title: PRO-cap from K562 (ENCLB275OYW)

description:
https://www.encodeproject.org/experiments/ENCSR604EBH/
***************
biological replicate number: 1
technical replicate number: 2
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR604EBH
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB275OYW

value: cell line

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Lis, Cornell

value: ATCC

value: ENCBS010FNJ at ENCODE; https://www.encodeproject.org/ENCBS010FNJ/

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


title: CRISPR RNA-seq from K562 (ENCLB064DMG)

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/ENCSR119PLU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGKcLV33)
experiment encode accession: ENCSR119PLU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB064DMG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c8a4cf90-e3f0-42f2-bf0d-eb6e895e18a8/@@download/attachment/L-RUVBL1-BGKcLV33-23.pdf

tag: antibody

tag: line

tag: description

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGKcLV33-23)

tag: biosample encode accession

tag: organism

tag: Sex

tag: health state

tag: dev stage

value: adult

tag: age

tag: lab

value: Brenton Graveley, UConn

tag: source

tag: link

value: ENCBS328MIH at ENCODE; https://www.encodeproject.org/ENCBS328MIH/


title: total RNA-seq from K562 (ENCLB712FPI)

description:
https://www.encodeproject.org/experiments/ENCSR115PIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Chaetocin for 48 hours
experiment encode accession: ENCSR115PIZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB712FPI
size range: 300-600

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

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

tag: treatments

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

value: ENCBS738ZPE at ENCODE; https://www.encodeproject.org/ENCBS738ZPE/


title: long read RNA-seq from layer of hippocampus (ENCLB278HSI)

description:
https://www.encodeproject.org/experiments/ENCSR214HSG/
***************
biological replicate number: 1
technical replicate number: 1
description: Hippocampus1 from 6 mo C57BL/6 male
experiment encode accession: ENCSR214HSG
assay title: long read RNA-seq
assembly: mm10
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB278HSI

organism: Mus musculus

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

value: layer of hippocampus

value: tissue

value: Hippocampus from 6 mo C57BL/6 male

value: Mus musculus

value: not collected

value: 6 month

value: Ali Mortazavi, UCI

value: Andrea Tenner

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

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


title: total RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB895OWI)

description:
https://www.encodeproject.org/experiments/ENCSR317HKT/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th0 (no diff Cytokines)(day 14)
experiment encode accession: ENCSR317HKT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB895OWI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (35 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: Homo sapiens

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS917FHP at ENCODE; https://www.encodeproject.org/ENCBS917FHP/

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


title: total RNA-seq from middle frontal area 46 (ENCLB867LNB)

description:
https://www.encodeproject.org/experiments/ENCSR693CVD/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7763031_BS210_ENC4_cDNA765
experiment encode accession: ENCSR693CVD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB867LNB
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: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS368BJM at ENCODE; https://www.encodeproject.org/ENCBS368BJM/

value: Derived from ENCODE donor ENCDO672KST; https://www.encodeproject.org/ENCDO672KST/


title: long read RNA-seq from left cerebral cortex (ENCLB516DGU)

description:
https://www.encodeproject.org/experiments/ENCSR340GWV/
***************
biological replicate number: 1
technical replicate number: 1
description: Cortex1 from 6 mo C57BL/6 male
experiment encode accession: ENCSR340GWV
assay title: long read RNA-seq
assembly: mm10
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB516DGU

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

value: left cerebral cortex

value: Cortex from 6 mo C57BL/6 male

value: Mus musculus

value: not collected

value: 6 month

value: Ali Mortazavi, UCI

value: Andrea Tenner

value: ENCBS668TCF at ENCODE; https://www.encodeproject.org/ENCBS668TCF/

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


title: long read RNA-seq from layer of hippocampus (ENCLB067AJF)

description:
https://www.encodeproject.org/experiments/ENCSR214HSG/
***************
biological replicate number: 2
technical replicate number: 1
description: Hippocampus1 from 6 mo C57BL/6 male
experiment encode accession: ENCSR214HSG
assay title: long read RNA-seq
assembly: mm10
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB067AJF

value: layer of hippocampus

value: Hippocampus from 6 mo C57BL/6 male

value: adult

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


title: total RNA-seq from K562 (ENCLB294QEZ)

description:
https://www.encodeproject.org/experiments/ENCSR115PIZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Chaetocin for 48 hours
experiment encode accession: ENCSR115PIZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB294QEZ
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS360EBB at ENCODE; https://www.encodeproject.org/ENCBS360EBB/

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


title: PRO-cap from K562 (ENCLB652JVN)

description:
https://www.encodeproject.org/experiments/ENCSR604EBH/
***************
biological replicate number: 2
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR604EBH
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB652JVN

source_name: Homo sapiens K562 cell line

value: John Lis, Cornell

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


title: PRO-cap from K562 (ENCLB888WSM)

description:
https://www.encodeproject.org/experiments/ENCSR149ZRX/
***************
biological replicate number: 2
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and PCR amplification was performed before sequencing.
experiment encode accession: ENCSR149ZRX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB888WSM

value: ENCBS396XJP at ENCODE; https://www.encodeproject.org/ENCBS396XJP/


title: PRO-cap from K562 (ENCLB623HEK)

description:
https://www.encodeproject.org/experiments/ENCSR604EBH/
***************
biological replicate number: 1
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR604EBH
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB623HEK

value: ENCBS010FNJ at ENCODE; https://www.encodeproject.org/ENCBS010FNJ/


title: PRO-cap from K562 (ENCLB822KAX)

description:
https://www.encodeproject.org/experiments/ENCSR114HGS/
***************
biological replicate number: 1
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and PCR amplification was performed before sequencing.
experiment encode accession: ENCSR114HGS
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB822KAX

value: adult

value: ENCBS687QFM at ENCODE; https://www.encodeproject.org/ENCBS687QFM/


title: PRO-seq from HCT116 (ENCLB695LGP)

description:
https://www.encodeproject.org/experiments/ENCSR673THD/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in CTCF_T
experiment encode accession: ENCSR673THD
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB695LGP
spikeins used: The drosophila spike-in reference used for alignment

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

value: cell line

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

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


title: long read RNA-seq from forelimb (ENCLB069KZQ)

description:
https://www.encodeproject.org/experiments/ENCSR082JMB/
***************
biological replicate number: 1
technical replicate number: 1
description: Mus musculus strain B6NCrl embryo (13 days) forelimb tissue
experiment encode accession: ENCSR082JMB
assay title: long read RNA-seq
assembly: mm10
encode release date: 2019-12-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB069KZQ

value: forelimb

value: tissue

value: Mus musculus

value: not collected

value: embryonic

value: 13 day

value: Ali Mortazavi, UCI

value: The Jackson Laboratory

value: ENCBS250SFS at ENCODE; https://www.encodeproject.org/ENCBS250SFS/

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


title: total RNA-seq from K562 (ENCLB911FMS)

description:
https://www.encodeproject.org/experiments/ENCSR114LNC/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Vorinostat for 4 hours
experiment encode accession: ENCSR114LNC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB911FMS
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 7.5 nM Vorinostat for 4 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS542MKJ at ENCODE; https://www.encodeproject.org/ENCBS542MKJ/

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


title: total RNA-seq from middle frontal area 46 (ENCLB343FEC)

description:
https://www.encodeproject.org/experiments/ENCSR675UIU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7469794_BS126_ENC4_cDNA688
experiment encode accession: ENCSR675UIU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB343FEC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

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: ENCBS904CGT at ENCODE; https://www.encodeproject.org/ENCBS904CGT/

value: Derived from ENCODE donor ENCDO980GMJ; https://www.encodeproject.org/ENCDO980GMJ/


title: PRO-cap from K562 (ENCLB179ISC)

description:
https://www.encodeproject.org/experiments/ENCSR114HGS/
***************
biological replicate number: 2
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and PCR amplification was performed before sequencing.
experiment encode accession: ENCSR114HGS
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB179ISC

value: cell line

value: Homo sapiens

value: John Lis, Cornell

value: ENCBS742LPB at ENCODE; https://www.encodeproject.org/ENCBS742LPB/


title: total RNA-seq from WTC11 (ENCLB285JEI)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 10
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB285JEI

source_name: Homo sapiens WTC11 cell line, preserved by flash-freezing

value: iPSC

value: male

value: adult

value: 30 year

value: Coriell

value: ENCBS441RWM at ENCODE; https://www.encodeproject.org/ENCBS441RWM/

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


title: PRO-seq from HCT116 (ENCLB431EEH)

description:
https://www.encodeproject.org/experiments/ENCSR242MOQ/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in BRD4_T
experiment encode accession: ENCSR242MOQ
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB431EEH
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 BRD4 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

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: ENCBS745VSI at ENCODE; https://www.encodeproject.org/ENCBS745VSI/

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


title: total RNA-seq from K562 (ENCLB434KTF)

description:
https://www.encodeproject.org/experiments/ENCSR114LNC/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Vorinostat for 4 hours
experiment encode accession: ENCSR114LNC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB434KTF
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS408PRS at ENCODE; https://www.encodeproject.org/ENCBS408PRS/

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


title: CRISPR RNA-seq from K562 (ENCLB319GWQ)

description:
https://www.encodeproject.org/experiments/ENCSR146YRO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGKcLV28)
experiment encode accession: ENCSR146YRO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB319GWQ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dd77c385-4d54-4bf0-89a6-c21e1e5c981b/@@download/attachment/L-CTTN-BGKcLV28-51.pdf

value: CTTN

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGKcLV28-51)

value: adult

value: Brenton Graveley, UConn

value: ENCBS056LXD at ENCODE; https://www.encodeproject.org/ENCBS056LXD/


title: total RNA-seq from WTC11 (ENCLB956RNW)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 8
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB956RNW

value: iPSC

value: male

value: 30 year

value: Coriell

value: ENCBS597FPH at ENCODE; https://www.encodeproject.org/ENCBS597FPH/

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


title: PRO-seq from HCT116 (ENCLB656WEJ)

description:
https://www.encodeproject.org/experiments/ENCSR242MOQ/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in BRD4_T
experiment encode accession: ENCSR242MOQ
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB656WEJ
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: Homo sapiens

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: ENCBS191ARH at ENCODE; https://www.encodeproject.org/ENCBS191ARH/

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


title: total RNA-seq from K562 (ENCLB616ZED)

description:
https://www.encodeproject.org/experiments/ENCSR591KOB/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Crizotinib for 24 hours
experiment encode accession: ENCSR591KOB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB616ZED
size range: 300-600

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

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS703VDG at ENCODE; https://www.encodeproject.org/ENCBS703VDG/

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


title: total RNA-seq from K562 (ENCLB695HSB)

description:
https://www.encodeproject.org/experiments/ENCSR105NQB/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Vorinostat for 12 hours
experiment encode accession: ENCSR105NQB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB695HSB
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 7.5 nM Vorinostat for 12 hours, preserved by flash-freezing

value: cell line

value: Homo sapiens

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

value: ENCBS128QWT at ENCODE; https://www.encodeproject.org/ENCBS128QWT/


title: total RNA-seq from WTC11 (ENCLB563MXN)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 6
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB563MXN

value: iPSC

value: male

value: 30 year

value: Coriell

value: ENCBS167CPD at ENCODE; https://www.encodeproject.org/ENCBS167CPD/

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


title: total RNA-seq from middle frontal area 46 (ENCLB733XPU)

description:
https://www.encodeproject.org/experiments/ENCSR252IPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2395615_BS177_ENC4_cDNA731
experiment encode accession: ENCSR252IPQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB733XPU
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: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS056ENN at ENCODE; https://www.encodeproject.org/ENCBS056ENN/

value: Derived from ENCODE donor ENCDO660TGP; https://www.encodeproject.org/ENCDO660TGP/


title: total RNA-seq from K562 (ENCLB391YVG)

description:
https://www.encodeproject.org/experiments/ENCSR105NQB/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Vorinostat for 12 hours
experiment encode accession: ENCSR105NQB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB391YVG
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

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

value: ENCBS208MUJ at ENCODE; https://www.encodeproject.org/ENCBS208MUJ/

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


title: total RNA-seq from K562 (ENCLB438OYF)

description:
https://www.encodeproject.org/experiments/ENCSR591KOB/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Crizotinib for 24 hours
experiment encode accession: ENCSR591KOB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB438OYF
size range: 300-600

value: female

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

value: ENCBS601WBA at ENCODE; https://www.encodeproject.org/ENCBS601WBA/


title: total RNA-seq from WTC11 (ENCLB365GJO)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB365GJO

value: iPSC

value: male

value: adult

value: 30 year

value: Coriell

value: ENCBS339RWG at ENCODE; https://www.encodeproject.org/ENCBS339RWG/

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


title: total RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB665GBA)

description:
https://www.encodeproject.org/experiments/ENCSR235PLU/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Naive_DONOR 6: 0 hour no activation
experiment encode accession: ENCSR235PLU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB665GBA
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) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: Homo sapiens

value: 50 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS881DDA at ENCODE; https://www.encodeproject.org/ENCBS881DDA/

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


title: BruChase-seq from Calu3 (ENCLB062MEP)

description:
https://www.encodeproject.org/experiments/ENCSR591KLL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR591KLL
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR692DCF
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB062MEP
size range: 400-500

source_name: Homo sapiens Calu3 cell line, subjected to a 2 hour pulse-chase

value: cell line

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS623ENG at ENCODE; https://www.encodeproject.org/ENCBS623ENG/

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


title: total RNA-seq from WTC11 (ENCLB857YUK)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB857YUK

value: iPSC

value: male

value: adult

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: ENCBS947MOM at ENCODE; https://www.encodeproject.org/ENCBS947MOM/


title: total RNA-seq from WTC11 (ENCLB790JXW)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 12
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB790JXW

value: Homo sapiens

value: ENCBS164SOA at ENCODE; https://www.encodeproject.org/ENCBS164SOA/

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


title: total RNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB658SHE)

description:
https://www.encodeproject.org/experiments/ENCSR241EBI/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Naive_DONOR 6: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR241EBI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB658SHE
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 naive CD4-positive, alpha-beta T primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: primary cell

value: 50 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: ENCBS616JKY at ENCODE; https://www.encodeproject.org/ENCBS616JKY/

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


title: BruChase-seq from Calu3 (ENCLB997BJQ)

description:
https://www.encodeproject.org/experiments/ENCSR591KLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR591KLL
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR692DCF
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB997BJQ
size range: 400-500

value: cell line

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS226EPG at ENCODE; https://www.encodeproject.org/ENCBS226EPG/

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


title: total RNA-seq from middle frontal area 46 (ENCLB875DYZ)

description:
https://www.encodeproject.org/experiments/ENCSR671FBB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1329219_BS173_ENC4_cDNA727
experiment encode accession: ENCSR671FBB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB875DYZ
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: adult

value: 86 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS352YCX at ENCODE; https://www.encodeproject.org/ENCBS352YCX/

value: Derived from ENCODE donor ENCDO418RWN; https://www.encodeproject.org/ENCDO418RWN/


title: PRO-seq from HCT116 (ENCLB915KUI)

description:
https://www.encodeproject.org/experiments/ENCSR673THD/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in CTCF_T
experiment encode accession: ENCSR673THD
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB915KUI
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: ENCBS637VLU at ENCODE; https://www.encodeproject.org/ENCBS637VLU/

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


title: CRISPR RNA-seq from HepG2 (ENCLB838OVR)

description:
https://www.encodeproject.org/experiments/ENCSR104RTM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGHcLV25)
experiment encode accession: ENCSR104RTM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB838OVR
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 BARD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9a4ef8bb-9621-4819-b7c1-69c1ac90b03c/@@download/attachment/L-BARD1-BGHcLV25-28.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGHcLV25-28)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS993GEA at ENCODE; https://www.encodeproject.org/ENCBS993GEA/

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


title: total RNA-seq from WTC11 (ENCLB366TJG)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 4
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB366TJG

value: cell line

value: iPSC

value: male

value: adult

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: ENCBS466IYK at ENCODE; https://www.encodeproject.org/ENCBS466IYK/

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


title: total RNA-seq from middle frontal area 46 (ENCLB743EOH)

description:
https://www.encodeproject.org/experiments/ENCSR669GBC/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2541828_BS179_ENC4_cDNA733
experiment encode accession: ENCSR669GBC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB743EOH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS554PHI at ENCODE; https://www.encodeproject.org/ENCBS554PHI/

value: Derived from ENCODE donor ENCDO776JEI; https://www.encodeproject.org/ENCDO776JEI/


title: CRISPR RNA-seq from HepG2 (ENCLB149OCI)

description:
https://www.encodeproject.org/experiments/ENCSR104RTM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGHcLV25)
experiment encode accession: ENCSR104RTM
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB149OCI
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/63e13667-16f0-4ed5-ba96-c15e2ed988c5/@@download/attachment/L-BARD1-BGHcLV25-27.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGHcLV25-27)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS297YGW at ENCODE; https://www.encodeproject.org/ENCBS297YGW/

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


title: PRO-seq from HCT116 (ENCLB741LCF)

description:
https://www.encodeproject.org/experiments/ENCSR222XCG/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in SMARCA5_T
experiment encode accession: ENCSR222XCG
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB741LCF
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 SMARCA5 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS540RKF at ENCODE; https://www.encodeproject.org/ENCBS540RKF/

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


title: total RNA-seq from K562 (ENCLB768BWT)

description:
https://www.encodeproject.org/experiments/ENCSR100VUY/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Chaetocin for 24 hours
experiment encode accession: ENCSR100VUY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB768BWT
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 nM Chaetocin for 24 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

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

value: ENCBS052NOA at ENCODE; https://www.encodeproject.org/ENCBS052NOA/

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


title: total RNA-seq from WTC11 (ENCLB239OZQ)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 5
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB239OZQ

value: iPSC

value: male

value: adult

value: 30 year

value: Coriell

value: ENCBS511GAV at ENCODE; https://www.encodeproject.org/ENCBS511GAV/

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


title: total RNA-seq from K562 (ENCLB851AEG)

description:
https://www.encodeproject.org/experiments/ENCSR100VUY/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Chaetocin for 24 hours
experiment encode accession: ENCSR100VUY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB851AEG
size range: 300-600

value: cell line

value: ATCC

value: ENCBS881WRE at ENCODE; https://www.encodeproject.org/ENCBS881WRE/


title: total RNA-seq from middle frontal area 46 (ENCLB203XBI)

description:
https://www.encodeproject.org/experiments/ENCSR233IVG/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3332236_BS97_ENC4_cDNA674
experiment encode accession: ENCSR233IVG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB203XBI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

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

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: female

value: 82 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS943VMJ at ENCODE; https://www.encodeproject.org/ENCBS943VMJ/

value: Derived from ENCODE donor ENCDO165PNJ; https://www.encodeproject.org/ENCDO165PNJ/


title: PRO-seq from HCT116 (ENCLB836IVV)

description:
https://www.encodeproject.org/experiments/ENCSR222XCG/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in SMARCA5_T
experiment encode accession: ENCSR222XCG
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB836IVV
spikeins used: The drosophila spike-in reference used for alignment

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS288BQH at ENCODE; https://www.encodeproject.org/ENCBS288BQH/

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


title: total RNA-seq from WTC11 (ENCLB140SEL)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 7
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB140SEL

value: cell line

value: iPSC

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: ENCBS622XGP at ENCODE; https://www.encodeproject.org/ENCBS622XGP/

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


title: total RNA-seq from WTC11 (ENCLB104ENH)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 11
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB104ENH

value: Homo sapiens

value: ENCBS114KZO at ENCODE; https://www.encodeproject.org/ENCBS114KZO/


title: total RNA-seq from WTC11 (ENCLB018YQI)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 3
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB018YQI

value: male

value: ENCBS825TMJ at ENCODE; https://www.encodeproject.org/ENCBS825TMJ/


title: total RNA-seq from middle frontal area 46 (ENCLB249NGQ)

description:
https://www.encodeproject.org/experiments/ENCSR216RNR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8259623_BS127_ENC4_cDNA689
experiment encode accession: ENCSR216RNR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB249NGQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens female adult (88 years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: adult

value: 88 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS485BXU at ENCODE; https://www.encodeproject.org/ENCBS485BXU/

value: Derived from ENCODE donor ENCDO430XKI; https://www.encodeproject.org/ENCDO430XKI/


title: total RNA-seq from K562 (ENCLB720IOO)

description:
https://www.encodeproject.org/experiments/ENCSR100JNS/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with DMSO for 24 hours
experiment encode accession: ENCSR100JNS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB720IOO
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 1% DMSO for 24 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:DMSO; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS576FYS at ENCODE; https://www.encodeproject.org/ENCBS576FYS/

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


title: total RNA-seq from K562 (ENCLB139AYM)

description:
https://www.encodeproject.org/experiments/ENCSR100JNS/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with DMSO for 24 hours
experiment encode accession: ENCSR100JNS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB139AYM
size range: 300-600

value: Homo sapiens

value: ENCBS099NKE at ENCODE; https://www.encodeproject.org/ENCBS099NKE/


title: CRISPR RNA-seq from K562 (ENCLB613JKD)

description:
https://www.encodeproject.org/experiments/ENCSR585UBH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGKcLV26)
experiment encode accession: ENCSR585UBH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB613JKD
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 ATXN2L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2aa4819a-4431-456f-8dd1-e9490c4d535e/@@download/attachment/L-ATXN2L-BGKcLV26-40.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGKcLV26-40)

value: female

value: adult

value: Brenton Graveley, UConn

value: ENCBS471JPC at ENCODE; https://www.encodeproject.org/ENCBS471JPC/


title: total RNA-seq from middle frontal area 46 (ENCLB206TGQ)

description:
https://www.encodeproject.org/experiments/ENCSR650SDA/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1805112_BS175_ENC4_cDNA729
experiment encode accession: ENCSR650SDA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB206TGQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS898EKF at ENCODE; https://www.encodeproject.org/ENCBS898EKF/

value: Derived from ENCODE donor ENCDO204VNL; https://www.encodeproject.org/ENCDO204VNL/


title: total RNA-seq from T-cell (ENCLB633VTU)

description:
https://www.encodeproject.org/experiments/ENCSR196KBV/
***************
biological replicate number: 1
technical replicate number: 1
description: CD3+_DONOR 4: 0 hour no activation
experiment encode accession: ENCSR196KBV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB633VTU
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) T-cell primary cell

value: T-cell

value: primary cell

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS698KGE at ENCODE; https://www.encodeproject.org/ENCBS698KGE/

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


title: CRISPR RNA-seq from K562 (ENCLB569EAR)

description:
https://www.encodeproject.org/experiments/ENCSR585UBH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGKcLV26)
experiment encode accession: ENCSR585UBH
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB569EAR
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/51e1ed23-105b-4016-b6c0-e50a09a62da6/@@download/attachment/L-ATXN2L-BGKcLV26-39.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGKcLV26-39)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS252NUU at ENCODE; https://www.encodeproject.org/ENCBS252NUU/

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


title: total RNA-seq from middle frontal area 46 (ENCLB178BIE)

description:
https://www.encodeproject.org/experiments/ENCSR209TIR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7886851_BS164_ENC4_cDNA714
experiment encode accession: ENCSR209TIR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB178BIE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: middle frontal area 46

value: tissue

value: male

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS544WUH at ENCODE; https://www.encodeproject.org/ENCBS544WUH/

value: Derived from ENCODE donor ENCDO741BVY; https://www.encodeproject.org/ENCDO741BVY/


title: total RNA-seq from WTC11 (ENCLB100KAD)

description:
https://www.encodeproject.org/experiments/ENCSR056TWA/
***************
biological replicate number: 9
technical replicate number: 1
description: Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.
experiment encode accession: ENCSR056TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB100KAD

source_name: Homo sapiens WTC11 cell line, preserved by flash-freezing

value: cell line

value: iPSC

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: ENCBS049BPX at ENCODE; https://www.encodeproject.org/ENCBS049BPX/

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


title: PRO-cap from HCT116 (ENCLB027EOY)

description:
https://www.encodeproject.org/experiments/ENCSR100EDZ/
***************
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 RAD21_T.
experiment encode accession: ENCSR100EDZ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB027EOY
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 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: Homo sapiens

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS257FWX at ENCODE; https://www.encodeproject.org/ENCBS257FWX/

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


title: total RNA-seq from middle frontal area 46 (ENCLB059OHW)

description:
https://www.encodeproject.org/experiments/ENCSR642FZN/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5410646_BS203_ENC4_cDNA758
experiment encode accession: ENCSR642FZN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB059OHW
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: ENCBS186ADK at ENCODE; https://www.encodeproject.org/ENCBS186ADK/

value: Derived from ENCODE donor ENCDO183VJV; https://www.encodeproject.org/ENCDO183VJV/


title: total RNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB380ZAP)

description:
https://www.encodeproject.org/experiments/ENCSR177CWW/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Naive_DONOR 5: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR177CWW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB380ZAP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (48 years) activated naive CD4-positive, alpha-beta T primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: primary cell

value: Homo sapiens

value: male

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: ENCBS710OBZ at ENCODE; https://www.encodeproject.org/ENCBS710OBZ/

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


title: total RNA-seq from middle frontal area 46 (ENCLB660BFQ)

description:
https://www.encodeproject.org/experiments/ENCSR641XXD/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3760550_BS198_ENC4_cDNA753
experiment encode accession: ENCSR641XXD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB660BFQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adult

value: ENCBS652ENJ at ENCODE; https://www.encodeproject.org/ENCBS652ENJ/

value: Derived from ENCODE donor ENCDO539ZHT; https://www.encodeproject.org/ENCDO539ZHT/


title: CRISPR RNA-seq from K562 (ENCLB852CBH)

description:
https://www.encodeproject.org/experiments/ENCSR096JMV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM26. (RBM26-BGKcLV30)
experiment encode accession: ENCSR096JMV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB852CBH
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 RBM26

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4c8c3e64-d2c1-4096-a76c-686d172e5f00/@@download/attachment/L-RBM26-BGKcLV30-14.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM26. (RBM26-BGKcLV30-14)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS384SFY at ENCODE; https://www.encodeproject.org/ENCBS384SFY/

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


title: total RNA-seq from middle frontal area 46 (ENCLB446YKM)

description:
https://www.encodeproject.org/experiments/ENCSR171ZNI/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1005516_BS117_ENC4_cDNA679
experiment encode accession: ENCSR171ZNI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB446YKM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

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: Homo sapiens

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS885BFB at ENCODE; https://www.encodeproject.org/ENCBS885BFB/

value: Derived from ENCODE donor ENCDO020BIL; https://www.encodeproject.org/ENCDO020BIL/


title: total RNA-seq from middle frontal area 46 (ENCLB201CHN)

description:
https://www.encodeproject.org/experiments/ENCSR171CLQ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8685549_BS169_ENC4_cDNA719
experiment encode accession: ENCSR171CLQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB201CHN
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 (81 years) with Alzheimer's disease; middle frontal area 46 tissue

value: adult

value: 81 year

value: ENCBS204HWF at ENCODE; https://www.encodeproject.org/ENCBS204HWF/

value: Derived from ENCODE donor ENCDO097MEH; https://www.encodeproject.org/ENCDO097MEH/


title: CRISPR RNA-seq from HepG2 (ENCLB872VUM)

description:
https://www.encodeproject.org/experiments/ENCSR585MSI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against API5. (API5-BGHcLV27)
experiment encode accession: ENCSR585MSI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB872VUM
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 API5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9c173fbf-8f6e-411e-9750-122219f17b66/@@download/attachment/L-API5-BGHcLV27-12.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against API5. (API5-BGHcLV27-12)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS026SMB at ENCODE; https://www.encodeproject.org/ENCBS026SMB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB657PYY)

description:
https://www.encodeproject.org/experiments/ENCSR585MSI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against API5. (API5-BGHcLV27)
experiment encode accession: ENCSR585MSI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB657PYY
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/d0c7d7a8-9315-4062-8e14-60de66623b1b/@@download/attachment/L-API5-BGHcLV27-11.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against API5. (API5-BGHcLV27-11)

value: Homo sapiens

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS509BGS at ENCODE; https://www.encodeproject.org/ENCBS509BGS/


title: CRISPR RNA-seq from HepG2 (ENCLB616DSP)

description:
https://www.encodeproject.org/experiments/ENCSR094AES/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGHcLV31)
experiment encode accession: ENCSR094AES
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB616DSP
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 SEC62

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c2c54688-b7ea-4898-86cb-030d073aed7f/@@download/attachment/L-SEC62-BGHcLV31-36.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGHcLV31-36)

value: ENCBS029UTH at ENCODE; https://www.encodeproject.org/ENCBS029UTH/


title: PRO-seq from HCT116 (ENCLB555KQA)

description:
https://www.encodeproject.org/experiments/ENCSR163WLJ/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in SUPT16H_U
experiment encode accession: ENCSR163WLJ
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB555KQA
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS465EAG at ENCODE; https://www.encodeproject.org/ENCBS465EAG/

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


title: total RNA-seq from middle frontal area 46 (ENCLB460HWN)

description:
https://www.encodeproject.org/experiments/ENCSR162SPJ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6018011_BS156_ENC4_cDNA706
experiment encode accession: ENCSR162SPJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB460HWN
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 (77 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 77 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS819GGD at ENCODE; https://www.encodeproject.org/ENCBS819GGD/

value: Derived from ENCODE donor ENCDO628ASW; https://www.encodeproject.org/ENCDO628ASW/


title: CRISPR RNA-seq from HepG2 (ENCLB645XAR)

description:
https://www.encodeproject.org/experiments/ENCSR094AES/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGHcLV31)
experiment encode accession: ENCSR094AES
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR452TFV
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB645XAR
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/a01bc278-1804-4bf7-96cf-bdcbf223d6b1/@@download/attachment/L-SEC62-BGHcLV31-35.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGHcLV31-35)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS391QCN at ENCODE; https://www.encodeproject.org/ENCBS391QCN/

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


title: microRNA-seq from HL-60 (ENCLB139HQU)

description:
https://www.encodeproject.org/experiments/ENCSR496QLS/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation HL-60 derived M1 macrophages (differentiated 12hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR496QLS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB139HQU
size range: <30

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

value: HL-60 derived M1 macrophages (12hr)

value: female

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: Ali Mortazavi, UCI

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

value: ENCBS706VCU at ENCODE; https://www.encodeproject.org/ENCBS706VCU/

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


title: total RNA-seq from middle frontal area 46 (ENCLB602RRZ)

description:
https://www.encodeproject.org/experiments/ENCSR631GOR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7469354_BS162_ENC4_cDNA712
experiment encode accession: ENCSR631GOR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB602RRZ
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: Homo sapiens

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS963VMK at ENCODE; https://www.encodeproject.org/ENCBS963VMK/

value: Derived from ENCODE donor ENCDO637GUS; https://www.encodeproject.org/ENCDO637GUS/


title: total RNA-seq from A549 (ENCLB763HSA)

description:
https://www.encodeproject.org/experiments/ENCSR584OXW/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR584OXW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB763HSA
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM AZD9567 (agonist) for 4 hours

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

value: cell line

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_name:AZD9567; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS304EXR at ENCODE; https://www.encodeproject.org/ENCBS304EXR/

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


title: microRNA-seq from HL-60 (ENCLB378ERM)

description:
https://www.encodeproject.org/experiments/ENCSR496QLS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HL-60 derived M1 macrophages (differentiated 12hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR496QLS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB378ERM
size range: <30

value: HL-60 derived M1 macrophages (12hr)

value: female

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: Ali Mortazavi, UCI

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

value: ENCBS887OHV at ENCODE; https://www.encodeproject.org/ENCBS887OHV/

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


title: microRNA-seq from HL-60 (ENCLB631MWG)

description:
https://www.encodeproject.org/experiments/ENCSR496QLS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HL-60 derived M1 macrophages (differentiated 12hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR496QLS
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB631MWG
size range: <30

value: cell line

value: Homo sapiens

value: ENCBS380AKB at ENCODE; https://www.encodeproject.org/ENCBS380AKB/


title: PRO-cap from HCT116 (ENCLB998ELB)

description:
https://www.encodeproject.org/experiments/ENCSR100EDZ/
***************
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 RAD21_T.
experiment encode accession: ENCSR100EDZ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB998ELB
spikeins used: The drosophila spike-in reference used for alignment

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS364ERK at ENCODE; https://www.encodeproject.org/ENCBS364ERK/

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


title: total RNA-seq from A549 (ENCLB460ZNQ)

description:
https://www.encodeproject.org/experiments/ENCSR584OXW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR584OXW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB460ZNQ
size range: 200-300

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_name:AZD9567; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS947ONF at ENCODE; https://www.encodeproject.org/ENCBS947ONF/

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


title: total RNA-seq from middle frontal area 46 (ENCLB790IDC)

description:
https://www.encodeproject.org/experiments/ENCSR158VWD/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7623847_BS163_ENC4_cDNA713
experiment encode accession: ENCSR158VWD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB790IDC
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: Homo sapiens

value: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

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

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


title: total RNA-seq from A549 (ENCLB039ORO)

description:
https://www.encodeproject.org/experiments/ENCSR584OXW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR584OXW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB039ORO
size range: 200-300

value: cell line

value: male

value: ENCBS983VUH at ENCODE; https://www.encodeproject.org/ENCBS983VUH/


title: total RNA-seq from middle frontal area 46 (ENCLB401EML)

description:
https://www.encodeproject.org/experiments/ENCSR158IHB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6590998_BS170_ENC4_cDNA720
experiment encode accession: ENCSR158IHB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB401EML
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 (75 years) middle frontal area 46 tissue

value: adult

value: 75 year

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 left cerebral cortex (ENCLB500FVL)

description:
https://www.encodeproject.org/experiments/ENCSR299GYD/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast L. cortex (brain)_8-10 months male
experiment encode accession: ENCSR299GYD
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB500FVL
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: Mus musculus strain 5xFAD/CAST male adult (8-10 months) left cerebral cortex tissue

value: left cerebral cortex

value: Mus musculus

value: 8-10 month

value: The Jackson Laboratory

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

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


title: total RNA-seq from A549 (ENCLB388QGT)

description:
https://www.encodeproject.org/experiments/ENCSR584OXW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR584OXW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB388QGT
size range: 200-300

value: Homo sapiens

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_name:AZD9567; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS360KJV at ENCODE; https://www.encodeproject.org/ENCBS360KJV/

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


title: total RNA-seq from A549 (ENCLB829GBJ)

description:
https://www.encodeproject.org/experiments/ENCSR584OXW/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR584OXW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB829GBJ
size range: 200-300

value: cell line

value: male

value: adult

value: ENCBS965KRL at ENCODE; https://www.encodeproject.org/ENCBS965KRL/


title: CRISPR RNA-seq from K562 (ENCLB880XMT)

description:
https://www.encodeproject.org/experiments/ENCSR096JMV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM26. (RBM26-BGKcLV30)
experiment encode accession: ENCSR096JMV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB880XMT
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/8b619a76-b2b0-4230-b2a0-6631922421f8/@@download/attachment/L-RBM26-BGKcLV30-13.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM26. (RBM26-BGKcLV30-13)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS603SIB at ENCODE; https://www.encodeproject.org/ENCBS603SIB/

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


title: total RNA-seq from left cerebral cortex (ENCLB321HLP)

description:
https://www.encodeproject.org/experiments/ENCSR299GYD/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast L. cortex (brain)_8-10 months male
experiment encode accession: ENCSR299GYD
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB321HLP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: left cerebral cortex

value: tissue

value: Mus musculus

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

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

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


title: PRO-seq from HCT116 (ENCLB393WYB)

description:
https://www.encodeproject.org/experiments/ENCSR163WLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in SUPT16H_U
experiment encode accession: ENCSR163WLJ
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB393WYB
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: Homo sapiens

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS984MQX at ENCODE; https://www.encodeproject.org/ENCBS984MQX/

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


title: total RNA-seq from middle frontal area 46 (ENCLB303ZTR)

description:
https://www.encodeproject.org/experiments/ENCSR154PNU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5387473_BS202_ENC4_cDNA757
experiment encode accession: ENCSR154PNU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB303ZTR
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: female

value: 90 or above year

value: Rush University

value: ENCBS685GIE at ENCODE; https://www.encodeproject.org/ENCBS685GIE/

value: Derived from ENCODE donor ENCDO893GME; https://www.encodeproject.org/ENCDO893GME/


title: Bru-seq from HCT116 (ENCLB272XUG)

description:
https://www.encodeproject.org/experiments/ENCSR093FVX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR093FVX
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR008ZZZ
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB272XUG
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 CDK7 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

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

value: ENCBS918VDA at ENCODE; https://www.encodeproject.org/ENCBS918VDA/


title: total RNA-seq from left cerebral cortex (ENCLB579LBW)

description:
https://www.encodeproject.org/experiments/ENCSR723XFW/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast L. cortex (brain)_8-10 months female
experiment encode accession: ENCSR723XFW
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB579LBW
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: Mus musculus strain 5xFAD/CAST female adult (8-10 months) left cerebral cortex tissue

value: left cerebral cortex

value: Mus musculus

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

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

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


title: total RNA-seq from middle frontal area 46 (ENCLB408VCN)

description:
https://www.encodeproject.org/experiments/ENCSR133PLR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1703237_BS141_ENC4_cDNA691
experiment encode accession: ENCSR133PLR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB408VCN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

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

value: middle frontal area 46

value: Homo sapiens

value: male

value: adult

value: 85 year

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

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


title: total RNA-seq from heart (ENCLB439AHA)

description:
https://www.encodeproject.org/experiments/ENCSR967IKT/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast heart_8-10 months female
experiment encode accession: ENCSR967IKT
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB439AHA
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: Mus musculus strain 5xFAD/CAST female adult (8-10 months) heart tissue

value: heart

value: tissue

value: female

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


title: CRISPR RNA-seq from HepG2 (ENCLB947EFS)

description:
https://www.encodeproject.org/experiments/ENCSR085GSF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGHcLV29)
experiment encode accession: ENCSR085GSF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB947EFS
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 CNDP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/48b84c29-1840-40fa-a373-a098e5e176dc/@@download/attachment/L-CNDP2-BGHcLV29-27.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGHcLV29-27)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS355KGS at ENCODE; https://www.encodeproject.org/ENCBS355KGS/

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


title: total RNA-seq from middle frontal area 46 (ENCLB409ZWK)

description:
https://www.encodeproject.org/experiments/ENCSR591ZCN/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6315900_BS205_ENC4_cDNA760
experiment encode accession: ENCSR591ZCN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB409ZWK
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: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS938TZB at ENCODE; https://www.encodeproject.org/ENCBS938TZB/

value: Derived from ENCODE donor ENCDO739EFE; https://www.encodeproject.org/ENCDO739EFE/


title: total RNA-seq from middle frontal area 46 (ENCLB065XLT)

description:
https://www.encodeproject.org/experiments/ENCSR138MMB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E4646042_BS99_ENC4_cDNA676
experiment encode accession: ENCSR138MMB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB065XLT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

value: tissue

value: female

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

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


title: Bru-seq from HCT116 (ENCLB933UXS)

description:
https://www.encodeproject.org/experiments/ENCSR093FVX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR093FVX
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR008ZZZ
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB933UXS
size range: 400-500

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS119YVC at ENCODE; https://www.encodeproject.org/ENCBS119YVC/

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


title: total RNA-seq from gastrocnemius (ENCLB976BUM)

description:
https://www.encodeproject.org/experiments/ENCSR960ZZW/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast gastrocnemius_8-10 months female
experiment encode accession: ENCSR960ZZW
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB976BUM
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: Mus musculus strain B6CASTF1/J female adult (8-10 months) gastrocnemius tissue

value: gastrocnemius

value: B6 X Cast gastrocnemius_8-10 months female animal 1_ENC4_cDNA_842

value: Mus musculus

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS266MYR at ENCODE; https://www.encodeproject.org/ENCBS266MYR/

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


title: CRISPR RNA-seq from K562 (ENCLB051KWA)

description:
https://www.encodeproject.org/experiments/ENCSR082BCP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGKcLV33)
experiment encode accession: ENCSR082BCP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB051KWA
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 SEPT7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/49a2185e-703a-4826-aaff-72f978f87c67/@@download/attachment/L-SEC63-BGKcLV33-41.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGKcLV33-41)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS840KHA at ENCODE; https://www.encodeproject.org/ENCBS840KHA/

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


title: CRISPR RNA-seq from K562 (ENCLB318NZC)

description:
https://www.encodeproject.org/experiments/ENCSR082BCP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGKcLV33)
experiment encode accession: ENCSR082BCP
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB318NZC
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/5666964e-4894-4140-b69a-72e13ee30f3a/@@download/attachment/L-SEC63-BGKcLV33-42.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGKcLV33-42)

value: ENCBS695AAR at ENCODE; https://www.encodeproject.org/ENCBS695AAR/


title: total RNA-seq from gastrocnemius (ENCLB360IRF)

description:
https://www.encodeproject.org/experiments/ENCSR960ZZW/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast gastrocnemius_8-10 months female
experiment encode accession: ENCSR960ZZW
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB360IRF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: gastrocnemius

value: tissue

value: B6 X Cast gastrocnemius_8-10 months female animal 3_ENC4_cDNA_843

value: Mus musculus

value: adult

value: 8-10 month

value: ENCBS720GRG at ENCODE; https://www.encodeproject.org/ENCBS720GRG/


title: CRISPR RNA-seq from HepG2 (ENCLB576SAS)

description:
https://www.encodeproject.org/experiments/ENCSR077MFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARS. (CARS-BGHcLV27)
experiment encode accession: ENCSR077MFQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB576SAS
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 CARS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/43c6083a-384c-4164-abc3-71835d980325/@@download/attachment/L-CARS-BGHcLV27-40.pdf

value: CARS

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARS. (CARS-BGHcLV27-40)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS104KVQ at ENCODE; https://www.encodeproject.org/ENCBS104KVQ/

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


title: total RNA-seq from heart (ENCLB056QSR)

description:
https://www.encodeproject.org/experiments/ENCSR967IKT/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast heart_8-10 months female
experiment encode accession: ENCSR967IKT
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB056QSR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: female

value: Barbara Wold, Caltech

value: The Jackson Laboratory

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

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


title: total RNA-seq from layer of hippocampus (ENCLB674CUH)

description:
https://www.encodeproject.org/experiments/ENCSR886NLC/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast hippocampus_8-10 months female
experiment encode accession: ENCSR886NLC
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB674CUH
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: Mus musculus strain 5xFAD/CAST female adult (8-10 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: Mus musculus

value: adult

value: 8-10 month

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