ENCSR965OKL/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2229963_BS176_ENC4_cDNA730
experiment encode accession: ENCSR965OKL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB878WIT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (78 years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 78 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS500QUI at ENCODE; https://www.encodeproject.org/ENCBS500QUI/

value: Derived from ENCODE donor ENCDO203GSG; https://www.encodeproject.org/ENCDO203GSG/


title: total RNA-seq from middle frontal area 46 (ENCLB635HXQ)

description:
https://www.encodeproject.org/experiments/ENCSR019ICB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_2327042_BS92_ENC4_cDNA669
experiment encode accession: ENCSR019ICB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB635HXQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: female

value: 90 or above year

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

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


title: total RNA-seq from activated T-helper 17 cell (ENCLB187IAQ)

description:
https://www.encodeproject.org/experiments/ENCSR964JRR/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Th17_DONOR 6: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR964JRR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB187IAQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

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

value: activated T-helper 17 cell

value: primary cell

value: Homo sapiens

value: male

value: adult

value: 50 year

value: ENCBS304KCD at ENCODE; https://www.encodeproject.org/ENCBS304KCD/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: total RNA-seq from K562 (ENCLB319WDF)

description:
https://www.encodeproject.org/experiments/ENCSR195JRH/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with JQ1 for 12 hours
experiment encode accession: ENCSR195JRH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB319WDF
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM JQ1 for 12 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:JQ1; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS172RKT at ENCODE; https://www.encodeproject.org/ENCBS172RKT/

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


title: CRISPR RNA-seq from HepG2 (ENCLB449WON)

description:
https://www.encodeproject.org/experiments/ENCSR191LWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGHcLV29)
experiment encode accession: ENCSR191LWZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB449WON
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 ARHGEF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5771067d-7c9c-4743-af5c-bf4adbd8feac/@@download/attachment/L-ARHGEF2-BGHcLV29-4.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGHcLV29-4)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS265LMY at ENCODE; https://www.encodeproject.org/ENCBS265LMY/

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


title: microRNA-seq from middle frontal area 46 (ENCLB972DYW)

description:
https://www.encodeproject.org/experiments/ENCSR507KCT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR507KCT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB972DYW
size range: <30

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

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

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


title: microRNA-seq from middle frontal area 46 (ENCLB192EGN)

description:
https://www.encodeproject.org/experiments/ENCSR015QSB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR015QSB
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB192EGN
size range: <30

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

value: ENCBS141EMN at ENCODE; https://www.encodeproject.org/ENCBS141EMN/

value: Derived from ENCODE donor ENCDO150EBZ; https://www.encodeproject.org/ENCDO150EBZ/


title: PRO-seq from HCT116 (ENCLB641ZZO)

description:
https://www.encodeproject.org/experiments/ENCSR954XDE/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in CDK7_T
experiment encode accession: ENCSR954XDE
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB641ZZO
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS369YWA at ENCODE; https://www.encodeproject.org/ENCBS369YWA/

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


title: total RNA-seq from activated T-cell (ENCLB363NWV)

description:
https://www.encodeproject.org/experiments/ENCSR995GRL/
***************
biological replicate number: 1
technical replicate number: 4
description: CD3+_DONOR 4: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR995GRL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB363NWV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: activated T-cell

value: primary cell

value: Homo sapiens

value: female

value: adult

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

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

value: ENCBS257FNC at ENCODE; https://www.encodeproject.org/ENCBS257FNC/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: CRISPR RNA-seq from HepG2 (ENCLB409RMC)

description:
https://www.encodeproject.org/experiments/ENCSR191LWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGHcLV29)
experiment encode accession: ENCSR191LWZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB409RMC
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/b96870d2-1df8-4098-85b6-690e2663ed51/@@download/attachment/L-ARHGEF2-BGHcLV29-3.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGHcLV29-3)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS813CQS at ENCODE; https://www.encodeproject.org/ENCBS813CQS/

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