title: polyA mRNA RNA-seq from embryonic fibroblast (ENCLB536UCE)

description:
https://www.encodeproject.org/experiments/ENCSR000CGV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse embryonic fibroblast (MEF)
experiment encode accession: ENCSR000CGV
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB536UCE
size range: >200
spikeins used: /references/ENCSR866KGS/

value: embryonic fibroblast

value: primary cell

value: Mouse Embryonic Fibroblast

value: ENCBS703ZIY at ENCODE; https://www.encodeproject.org/ENCBS703ZIY/


title: TOV-1946

status: Public on Feb 03 2017

type: SRA

city: Toronto

first: Mauricio

last: Medrano

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

library_source: transcriptomic

data_processing:
Basecalls files were converted to sequences in FASTQ format using BCLToFastq CASAVA 1.8.2
Fragments were mapped to build GRCh37 of the human genome using TopHat 1.4.1 and Bowtie 1.0.
Transcript abundance was determined using cufflinks 1.3.0
Genome_build: GRCh37
Supplementary_files_format_and_content: cufflinks gene-level quantification; expression estimates (cufflinks output)

molecule: total RNA

organism: Homo sapiens

source_name: ovarian serous adenocarcinoma

extract_protocol:
Total RNA was extracted from 40 epithelial ovarian cancer cell lines and one immortalized line derived from ovarian surface epithelium (OE-E6/E7) using RNeasy plus mini kit (QIAGEN, 74134). mRNA was quantified using QubitRNA (Invitrogen) and quality control was assessed with bioanalyzer total RNA nano chip. One μg of mRNA was fragmented to an average length of 200 bp by incubation for 5 minutes at 94°C with 5X fragmentation buffer (Illumina, RS-100-0801). Efficiency of the fragmentation was defined on Bioanalyzer RNA Pico Chip. The fragmented mRNA was randomly primed and reverse transcribed using Super Script II cDNA synthesis kit (Invitrogen, 18064-014). After second-strand synthesis, the cDNA went through end-repair and ligation reactions according to the Illumina mRNA-Seq Sample Prep Kit protocol. The cDNA library was size-fractioned on a 2% TBE agarose gel. Material in the 350-400 bp range was excised and purified (Zymo Research, D4001). Half of the eluted cDNA library was used as a template for amplification according mRNA-Seq Sample Prep Kit protocol. The PCR product was purified using the PureLink PCR micro purification kit (Invitrogen, K310050). The library size (350-400 bp) was validated on a Bioanalyzer DNA 1000 Chip and the concentration was estimated using Qubit fluorometer and Quant-iT dsDNA BR Assay Kit (Invitrogen, Q32850). The library was then used to build clusters on the Illumina flow cell and analysis was done using Illumina Hiseq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: high-grade serous ovarian cancer (HGSC) cell line

tag: cell subtype

value: ovarian serous adenocarcinoma


title: TOV-21G

source_name: clear cell

value: clear cell


title: TOV-2223G


title: SKOV3


title: polyA mRNA RNA-seq from lung (ENCLB579BBP)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000CHC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse lung
experiment encode accession: ENCSR000CHC
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB579BBP
size range: >200
spikeins used: /references/ENCSR866KGS/

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

organism: Mus musculus

source_name: Mus musculus strain B6NCrl lung tissue male adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0a7c7860-4801-456d-baaa-0f3ac6d99aa7/@@download/attachment/Ren_mRNA-seq_protocols_v090113.pdf

value: lung

value: tissue

tag: description

value: Lung from an individual mouse

tag: biosample encode accession

tag: dev stage

value: adult

tag: age

value: 8 week

tag: Sex

value: male

tag: lab

value: Bing Ren, UCSD

tag: link

value: ENCBS678KJQ at ENCODE; https://www.encodeproject.org/ENCBS678KJQ/

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

value: ENCODE dbxrefs Lung; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Lung


title: TOV-3133G


title: TOV-1369TR


title: RMG-1


title: PEO23


title: PEO6


title: polyA mRNA RNA-seq from spleen (ENCLB809NWC)

description:
https://www.encodeproject.org/experiments/ENCSR000CGW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse spleen
experiment encode accession: ENCSR000CGW
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB809NWC
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl spleen tissue male adult (8 weeks)

value: spleen

value: Spleen from a single mouse

value: ENCBS690SSU at ENCODE; https://www.encodeproject.org/ENCBS690SSU/

value: ENCODE dbxrefs Spleen; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Spleen


title: polyA mRNA RNA-seq from cerebellum (ENCLB001HUO)

description:
https://www.encodeproject.org/experiments/ENCSR000CGX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse cerebellum
experiment encode accession: ENCSR000CGX
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB001HUO
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl cerebellum tissue male adult (8 weeks)

value: cerebellum

value: Cerebellum from an individual mouse

value: ENCBS173NCK at ENCODE; https://www.encodeproject.org/ENCBS173NCK/

value: ENCODE dbxrefs Cerebellum; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Cerebellum


title: PEO1L

value: high-grade serous ovarian cancer (HGSC) cell line

value: ovarian serous adenocarcinoma


title: PEA2


title: PEO1C


title: PEO14


title: PEO4


title: OVSH-1

value: clear cell


title: OVCAR5


title: PEA1


title: OVCAR8


title: OVCAR420


title: OVCAR433


title: OVCAR432


title: OV-56


title: OV-3133(2)


title: OV-3133


title: OV-1946


title: OV-2295


title: OV-2295(2)


title: OV-90


title: OV-1369(2)


title: OV-17R


title: JHOC5


title: COV504


title: OAW42


title: OE E6/E7

source_name: immortalized human oviductal epithelium

value: OE E6/E7

value: immortalized human oviductal epithelium


title: A2780

source_name: unknown histotype - ovarian origin

value: unknown histotype - ovarian origin


title: A2780Cis


title: ES-2


title: JHOC9


title: OVCAR3


title: 60905OM


title: COV318


title: ATAC-seq from dendritic cell (ENCLB936LKP)

description:
https://www.encodeproject.org/experiments/ENCSR926GDT/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR926GDT
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB936LKP
size range: 175-500

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens dendritic in vitro differentiated cells treated with 100 ng/mL Lipopolysaccharide for 4 hours

extract_protocol:
general protocol: https://www.encodeproject.org/documents/8ddcf49f-5e65-4158-b21c-b1b2620ef7b8/@@download/attachment/ATAC%20modified%20protocol.pdf
extraction method: ATAC-seq (Greenleaf & Chang Lab protocol)

value: dendritic cell

value: in vitro differentiated cells

value: unknown

tag: treatments

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:4; duration_units:hour;

value: not collected

value: Manuel Garber, UMass

value: ENCBS466HYD at ENCODE; https://www.encodeproject.org/ENCBS466HYD/

value: Derived from ENCODE donor ENCDO349SMJ; https://www.encodeproject.org/ENCDO349SMJ/


title: ATAC-seq from dendritic cell (ENCLB811FLK)

description:
https://www.encodeproject.org/experiments/ENCSR940QJU/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR940QJU
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB811FLK
size range: 175-500

source_name: Homo sapiens dendritic in vitro differentiated cells treated with 0 ng/mL Lipopolysaccharide for 0 hours

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration_units:hour;

value: ENCBS398DZA at ENCODE; https://www.encodeproject.org/ENCBS398DZA/

value: Derived from ENCODE donor ENCDO103KOF; https://www.encodeproject.org/ENCDO103KOF/


title: total RNA-seq from dendritic cell (ENCLB644BML)

description:
https://www.encodeproject.org/experiments/ENCSR975YGW/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR975YGW
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB644BML
size range: 100-350

source_name: Homo sapiens dendritic in vitro differentiated cells treated with 100 ng/mL Lipopolysaccharide for 2 hours

extract_protocol:
general protocol: https://www.encodeproject.org/documents/0d4acdae-dcfc-42a6-bd30-2833b1c9c5c9/@@download/attachment/Luban%20Lab%20RNA-seq%20protocol.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS064ORL at ENCODE; https://www.encodeproject.org/ENCBS064ORL/

value: Derived from ENCODE donor ENCDO336RRQ; https://www.encodeproject.org/ENCDO336RRQ/


title: total RNA-seq from dendritic cell (ENCLB223MGX)

description:
https://www.encodeproject.org/experiments/ENCSR670MXT/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR670MXT
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB223MGX
size range: 100-350

value: ENCBS301RHJ at ENCODE; https://www.encodeproject.org/ENCBS301RHJ/

value: Derived from ENCODE donor ENCDO681AUF; https://www.encodeproject.org/ENCDO681AUF/


title: ATAC-seq from dendritic cell (ENCLB892RWD)

description:
https://www.encodeproject.org/experiments/ENCSR926TFY/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR926TFY
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB892RWD
size range: 175-500

value: ENCBS303XVD at ENCODE; https://www.encodeproject.org/ENCBS303XVD/

value: Derived from ENCODE donor ENCDO166AGO; https://www.encodeproject.org/ENCDO166AGO/


title: ATAC-seq from dendritic cell (ENCLB371MUO)

description:
https://www.encodeproject.org/experiments/ENCSR679NRJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR679NRJ
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB371MUO
size range: 175-500

source_name: Homo sapiens dendritic in vitro differentiated cells treated with 100 ng/mL Lipopolysaccharide for 1 hour

value: dendritic cell

value: in vitro differentiated cells

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

value: ENCBS874KRV at ENCODE; https://www.encodeproject.org/ENCBS874KRV/


title: total RNA-seq from dendritic cell (ENCLB345SHX)

description:
https://www.encodeproject.org/experiments/ENCSR652RSO/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR652RSO
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB345SHX
size range: 100-350

source_name: Homo sapiens dendritic in vitro differentiated cells treated with 100 ng/mL Lipopolysaccharide for 6 hours

value: unknown

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:6; duration_units:hour;

value: not collected

value: Manuel Garber, UMass

value: ENCBS987IYA at ENCODE; https://www.encodeproject.org/ENCBS987IYA/


title: total RNA-seq from dendritic cell (ENCLB704CMV)

description:
https://www.encodeproject.org/experiments/ENCSR760INS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR760INS
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB704CMV
size range: 100-100

value: ENCBS293BSG at ENCODE; https://www.encodeproject.org/ENCBS293BSG/

value: Derived from ENCODE donor ENCDO342GLT; https://www.encodeproject.org/ENCDO342GLT/


title: ATAC-seq from dendritic cell (ENCLB275NZH)

description:
https://www.encodeproject.org/experiments/ENCSR648JJT/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR648JJT
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB275NZH
size range: 175-500

source_name: Homo sapiens dendritic in vitro differentiated cells treated with 100 ng/mL Lipopolysaccharide for 30 minutes

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS214CSU at ENCODE; https://www.encodeproject.org/ENCBS214CSU/

value: Derived from ENCODE donor ENCDO521EVK; https://www.encodeproject.org/ENCDO521EVK/


title: ATAC-seq from dendritic cell (ENCLB223DKL)

description:
https://www.encodeproject.org/experiments/ENCSR605EGR/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR605EGR
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB223DKL
size range: 175-500


title: ATAC-seq from dendritic cell (ENCLB975DIV)

description:
https://www.encodeproject.org/experiments/ENCSR628SXX/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR628SXX
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB975DIV
size range: 175-500

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS784GSL at ENCODE; https://www.encodeproject.org/ENCBS784GSL/

value: Derived from ENCODE donor ENCDO280UGN; https://www.encodeproject.org/ENCDO280UGN/


title: total RNA-seq from dendritic cell (ENCLB895XSE)

description:
https://www.encodeproject.org/experiments/ENCSR571IUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR571IUZ
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB895XSE
size range: 100-350

value: dendritic cell

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS935MDW at ENCODE; https://www.encodeproject.org/ENCBS935MDW/

value: Derived from ENCODE donor ENCDO681AUF; https://www.encodeproject.org/ENCDO681AUF/


title: total RNA-seq from dendritic cell (ENCLB503UPX)

description:
https://www.encodeproject.org/experiments/ENCSR870DRE/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR870DRE
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB503UPX
size range: 100-350

value: in vitro differentiated cells

value: unknown

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration_units:hour;

value: ENCBS026AWG at ENCODE; https://www.encodeproject.org/ENCBS026AWG/

value: Derived from ENCODE donor ENCDO336RRQ; https://www.encodeproject.org/ENCDO336RRQ/


title: ATAC-seq from dendritic cell (ENCLB460BFR)

description:
https://www.encodeproject.org/experiments/ENCSR589ROM/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR589ROM
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB460BFR
size range: 175-500

value: not collected

value: Manuel Garber, UMass

value: ENCBS670ABO at ENCODE; https://www.encodeproject.org/ENCBS670ABO/


title: ATAC-seq from dendritic cell (ENCLB072MNJ)

description:
https://www.encodeproject.org/experiments/ENCSR544YXV/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR544YXV
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB072MNJ
size range: 175-500

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

value: ENCBS307KOL at ENCODE; https://www.encodeproject.org/ENCBS307KOL/

value: Derived from ENCODE donor ENCDO349SMJ; https://www.encodeproject.org/ENCDO349SMJ/


title: ATAC-seq from dendritic cell (ENCLB313ORP)

description:
https://www.encodeproject.org/experiments/ENCSR535NOD/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR535NOD
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB313ORP
size range: 175-500

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS091OOD at ENCODE; https://www.encodeproject.org/ENCBS091OOD/


title: total RNA-seq from dendritic cell (ENCLB184JJV)

description:
https://www.encodeproject.org/experiments/ENCSR519NFO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR519NFO
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB184JJV
size range: 100-100

value: dendritic cell

value: ENCBS693UNQ at ENCODE; https://www.encodeproject.org/ENCBS693UNQ/

value: Derived from ENCODE donor ENCDO342GLT; https://www.encodeproject.org/ENCDO342GLT/


title: total RNA-seq from dendritic cell (ENCLB558IGX)

description:
https://www.encodeproject.org/experiments/ENCSR536GUD/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR536GUD
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB558IGX
size range: 100-350

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS445XAO at ENCODE; https://www.encodeproject.org/ENCBS445XAO/


title: ATAC-seq from dendritic cell (ENCLB305NJC)

description:
https://www.encodeproject.org/experiments/ENCSR459AYS/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR459AYS
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB305NJC
size range: 175-500

value: in vitro differentiated cells

value: unknown

value: ENCBS549OUK at ENCODE; https://www.encodeproject.org/ENCBS549OUK/

value: Derived from ENCODE donor ENCDO521EVK; https://www.encodeproject.org/ENCDO521EVK/


title: total RNA-seq from dendritic cell (ENCLB951KJZ)

description:
https://www.encodeproject.org/experiments/ENCSR475TVN/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR475TVN
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB951KJZ
size range: 100-350

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:6; duration_units:hour;

value: not collected

value: ENCBS920LQC at ENCODE; https://www.encodeproject.org/ENCBS920LQC/

value: Derived from ENCODE donor ENCDO565FMK; https://www.encodeproject.org/ENCDO565FMK/


title: total RNA-seq from dendritic cell (ENCLB328MWF)

description:
https://www.encodeproject.org/experiments/ENCSR476TKU/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR476TKU
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB328MWF
size range: 100-350

value: Manuel Garber, UMass

value: ENCBS737RZU at ENCODE; https://www.encodeproject.org/ENCBS737RZU/


title: total RNA-seq from dendritic cell (ENCLB605YPO)

description:
https://www.encodeproject.org/experiments/ENCSR916YUR/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR916YUR
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB605YPO
size range: 100-350

value: ENCBS090FYD at ENCODE; https://www.encodeproject.org/ENCBS090FYD/

value: Derived from ENCODE donor ENCDO336RRQ; https://www.encodeproject.org/ENCDO336RRQ/


title: ATAC-seq from dendritic cell (ENCLB065VMV)

description:
https://www.encodeproject.org/experiments/ENCSR370QWN/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR370QWN
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB065VMV
size range: 175-500

value: dendritic cell

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration_units:hour;

value: ENCBS770SDC at ENCODE; https://www.encodeproject.org/ENCBS770SDC/

value: Derived from ENCODE donor ENCDO349SMJ; https://www.encodeproject.org/ENCDO349SMJ/


title: ATAC-seq from dendritic cell (ENCLB486ZGV)

description:
https://www.encodeproject.org/experiments/ENCSR901IEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR901IEQ
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB486ZGV
size range: 175-500

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS144RZK at ENCODE; https://www.encodeproject.org/ENCBS144RZK/

value: Derived from ENCODE donor ENCDO103KOF; https://www.encodeproject.org/ENCDO103KOF/


title: ATAC-seq from dendritic cell (ENCLB685FCM)

description:
https://www.encodeproject.org/experiments/ENCSR290AUK/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR290AUK
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB685FCM
size range: 175-500

value: in vitro differentiated cells

value: unknown

value: ENCBS289TMG at ENCODE; https://www.encodeproject.org/ENCBS289TMG/

value: Derived from ENCODE donor ENCDO280UGN; https://www.encodeproject.org/ENCDO280UGN/


title: ATAC-seq from dendritic cell (ENCLB384NOX)

description:
https://www.encodeproject.org/experiments/ENCSR204FCV/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR204FCV
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB384NOX
size range: 175-500

value: not collected

value: ENCBS903EGN at ENCODE; https://www.encodeproject.org/ENCBS903EGN/

value: Derived from ENCODE donor ENCDO166AGO; https://www.encodeproject.org/ENCDO166AGO/


title: total RNA-seq from dendritic cell (ENCLB278EWD)

description:
https://www.encodeproject.org/experiments/ENCSR682CFV/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR682CFV
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB278EWD
size range: 100-350

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:2; duration_units:hour;

value: Manuel Garber, UMass

value: ENCBS610TYE at ENCODE; https://www.encodeproject.org/ENCBS610TYE/

value: Derived from ENCODE donor ENCDO565FMK; https://www.encodeproject.org/ENCDO565FMK/


title: total RNA-seq from dendritic cell (ENCLB615TIK)

description:
https://www.encodeproject.org/experiments/ENCSR178SNP/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR178SNP
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB615TIK
size range: 100-350

value: dendritic cell

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

value: ENCBS725FYS at ENCODE; https://www.encodeproject.org/ENCBS725FYS/


title: ATAC-seq from dendritic cell (ENCLB455GDX)

description:
https://www.encodeproject.org/experiments/ENCSR156FDX/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR156FDX
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB455GDX
size range: 175-500

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS271EMZ at ENCODE; https://www.encodeproject.org/ENCBS271EMZ/


title: total RNA-seq from dendritic cell (ENCLB626EYP)

description:
https://www.encodeproject.org/experiments/ENCSR146PLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146PLL
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB626EYP
size range: 100-100

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS679AZN at ENCODE; https://www.encodeproject.org/ENCBS679AZN/

value: Derived from ENCODE donor ENCDO342GLT; https://www.encodeproject.org/ENCDO342GLT/


title: ATAC-seq from dendritic cell (ENCLB683LFW)

description:
https://www.encodeproject.org/experiments/ENCSR131CHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR131CHJ
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB683LFW
size range: 175-500

value: in vitro differentiated cells

value: unknown

value: ENCBS647HIX at ENCODE; https://www.encodeproject.org/ENCBS647HIX/


title: total RNA-seq from dendritic cell (ENCLB578MBD)

description:
https://www.encodeproject.org/experiments/ENCSR084JIA/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR084JIA
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB578MBD
size range: 100-350

value: not collected

value: ENCBS913SBA at ENCODE; https://www.encodeproject.org/ENCBS913SBA/

value: Derived from ENCODE donor ENCDO336RRQ; https://www.encodeproject.org/ENCDO336RRQ/


title: total RNA-seq from dendritic cell (ENCLB211RGM)

description:
https://www.encodeproject.org/experiments/ENCSR022BYE/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR022BYE
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB211RGM
size range: 100-350

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration_units:hour;

value: Manuel Garber, UMass

value: ENCBS426AOO at ENCODE; https://www.encodeproject.org/ENCBS426AOO/


title: ATAC-seq from dendritic cell (ENCLB586KIS)

description:
https://www.encodeproject.org/experiments/ENCSR566LZT/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR566LZT
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB586KIS
size range: 175-500

value: dendritic cell

value: ENCBS004CRM at ENCODE; https://www.encodeproject.org/ENCBS004CRM/

value: Derived from ENCODE donor ENCDO280UGN; https://www.encodeproject.org/ENCDO280UGN/


title: polyA mRNA RNA-seq from adrenal gland (ENCLB603REP)

description:
https://www.encodeproject.org/experiments/ENCSR680AAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human adrenal gland. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR680AAZ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB603REP
size range: 350-450

source_name: Homo sapiens adrenal gland tissue male adult (21 year)

extract_protocol:
general protocol: https://www.encodeproject.org/documents/ffef687e-f74d-429e-8799-d16f991bbb11/@@download/attachment/wgEncodeSydhRnaSeq.patch.html.pdf
extraction method: RNeasy Lipid Tissue Mini Kit (QIAGEN cat#74804)

value: adrenal gland

value: tissue

value: adult

value: 21 year

value: male

value: Michael Snyder, Stanford

value: ENCBS629YZU at ENCODE; https://www.encodeproject.org/ENCBS629YZU/

value: Derived from ENCODE donor ENCDO637AUB; https://www.encodeproject.org/ENCDO637AUB/


title: polyA mRNA RNA-seq from spleen (ENCLB138JMP)

description:
https://www.encodeproject.org/experiments/ENCSR448VSW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human spleen tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR448VSW
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB138JMP
size range: 350-450

source_name: Homo sapiens spleen tissue female adult (30 years)

value: spleen

value: 30 year

value: female

value: ENCBS167WVB at ENCODE; https://www.encodeproject.org/ENCBS167WVB/

value: Derived from ENCODE donor ENCDO871RXV; https://www.encodeproject.org/ENCDO871RXV/


title: polyA mRNA RNA-seq from heart (ENCLB797GKI)

description:
https://www.encodeproject.org/experiments/ENCSR635GTY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human heart tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR635GTY
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB797GKI
size range: 350-450

source_name: Homo sapiens heart tissue female adult (30 years)

value: heart

value: ENCBS227BAN at ENCODE; https://www.encodeproject.org/ENCBS227BAN/

value: Derived from ENCODE donor ENCDO449QPH; https://www.encodeproject.org/ENCDO449QPH/


title: polyA mRNA RNA-seq from sigmoid colon (ENCLB521TPI)

description:
https://www.encodeproject.org/experiments/ENCSR270OKS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human sigmoid colon tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR270OKS
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB521TPI
size range: 350-450

source_name: Homo sapiens sigmoid colon tissue male adult (21 year)

value: sigmoid colon

value: ENCBS511JYL at ENCODE; https://www.encodeproject.org/ENCBS511JYL/


title: polyA mRNA RNA-seq from lung (ENCLB793NOU)

description:
https://www.encodeproject.org/experiments/ENCSR129KCJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human lung tissue tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR129KCJ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB793NOU
size range: 350-450

source_name: Homo sapiens lung tissue female adult (30 years)

value: lung

value: tissue

value: ENCBS973FZI at ENCODE; https://www.encodeproject.org/ENCBS973FZI/


title: polyA mRNA RNA-seq from small intestine (ENCLB670VDL)

description:
https://www.encodeproject.org/experiments/ENCSR612HYR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human small intestine tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR612HYR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB670VDL
size range: 350-450

source_name: Homo sapiens small intestine tissue female adult (30 years)

value: small intestine

value: adult

value: ENCBS487EXT at ENCODE; https://www.encodeproject.org/ENCBS487EXT/


title: polyA mRNA RNA-seq from adipose tissue (ENCLB236EKW)

description:
https://www.encodeproject.org/experiments/ENCSR236OON/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human adipose tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR236OON
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB236EKW
size range: 350-450

source_name: Homo sapiens adipose tissue female adult (63 years)

value: adipose tissue

value: 63 year

value: Michael Snyder, Stanford

value: ENCBS116JOH at ENCODE; https://www.encodeproject.org/ENCBS116JOH/

value: Derived from ENCODE donor ENCDO828UYN; https://www.encodeproject.org/ENCDO828UYN/


title: polyA mRNA RNA-seq from kidney (ENCLB947ZCC)

description:
https://www.encodeproject.org/experiments/ENCSR071ZMO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human kidney tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR071ZMO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB947ZCC
size range: 350-450

source_name: Homo sapiens kidney tissue male adult (41 year)

value: kidney

value: 41 year

value: male

value: ENCBS314EFM at ENCODE; https://www.encodeproject.org/ENCBS314EFM/

value: Derived from ENCODE donor ENCDO304TKO; https://www.encodeproject.org/ENCDO304TKO/


title: polyA mRNA RNA-seq from brain (ENCLB187ZUS)

description:
https://www.encodeproject.org/experiments/ENCSR274JRR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human brain tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR274JRR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB187ZUS
size range: 350-450

source_name: Homo sapiens brain tissue female adult (66 years)

value: brain

value: 66 year

value: female

value: ENCBS534KWT at ENCODE; https://www.encodeproject.org/ENCBS534KWT/

value: Derived from ENCODE donor ENCDO691SXZ; https://www.encodeproject.org/ENCDO691SXZ/


title: polyA mRNA RNA-seq from liver (ENCLB828MEI)

description:
https://www.encodeproject.org/experiments/ENCSR085HNI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human liver tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR085HNI
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB828MEI
size range: 350-450

source_name: Homo sapiens liver tissue male adult (18 years)

value: liver

value: tissue

value: adult

value: 18 year

value: ENCBS082KWE at ENCODE; https://www.encodeproject.org/ENCBS082KWE/

value: Derived from ENCODE donor ENCDO481HRF; https://www.encodeproject.org/ENCDO481HRF/


title: polyA mRNA RNA-seq from pancreas (ENCLB602LZJ)

description:
https://www.encodeproject.org/experiments/ENCSR001UXR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human pancreas tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR001UXR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB602LZJ
size range: 350-450

source_name: Homo sapiens pancreas tissue female adult (30 years)

value: pancreas

value: 30 year

value: Michael Snyder, Stanford

value: ENCBS526GJF at ENCODE; https://www.encodeproject.org/ENCBS526GJF/

value: Derived from ENCODE donor ENCDO871RXV; https://www.encodeproject.org/ENCDO871RXV/


title: polyA mRNA RNA-seq from ovary (ENCLB178YZR)

description:
https://www.encodeproject.org/experiments/ENCSR046XHI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq in human ovary.
experiment encode accession: ENCSR046XHI
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB178YZR
size range: 350-450

source_name: Homo sapiens ovary tissue female adult (47 years)

value: ovary

value: 47 year

value: ENCBS463ZCZ at ENCODE; https://www.encodeproject.org/ENCBS463ZCZ/

value: Derived from ENCODE donor ENCDO949QAW; https://www.encodeproject.org/ENCDO949QAW/


title: polyA mRNA RNA-seq from testis (ENCLB492VNE)

description:
https://www.encodeproject.org/experiments/ENCSR693GGB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of human testis tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR693GGB
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB492VNE
size range: 350-450

source_name: Homo sapiens testis tissue male adult (44 years)

value: testis

value: 44 year

value: male

value: ENCBS021ARD at ENCODE; https://www.encodeproject.org/ENCBS021ARD/

value: Derived from ENCODE donor ENCDO730LED; https://www.encodeproject.org/ENCDO730LED/


title: bisfulfite treated genomic DNA from arrested, G0 fibroblasts B

city: Baltimore

first: Andrew

last: Feinberg

state: Maryland

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

data_processing:
Alignment performed using BSmooth bisulfite alignment pipeline, Bowtie2 version 2.1.0
Filtered measurments with mapping quality <20 or nucleotide base quality <10, removed measurements from 5' most 10 nucleotides of both mates.
Genome_build: Hg19
Supplementary_files_format_and_content: A tabe of raw methylation values for CpGs with coverage >2 in 2 or more samples from each cell cycle phase, extracted using Bsmooth. Chromosome and position are indicated in the "chr" and "loc" columns.

source_name: G0 fibroblasts B

growth_protocol: Primary dermal fibroblasts were grown in DMEM with 15% FBS, penicllin and streptomycin.

extract_protocol:
Epicentre Masterpure Genomic DNA Extraction
Bisulfite converted Illumina TruSeq DNA library

treatment_protocol: Growth arrested cells were grown to confluency and maintained for 1 week without passaging.

value: Primary dermal fibroblasts

tag: cell stge


title: bisfulfite treated genomic DNA from G2 fibroblasts C

source_name: G2 fibroblasts C


title: bisfulfite treated genomic DNA from G1 fibroblasts C

source_name: G1 fibroblasts C


title: bisfulfite treated genomic DNA from arrested, G0 fibroblasts C

source_name: G0 fibroblasts C


title: bisfulfite treated genomic DNA from G2 fibroblasts B

source_name: G2 fibroblasts B


title: bisfulfite treated genomic DNA from arrested, G0 fibroblasts A

source_name: G0 fibroblasts A


title: bisfulfite treated genomic DNA from G0 fibroblasts B


title: bisfulfite treated genomic DNA from G1 fibroblasts B

source_name: G1 fibroblasts B


title: bisfulfite treated genomic DNA from G2 fibroblasts A

source_name: G2 fibroblasts A


title: polyA mRNA RNA-seq from K562 (ENCLB555AJH)

description:
https://www.encodeproject.org/experiments/ENCSR000BZV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human K562 cytosol long polyadenalated RNA
experiment encode accession: ENCSR000BZV
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2010-11-17
lab: Yijun Ruan, GIS
library encode accession: ENCLB555AJH
size range: >200

source_name: Homo sapiens K562 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2a2db777-e505-455f-a0ba-1ed6451d29ad/@@download/attachment/wgEncodeGisRnaSeq.html.pdf

tag: line

value: immortalized cell line

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: adult

tag: subcellular fraction term name

value: cytosol

value: 53 year

value: female

value: Yijun Ruan, GIS

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS810AAA at ENCODE; https://www.encodeproject.org/ENCBS810AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: bisfulfite treated genomic DNA from G1 fibroblasts A

source_name: G1 fibroblasts A


title: polyA mRNA RNA-seq from K562 (ENCLB555AJR)

description:
https://www.encodeproject.org/experiments/ENCSR000BZV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human K562 cytosol long polyadenalated RNA
experiment encode accession: ENCSR000BZV
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2010-11-17
lab: Yijun Ruan, GIS
library encode accession: ENCLB555AJR
size range: >200

value: ENCBS811AAA at ENCODE; https://www.encodeproject.org/ENCBS811AAA/


title: ATAC-seq from dendritic cell (ENCLB676XDS)

description:
https://www.encodeproject.org/experiments/ENCSR984HFU/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR984HFU
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB676XDS
size range: 175-500

source_name: Mus musculus dendritic in vitro differentiated cells derived from multi-cellular organism treated with 0 ng/mL Lipopolysaccharide for 0 hours

extract_protocol:
general protocol: https://www.encodeproject.org/documents/860c95a8-fdc4-46bd-b9b5-d44242ff20ef/@@download/attachment/ATAC_garberlab_protocol.pdf
extraction method: ATAC-seq (Greenleaf & Chang Lab protocol)

value: dendritic cell

value: in vitro differentiated cells

value: unknown

value: not collected

value: Manuel Garber, UMass

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration_units:hour;

value: ENCBS445ZSR at ENCODE; https://www.encodeproject.org/ENCBS445ZSR/

value: Derived from ENCODE donor ENCDO088AAA; https://www.encodeproject.org/ENCDO088AAA/


title: ATAC-seq from dendritic cell (ENCLB409HKJ)

description:
https://www.encodeproject.org/experiments/ENCSR984HFU/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR984HFU
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB409HKJ
size range: 175-500

value: ENCBS087APK at ENCODE; https://www.encodeproject.org/ENCBS087APK/


title: bisfulfite treated genomic DNA from G0 fibroblasts C

value: Primary dermal fibroblasts


title: bisfulfite treated genomic DNA from G0 fibroblasts A


title: total RNA-seq from dendritic cell (ENCLB644YDO)

description:
https://www.encodeproject.org/experiments/ENCSR945SYV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR945SYV
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB644YDO
size range: 175-500

extract_protocol:
general protocol: https://www.encodeproject.org/documents/a272c1bd-ad80-490d-9ff8-0742c8a8ab92/@@download/attachment/Garber_lab_RNA-seq_protocol.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment


title: total RNA-seq from dendritic cell (ENCLB029VYW)

description:
https://www.encodeproject.org/experiments/ENCSR945SYV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR945SYV
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB029VYW
size range: 175-500


title: total RNA-seq from dendritic cell (ENCLB373FTS)

description:
https://www.encodeproject.org/experiments/ENCSR867RTO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR867RTO
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB373FTS
size range: 175-500

source_name: Mus musculus dendritic in vitro differentiated cells derived from multi-cellular organism treated with 100 ng/mL Lipopolysaccharide for 6 hours

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS139NUH at ENCODE; https://www.encodeproject.org/ENCBS139NUH/


title: ATAC-seq from dendritic cell (ENCLB297GDC)

description:
https://www.encodeproject.org/experiments/ENCSR939XWM/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR939XWM
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB297GDC
size range: 175-500

source_name: Mus musculus dendritic in vitro differentiated cells derived from multi-cellular organism treated with 100 ng/mL Lipopolysaccharide for 1 hour

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

value: ENCBS795OWW at ENCODE; https://www.encodeproject.org/ENCBS795OWW/


title: ATAC-seq from dendritic cell (ENCLB543XCD)

description:
https://www.encodeproject.org/experiments/ENCSR787YJK/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR787YJK
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB543XCD
size range: 175-500

source_name: Mus musculus dendritic in vitro differentiated cells derived from multi-cellular organism treated with 100 ng/mL Lipopolysaccharide for 2 hours

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS688SEU at ENCODE; https://www.encodeproject.org/ENCBS688SEU/


title: Single.BLA-M-3_RNA-seq

status: Public on Feb 04 2017

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

country: China

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

description: Sample name: Single.BLA.M.3

data_processing:
Reads quality was examined by “fastQC”
Filtered reads were aligned to rhesus monkey genome database (AV et al. 2014) by tophat v2.1.0
Only uniquely mapped reads were used to calculate the counts of each gene by HTSeq (Anders et al. 2015).
Reads counts were normalized to library size by DESeq2 (Love et al. 2014), and normalized reads were then used for calculate the FPKM (Fragments Per Kilobase of transcript per Million fragments mapped).
Genome_build: MacaM
Supplementary_files_format_and_content: Contains the expression level of each gene in all samples, measured by FPKM

organism: Macaca mulatta

source_name: blastocyst

growth_protocol: Embryos were cultured at 37℃ in 50 μl drops of equilibrated HECM-9 containing 10% FBS (HyClone Laboratories Inc.) in a humidified atmosphere of 5% CO2 in air. Culture medium was changed every other day. Morphologically normal embryos with few fragments were selected for RNA-seq.

extract_protocol:
Dynabeads mRNA DIRECT kit (Invitrogen) was utilized to extract RNAs from oocytes and embryos. Oocytes or embryos were washed in PBS containing 0.03% PVP and transferred into a RNase-free Eppendorf tube (500 μl) containing 200 μl lysis/binding buffer from the Kit (Invitrogen). Complete lysis was achieved by gently flicking the tube for 2 min. The sample lysis were then temporarily stored at -80 ℃ until RNA extraction. RNA was extracted following manufactures instruction.
RNAs were subject to low input RNA-seq library construction based on Tang's protocol (Tang et al. 2010). In case of overloading, pooled RNA were aliquoted into several tubes and each tube was independently amplified, after 20 rounds of PCR amplification, all tubes contained the same stage samples were mixed together and sent to another 9 rounds of PCR amplification, PCR products was purified and the quality of library were checked by qPCR analysis of a set of house-keeping genes, Agilent 2100 bioanalyzer and QUBIT (Life Technologies) were also employed for quality control. The libraries were deep sequenced on Illumina HiSeq 2000 platform using 90-bp paired-end strategy.

tag: tissue

value: blastocyst

tag: oocyte/embryo number

tag: donator monkey number

tag: source of female

value: M


title: ATAC-seq from dendritic cell (ENCLB690QLA)

description:
https://www.encodeproject.org/experiments/ENCSR780HBP/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR780HBP
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB690QLA
size range: 175-500

value: dendritic cell

value: in vitro differentiated cells

value: ENCBS132PYZ at ENCODE; https://www.encodeproject.org/ENCBS132PYZ/


title: ATAC-seq from dendritic cell (ENCLB952DVH)

description:
https://www.encodeproject.org/experiments/ENCSR780HBP/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR780HBP
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB952DVH
size range: 175-500

value: unknown

value: not collected

value: Manuel Garber, UMass


title: total RNA-seq from dendritic cell (ENCLB798MHL)

description:
https://www.encodeproject.org/experiments/ENCSR602ODY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR602ODY
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB798MHL
size range: 175-500

value: ENCBS155QBX at ENCODE; https://www.encodeproject.org/ENCBS155QBX/

value: Derived from ENCODE donor ENCDO088AAA; https://www.encodeproject.org/ENCDO088AAA/


title: ATAC-seq from dendritic cell (ENCLB160HOT)

description:
https://www.encodeproject.org/experiments/ENCSR347RZI/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR347RZI
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB160HOT
size range: 175-500

source_name: Mus musculus dendritic in vitro differentiated cells derived from multi-cellular organism treated with 100 ng/mL Lipopolysaccharide for 4 hours

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS230UHY at ENCODE; https://www.encodeproject.org/ENCBS230UHY/


title: total RNA-seq from dendritic cell (ENCLB478RXH)

description:
https://www.encodeproject.org/experiments/ENCSR602ODY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR602ODY
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB478RXH
size range: 175-500


title: total RNA-seq from dendritic cell (ENCLB086QSP)

description:
https://www.encodeproject.org/experiments/ENCSR198JTV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR198JTV
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB086QSP
size range: 175-500


title: ATAC-seq from dendritic cell (ENCLB888LUQ)

description:
https://www.encodeproject.org/experiments/ENCSR116SPR/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR116SPR
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB888LUQ
size range: 175-500

source_name: Mus musculus dendritic in vitro differentiated cells derived from multi-cellular organism treated with 100 ng/mL Lipopolysaccharide for 30 minutes

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS520XKE at ENCODE; https://www.encodeproject.org/ENCBS520XKE/


title: total RNA-seq from dendritic cell (ENCLB892EBL)

description:
https://www.encodeproject.org/experiments/ENCSR198JTV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR198JTV
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB892EBL
size range: 175-500

value: ENCBS893OJB at ENCODE; https://www.encodeproject.org/ENCBS893OJB/


title: mammary epithelial cells, plate 2, library 4

city: Utrecht

first: Mauro

last: Muraro

state: Utrecht

address: Uppsalalaan, 8

country: Netherlands

institute: Single Cell Discoveries

data_processing:
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mm10 mouse genome release downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Genome_build: mm10
Supplementary_files_format_and_content: J2_mammary_gland_singlecells.csv: Tab separated data file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples. Column name indicates the experiment name (J2),  plate number (P*) and library number, separated by dots, followed by the cell number of the library, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: mammary gland

extract_protocol:
Cells were sorted into 5µl Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius for 5 minutes. mRNA was then reverse transcribed by adding RT mix.
RNA was processed by SORT-Seq, an automated version of the previously described Cel-Seq2 technique. Libraries were sequenced on a Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain

value: mixed


title: ATAC-seq from dendritic cell (ENCLB704IAI)

description:
https://www.encodeproject.org/experiments/ENCSR347RZI/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR347RZI
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB704IAI
size range: 175-500

value: ENCBS216NIS at ENCODE; https://www.encodeproject.org/ENCBS216NIS/


title: total RNA-seq from dendritic cell (ENCLB219HCZ)

description:
https://www.encodeproject.org/experiments/ENCSR085TSA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR085TSA
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB219HCZ
size range: 175-500


title: total RNA-seq from dendritic cell (ENCLB542YDS)

description:
https://www.encodeproject.org/experiments/ENCSR085TSA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR085TSA
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB542YDS
size range: 175-500


title: mammary epithelial cells, plate 1, library 3


title: mammary epithelial cells, plate 2, library 3


title: mammary epithelial cells, plate 2, library 2


title: mammary epithelial cells, plate 2, library 1


title: ATAC-seq from dendritic cell (ENCLB607DLY)

description:
https://www.encodeproject.org/experiments/ENCSR939XWM/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR939XWM
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB607DLY
size range: 175-500

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


title: mammary epithelial cells, plate 1, library 2


title: total RNA-seq from dendritic cell (ENCLB797VMN)

description:
https://www.encodeproject.org/experiments/ENCSR867RTO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq
experiment encode accession: ENCSR867RTO
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB797VMN
size range: 175-500

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:6; duration_units:hour;


title: ATAC-seq from dendritic cell (ENCLB230ZEV)

description:
https://www.encodeproject.org/experiments/ENCSR787YJK/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR787YJK
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB230ZEV
size range: 175-500

value: dendritic cell

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:2; duration_units:hour;


title: mammary epithelial cells, plate 1, library 1


title: L_Pro_LIF_rep1

city: Naples

first: Cristina

last: D'Aniello

address: Via Pietro Castellino, 111

country: Italy

institute: IGB-CNR

description: Sample 8

data_processing:
Illumina casava base calling
RNA-seq data were mapped to mm9 whole genome using TopHat v 2.0.13 using the annotation file (Mus musculus NCBIM37 release 67) as guide (parameter -G). All the other parameters are set as default. For RNA-seq data analysis of FBS/LIF ± VitC, L-Pro, naïve/2i and F/A EpiSCs, raw data were aligned to the Mus musculus NCBIM37.67 (mm9) transcriptome using Bowtie 1 with the following setting: -a --best --strata -S -m 100 -X 500. Quantification of gene expression was performed using MMSEQ.
raw counts have been obtained using HTSeq  (version 0.6.1p1) on intersection-nonempty mode and mmseq
individual raw count were comnined in a single table of counts and underwent to upper quantile normalization and proportional test filtering
normalization of combined raw counts, filtering and the analysis of differentially expressed genes was performad using RNAseqGUI, mmseq and DESeq
Genome_build: mm9
Supplementary_files_format_and_content: log expression measure

source_name: embryonic stem cells (ESC)

growth_protocol: mir-290_mCherry/mir-302_eGFP dual reporter ESCs (DRESCs) were plated at low density in FBS/LIF ± VitC (500 μM), 2i, L-Pro or in N2B27 supplemented with Activin A (20 ng/ml, Invitrogen) and bFGF (12 ng/ml) and cultured for 5 days.

extract_protocol:
Total RNAs were isolated using Trizol (samples 1-4) and RNeasy kit (samples 5-14)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell population


title: VitC_LIF_rep1

description: Sample 7

value: mir-290_mCherry/mir-302_eGFP dual reporter ESCs (DRESCs)


title: 2i_LIF_rep1

description: Sample 6


title: FBS_LIF_rep2

description: Sample 10


title: Fgf_ActivinA_rep2

description: Sample 14


title: RNAseq_AT3G45810_DIG1_Dex_10d_rep2

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Base-calling were performed by Illumina Real-Time Analysis software v1.17.20 to v1.18.61.
Sequencing reads were mapped to Arabidopsis TAIR10 genome assembly by tophat2.0.8 using default settings. Mapped reads with of mapping score equal to or larger than 10 were counted by HTSeq (v0.5.4) and analyzed by edgeR (v3.6.2) to identify differentially expressed genes using contrasts between ABA- and mock-treated samples at each time point and false discovery rate 0.01 or 0.05 as thresholds.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Etiolated seedlings were germinated and grown in dark for 3 days in 24-well plates with 1x Linsmaier and Skoog (LS) pH buffered basal salts, pH 5.7. Light-grown seedlings were germinated and grown on plates containing 1x LS media with 0.7% agar, 0.5% sucrose and 500 mM Dexamethasone.

extract_protocol:
Total RNA was extracted using Plant RNeasy mini Kit (Qiagen) according to manufacturer's instructions.
Libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit and sequenced by Illumina HiSeq 2500 according to the manufacturers' instructions.

treatment_protocol: Three-day old etiolated seedlings were treated by 10 uM Dex for 4 hours in dark. Light-grown seedlings were grown on plates containing 500 nM Dex for 10 days.

tag: accession

value: 10 day

tag: light condition

value: long day

tag: treatment

value: 500 nM dexamethasone,  10 days


title: RNAseq_GFP_Dex_10d_rep2

tag: age


title: 2i_LIF_rep2

description: Sample 11


title: L_Pro_LIF_rep2

description: Sample 13


title: Fgf_ActivinA_rep1

description: Sample 9


title: FBS_LIF_rep1

description: Sample 5


title: RNAseq_GFP_Dex_10d_rep1


title: mammary epithelial cells, plate 1, library 4


title: RNAseq_AT3G45810_DIG1_Dex_4h_rep2

value: 3 day

value: dark

value: 10 uM dexamethasone, 4 hours


title: AT5G50360_DIG2_Dex_6h_ChIP

data_processing:
Base-calling were performed by Illumina Real-Time Analysis software v1.17.20 to v1.18.61.
Reads were aligned by bowtie version 0.12.7 against the Arabidopsis TAIR10 genome assembly with parameters  "-m 1 --best --strata -S -3 30 --chunkmbs 256".
Genome_build: TAIR10
Supplementary_files_format_and_content: Peaks were called by using GFP-DIG as treatment and GFP as control with macs2.1.0 parameters "-g 1.19e8 --keep-dup auto --call-summits". The resulting peaks were then filtered by a p-value cutoff of 1e-16.

growth_protocol: Seedling were germinated and grown on nylon mesh in hydroponics for 4 days in dark before Dex treatment.

extract_protocol:
After formaldehyde crosslink and nuclei isolation, chromatin was sonicated to 100-500 bp fragments. GFP or GFP-DTAF was immunoprecipitated by a rabbit polyclonal GFP antibody (cat #A11122, Thermo Fisher USA). Detailed ChIP protocol is described in Song et al. Curr. Protoc. plant Biol. 2016.
Libraries were prepared according to Illumina's instructions accompanying TruSeq DNA sample prep kit and sequenced by Illumina HiSeq 2500 according to the manufacturer's instructions.

treatment_protocol: 10 uM Dex treatment for 6 hours.

value: 4 day

value: 10 uM dexamethasone, 6 hours

tag: chip antibody

value: GFP (ThermoFisher #A11122)


title: GFP_Dex_6h_ChIP


title: RNAseq_EtOH_60h_rep2

growth_protocol: Seedling were germinated and grown on nylon mesh in hydroponics for 3 days in dark before ABA or mock treatment.

treatment_protocol: 10 uM ABA treatment or ethanol mock treatment for 1 to 60 hours.

value: EtOH mock treatment, 60 hours


title: AT3G45810_DIG1_Dex_6h_ChIP


title: RNAseq_AT3G45810_DIG1_Dex_10d_rep1


title: RNAseq_ABA_60h_rep2

value: 10 uM abscisic acid, 60 hours


title: RNAseq_GFP_Dex_4h_rep1


title: RNAseq_EtOH_36h_rep2

value: EtOH mock treatment, 36 hours


title: RNAseq_ABA_36h_rep2

value: 10 uM abscisic acid, 36 hours


title: RNAseq_AT5G50360_DIG2_Dex_4h_rep2


title: RNAseq_EtOH_24h_rep2

value: EtOH mock treatment, 24 hours


title: RNAseq_AT3G45810_DIG1_Dex_4h_rep1


title: RNAseq_ABA_24h_rep2

value: 10 uM abscisic acid, 24 hours


title: RNAseq_EtOH_12h_rep2

value: EtOH mock treatment, 12 hours


title: RNAseq_GFP_Dex_4h_rep2


title: RNAseq_EtOH_08h_rep2

value: EtOH mock treatment, 8 hours


title: RNAseq_EtOH_01h_rep2

value: EtOH mock treatment, 1 hours


title: RNAseq_AT5G50360_DIG2_Dex_4h_rep1


title: RNAseq_ABA_01h_rep2

value: 10 uM abscisic acid, 1 hours


title: RNAseq_EtOH_04h_rep2

value: EtOH mock treatment, 4 hours


title: VitC_LIF_rep2

description: Sample 12

value: mir-290_mCherry/mir-302_eGFP dual reporter ESCs (DRESCs)


title: RNAseq_EtOH_36h_rep1

value: 3 day

value: dark


title: RNAseq_ABA_04h_rep2

value: 10 uM abscisic acid, 4 hours


title: RNAseq_EtOH_12h_rep1


title: RNAseq_ABA_12h_rep1

value: 10 uM abscisic acid, 12 hours


title: RNAseq_ABA_08h_rep2

value: 10 uM abscisic acid, 8 hours


title: RNAseq_ABA_04h_rep1


title: RNAseq_EtOH_01h_rep1


title: RNAseq_ABA_24h_rep1


title: RNAseq_ABA_36h_rep1


title: RNAseq_EtOH_08h_rep1


title: AT4G34000_ABF3_EtOH_ChIP_rep3

description: AT4G34000_ABF3_EtOH_optimal_narrowPeak_p16.bed

data_processing:
Base-calling were performed by Illumina Real-Time Analysis software v1.17.20 to v1.18.61.
Reads were aligned by bowtie version 0.12.7 against the Arabidopsis TAIR10 genome assembly with parameters " -m 1 --best --strata -S --chunkmbs 256" for 100 bp reads or "-m 1 --best --strata -S -3 30 --chunkmbs 256" for 130 bp reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by the Irreproducible Discovery Rate (IDR) pipeline using initial peak calls from MACS2 version 2.0.10, with q-value thresholds of 0.05, 0.01, and 0.001 for replicate consistency. The resulting optimal set of peaks were then filtered by a p-value cutoff of 1e-16.

growth_protocol: Recombineering tagging of YPet to TF genes was carried out as described previously (Zhou et al., The Plant Journal 2011; PMID 21294796).  Seedling were germinated and grown on nylon mesh in hydroponics for 3 days in dark before ABA or mock treatment.

extract_protocol:
After formaldehyde crosslink and nuclei isolation, chromatin was sonicated to 100-500 bp fragments. YPet-tagged TF of interest was immunoprecipitated by a rabbit polyclonal GFP antibody (cat #A11122, Thermo Fisher USA). Mock ChIP was carried out by immunoprecipitating Col-0 with the same GFP antibody. Detailed ChIP protocol is described in Song et al. Curr. Protoc. plant Biol. 2016.
Libraries were prepared according to Illumina's instructions accompanying TruSeq DNA sample prep kit and sequenced by Illumina HiSeq 2500 according to the manufacturer's instructions.

treatment_protocol: 10 uM ABA treatment or ethanol mock treatment for 4 hours.

value: GFP (ThermoFisher #A11122)


title: Col0_mockChIP_rep2

data_processing:
Base-calling were performed by Illumina Real-Time Analysis software v1.17.20 to v1.18.61.
Reads were aligned by bowtie version 0.12.7 against the Arabidopsis TAIR10 genome assembly with parameters " -m 1 --best --strata -S --chunkmbs 256" for 100 bp reads or "-m 1 --best --strata -S -3 30 --chunkmbs 256" for 130 bp reads.
Col0_mockChIP_rep1 and Col0_mockChIP_rep2 are used as the mock control datasets to generate the processed data (peaks)
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by the Irreproducible Discovery Rate (IDR) pipeline using initial peak calls from MACS2 version 2.0.10, with q-value thresholds of 0.05, 0.01, and 0.001 for replicate consistency. The resulting optimal set of peaks were then filtered by a p-value cutoff of 1e-16.


title: RNAseq_ABA_08h_rep1


title: RNAseq_EtOH_24h_rep1


title: RNAseq_ABA_01h_rep1


title: AT3G19290_ABF4_EtOH_ChIP_rep2

description: AT3G19290_ABF4_EtOH_optimal_narrowPeak_p16.bed


title: AT3G19290_ABF4_EtOH_ChIP_rep3


title: Col0_mockChIP_rep1


title: AT4G34000_ABF3_ABA_ChIP_rep2

description: AT4G34000_ABF3_ABA_optimal_narrowPeak_p16.bed


title: AT3G19290_ABF4_ABA_ChIP_rep2

description: AT3G19290_ABF4_ABA_optimal_narrowPeak_p16.bed


title: AT3G19290_ABF4_ABA_ChIP_rep1


title: ATAC-seq from dendritic cell (ENCLB570NPV)

description:
https://www.encodeproject.org/experiments/ENCSR116SPR/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR116SPR
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB570NPV
size range: 175-500

value: dendritic cell

value: in vitro differentiated cells

tag: biosample encode accession

tag: dev stage

value: unknown

tag: Sex

value: not collected

tag: lab

value: Manuel Garber, UMass

value: treatment_term_id:CHEBI:16412; treatment_term_name:Lipopolysaccharide; treatment_type:chemical; duration:30; duration_units:minute;

tag: link

value: ENCBS281JFK at ENCODE; https://www.encodeproject.org/ENCBS281JFK/

value: Derived from ENCODE donor ENCDO088AAA; https://www.encodeproject.org/ENCDO088AAA/


title: AT3G19290_ABF4_ABA_ChIP_rep3


title: RNAseq_ABA_12h_rep2


title: AT4G34000_ABF3_EtOH_ChIP_rep2


title: AT4G34000_ABF3_ABA_ChIP_rep3


title: AT2G46680_HB7_EtOH_ChIP_rep2

description: AT2G46680_HB7_EtOH_optimal_narrowPeak_p16.bed


title: AT2G46680_HB7_ABA_ChIP_rep3

description: AT2G46680_HB7_ABA_optimal_narrowPeak_p16.bed


title: RNAseq_ABA_60h_rep1

value: 10 uM abscisic acid, 60 hours


title: AT5G04760_EtOH_ChIP_rep1

description: AT5G04760_EtOH_optimal_narrowPeak_p16.bed

value: EtOH mock treatment, 4 hours


title: AT5G04760_ABA_ChIP_rep2

description: AT5G04760_ABA_optimal_narrowPeak_p16.bed


title: AT4G34000_ABF3_EtOH_ChIP_rep1


title: AT4G34000_ABF3_ABA_ChIP_rep1


title: AT3G19290_ABF4_EtOH_ChIP_rep1


title: AT2G22430_HB6_EtOH_ChIP_rep3

description: AT2G22430_HB6_EtOH_optimal_narrowPeak_p16.bed


title: AT5G04340_ZAT6_EtOH_ChIP_rep2

description: AT5G04340_ZAT6_EtOH_optimal_narrowPeak_p16.bed


title: AT5G04760_ABA_ChIP_rep1


title: AT2G22430_HB6_ABA_ChIP_rep2

description: AT2G22430_HB6_ABA_optimal_narrowPeak_p16.bed


title: RNAseq_EtOH_04h_rep1


title: AT2G22430_HB6_EtOH_ChIP_rep1


title: AT2G22430_HB6_ABA_ChIP_rep3


title: AT5G65310_HB5_EtOH_ChIP_rep3

description: AT5G65310_HB5_EtOH_optimal_narrowPeak_p16.bed


title: AT5G65310_HB5_ABA_ChIP_rep3

description: AT5G65310_HB5_ABA_optimal_narrowPeak_p16.bed


title: AT2G46680_HB7_ABA_ChIP_rep2


title: AT5G65310_HB5_ABA_ChIP_rep2


title: AT2G46680_HB7_EtOH_ChIP_rep3


title: AT2G46680_HB7_EtOH_ChIP_rep1


title: AT5G65310_HB5_EtOH_ChIP_rep2


title: AT5G65310_HB5_EtOH_ChIP_rep1


title: AT5G04340_ZAT6_ABA_ChIP_rep2

description: AT5G04340_ZAT6_ABA_optimal_narrowPeak_p16.bed


title: AT5G04340_ZAT6_EtOH_ChIP_rep1


title: AT5G67300_MYB44_EtOH_ChIP_rep3

description: AT5G67300_MYB44_EtOH_optimal_narrowPeak_p16.bed


title: AT5G04760_EtOH_ChIP_rep2


title: AT5G04760_EtOH_ChIP_rep3


title: AT5G67300_MYB44_EtOH_ChIP_rep2


title: AT5G04340_ZAT6_ABA_ChIP_rep1


title: AT2G22430_HB6_EtOH_ChIP_rep2


title: RNAseq_EtOH_60h_rep1

value: EtOH mock treatment, 60 hours


title: AT5G43840_HSFA6A_ABA_ChIP_rep3

description: AT5G43840_HSFA6A_ABA_optimal_narrowPeak_p16.bed

value: 3 day


title: AT5G43840_HSFA6A_EtOH_ChIP_rep3

description: AT5G43840_HSFA6A_EtOH_optimal_narrowPeak_p16.bed

value: dark


title: AT5G67300_MYB44_ABA_ChIP_rep2

description: AT5G67300_MYB44_ABA_optimal_narrowPeak_p16.bed

value: 10 uM abscisic acid, 4 hours


title: AT5G04760_ABA_ChIP_rep3


title: AT2G22430_HB6_ABA_ChIP_rep1


title: AT5G43840_HSFA6A_EtOH_ChIP_rep1


title: AT5G65310_HB5_ABA_ChIP_rep1


title: AT4G27410_RD26_EtOH_ChIP_rep2

description: AT4G27410_RD26_EtOH_optimal_narrowPeak_p16.bed


title: AT5G67300_MYB44_ABA_ChIP_rep3


title: AT5G67300_MYB44_ABA_ChIP_rep1


title: AT5G67300_MYB44_EtOH_ChIP_rep1


title: AT4G27410_RD26_ABA_ChIP_rep2

description: AT4G27410_RD26_ABA_optimal_narrowPeak_p16.bed


title: AT5G43840_HSFA6A_EtOH_ChIP_rep2


title: AT4G27410_RD26_EtOH_ChIP_rep1


title: AT4G27410_RD26_ABA_ChIP_rep1


title: AT4G27410_RD26_EtOH_ChIP_rep3


title: AT5G05410_DREB2A_EtOH_ChIP_rep3

description: AT5G05410_DREB2A_EtOH_optimal_narrowPeak_p16.bed


title: polyA mRNA RNA-seq from ovary (ENCLB854BJZ)

description:
https://www.encodeproject.org/experiments/ENCSR516UNF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq in mouse ovary.
experiment encode accession: ENCSR516UNF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB854BJZ
size range: 350-450

source_name: Mus musculus strain C57BL/6J ovary tissue female adult (10 weeks)

extract_protocol:
general protocol: https://www.encodeproject.org/documents/6f6a5d8c-0b06-4457-bfbb-ee4944eab1d6/@@download/attachment/wgEncodeSydhRnaSeq.release2.html.pdf
extraction method: RNeasy Lipid Tissue Mini Kit (QIAGEN cat#74804)

value: ovary

value: tissue

value: adult

value: 10 week

value: female

value: Michael Snyder, Stanford

value: ENCBS887UIO at ENCODE; https://www.encodeproject.org/ENCBS887UIO/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: AT4G27410_RD26_ABA_ChIP_rep3

value: GFP (ThermoFisher #A11122)


title: polyA mRNA RNA-seq from kidney (ENCLB103JFV)

description:
https://www.encodeproject.org/experiments/ENCSR394YLM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse kidney tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR394YLM
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB103JFV
size range: 350-450

source_name: Mus musculus strain C57BL/6J kidney tissue female adult (10 weeks)

value: kidney

value: ENCBS618GAD at ENCODE; https://www.encodeproject.org/ENCBS618GAD/


title: AT5G43840_HSFA6A_ABA_ChIP_rep1


title: AT5G05410_DREB2A_ABA_ChIP_rep2

description: AT5G05410_DREB2A_ABA_optimal_narrowPeak_p16.bed


title: polyA mRNA RNA-seq from lung (ENCLB862USP)

description:
https://www.encodeproject.org/experiments/ENCSR870AQU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse lung tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR870AQU
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB862USP
size range: 350-450

source_name: Mus musculus strain C57BL/6J lung tissue female adult (10 weeks)

value: lung

value: ENCBS964PGO at ENCODE; https://www.encodeproject.org/ENCBS964PGO/


title: polyA mRNA RNA-seq from adipose tissue (ENCLB634OTW)

description:
https://www.encodeproject.org/experiments/ENCSR288TLO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse adipose tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR288TLO
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB634OTW
size range: 350-450

source_name: Mus musculus strain C57BL/6J adipose tissue male adult (10 weeks)

value: adipose tissue

value: male

value: ENCBS298QDT at ENCODE; https://www.encodeproject.org/ENCBS298QDT/


title: polyA mRNA RNA-seq from spleen (ENCLB601GXX)

description:
https://www.encodeproject.org/experiments/ENCSR966JPL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse spleen tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR966JPL
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB601GXX
size range: 350-450

source_name: Mus musculus strain C57BL/6J spleen tissue male adult (10 weeks)

value: spleen

value: ENCBS614NNG at ENCODE; https://www.encodeproject.org/ENCBS614NNG/


title: AT5G05410_DREB2A_EtOH_ChIP_rep1

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours


title: AT5G05410_DREB2A_ABA_ChIP_rep1

value: 10 uM abscisic acid, 4 hours


title: polyA mRNA RNA-seq from liver (ENCLB183BBK)

description:
https://www.encodeproject.org/experiments/ENCSR216KLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse liver tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR216KLZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB183BBK
size range: 350-450

source_name: Mus musculus strain C57BL/6J liver tissue female adult (10 weeks)

value: liver

value: tissue

value: adult

value: 10 week

value: female

value: Michael Snyder, Stanford

value: ENCBS391ULH at ENCODE; https://www.encodeproject.org/ENCBS391ULH/


title: polyA mRNA RNA-seq from adrenal gland (ENCLB752CPU)

description:
https://www.encodeproject.org/experiments/ENCSR713OCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse adrenal gland tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR713OCQ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB752CPU
size range: 350-450

source_name: Mus musculus strain C57BL/6J adrenal gland tissue female adult (10 weeks)

value: adrenal gland

value: ENCBS816ZVY at ENCODE; https://www.encodeproject.org/ENCBS816ZVY/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: AT1G22640_MYB3_EtOH_ChIP_rep2

description: AT1G22640_MYB3_EtOH_optimal_narrowPeak_p16.bed

value: GFP (ThermoFisher #A11122)


title: polyA mRNA RNA-seq from heart (ENCLB129EEJ)

description:
https://www.encodeproject.org/experiments/ENCSR164BAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse heart tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR164BAZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB129EEJ
size range: 350-450

source_name: Mus musculus strain C57BL/6J heart tissue female adult (10 weeks)

value: heart

value: ENCBS183QIH at ENCODE; https://www.encodeproject.org/ENCBS183QIH/


title: polyA mRNA RNA-seq from MEL cell line (ENCLB176ESU)

description:
https://www.encodeproject.org/experiments/ENCSR000CIE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse erythroleukemia cells treated with dimethylsulfoxide 2.0% (single end)
experiment encode accession: ENCSR000CIE
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB176ESU
size range: >175

source_name: Mus musculus strain MEL MEL immortalized cell line treated with 2% dimethyl sulfoxide for 5 days

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d6ec08a9-8b45-424d-aad9-55cbc02d527f/@@download/attachment/wgEncodePsuRnaSeq.html.pdf

tag: line

value: MEL cell line

value: immortalized cell line

tag: description

value: Leukemia (K562 analog)

value: unknown

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:5; duration_units:day; UCSC-ENCODE-cv:DMSO_2.0pct;

value: not collected

tag: health state

value: ENCBS050ENC at ENCODE; https://www.encodeproject.org/ENCBS050ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: AT1G22640_MYB3_EtOH_ChIP_rep1

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours


title: polyA mRNA RNA-seq from brain (ENCLB226LNT)

description:
https://www.encodeproject.org/experiments/ENCSR554PHF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse brain tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR554PHF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB226LNT
size range: 350-450

source_name: Mus musculus strain C57BL/6J brain tissue male adult (10 weeks)

value: brain

value: tissue

value: adult

value: 10 week

value: male

value: Michael Snyder, Stanford

value: ENCBS693QXI at ENCODE; https://www.encodeproject.org/ENCBS693QXI/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: AT5G05410_DREB2A_EtOH_ChIP_rep2

value: GFP (ThermoFisher #A11122)


title: polyA mRNA RNA-seq from sigmoid colon (ENCLB897OWT)

description:
https://www.encodeproject.org/experiments/ENCSR518GDK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse sigmoid colon tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR518GDK
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB897OWT
size range: 350-450

source_name: Mus musculus strain C57BL/6J sigmoid colon tissue female adult (10 weeks)

value: sigmoid colon

value: female

value: ENCBS400IVQ at ENCODE; https://www.encodeproject.org/ENCBS400IVQ/


title: polyA mRNA RNA-seq from bone marrow macrophage (ENCLB619FLT)

description:
https://www.encodeproject.org/experiments/ENCSR000CHO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse bone marrow derived macrophage
experiment encode accession: ENCSR000CHO
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB619FLT
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain Bruce4 bone marrow macrophage primary cell male adult (8 weeks)

value: bone marrow macrophage

value: primary cell

value: Bone marrow derived macrophage from an individual mouse

value: 8 week

value: Bing Ren, UCSD

value: unknown

value: ENCBS182ENC at ENCODE; https://www.encodeproject.org/ENCBS182ENC/

value: Derived from ENCODE donor ENCDO081AAA; https://www.encodeproject.org/ENCDO081AAA/

value: ENCODE dbxrefs BMDM; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=BMDM


title: AT1G51140_FBH3_ABA_ChIP_rep3

description: AT1G51140_FBH3_ABA_optimal_narrowPeak_p16.bed

value: 3 day

value: dark

value: 10 uM abscisic acid, 4 hours


title: polyA mRNA RNA-seq from bone marrow macrophage (ENCLB193VSG)

description:
https://www.encodeproject.org/experiments/ENCSR000CHO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse bone marrow derived macrophage
experiment encode accession: ENCSR000CHO
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB193VSG
size range: >200
spikeins used: /references/ENCSR866KGS/

value: adult

value: male

value: ENCBS875ICW at ENCODE; https://www.encodeproject.org/ENCBS875ICW/


title: AT5G05410_DREB2A_ABA_ChIP_rep3

value: GFP (ThermoFisher #A11122)


title: AT5G43840_HSFA6A_ABA_ChIP_rep2

description: AT5G43840_HSFA6A_ABA_optimal_narrowPeak_p16.bed


title: polyA mRNA RNA-seq from pancreas (ENCLB238YXU)

description:
https://www.encodeproject.org/experiments/ENCSR248XKS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse pancreas tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR248XKS
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB238YXU
size range: 350-450

source_name: Mus musculus strain C57BL/6J pancreas tissue female adult (10 weeks)

value: pancreas

value: tissue

value: 10 week

value: female

value: Michael Snyder, Stanford

value: ENCBS508NKR at ENCODE; https://www.encodeproject.org/ENCBS508NKR/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA mRNA RNA-seq from testis (ENCLB219TSB)

description:
https://www.encodeproject.org/experiments/ENCSR266ESZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse testis tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR266ESZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB219TSB
size range: 350-450

source_name: Mus musculus strain C57BL/6J testis tissue male adult (10 weeks)

value: testis

value: ENCBS928FOT at ENCODE; https://www.encodeproject.org/ENCBS928FOT/


title: polyA mRNA RNA-seq from MEL cell line (ENCLB409VHC)

description:
https://www.encodeproject.org/experiments/ENCSR000CIE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse erythroleukemia cells treated with dimethylsulfoxide 2.0% (single end)
experiment encode accession: ENCSR000CIE
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB409VHC
size range: >175

value: MEL cell line

value: immortalized cell line

value: Leukemia (K562 analog)

value: unknown

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:5; duration_units:day; UCSC-ENCODE-cv:DMSO_2.0pct;

value: not collected

value: ENCBS050ENC at ENCODE; https://www.encodeproject.org/ENCBS050ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: AT4G37790_HAT22_EtOH_ChIP_rep3

description: AT4G37790_HAT22_EtOH_optimal_narrowPeak_p16.bed

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours

value: GFP (ThermoFisher #A11122)


title: AT1G22640_MYB3_EtOH_ChIP_rep3


title: AT4G37790_HAT22_ABA_ChIP_rep3

description: AT4G37790_HAT22_ABA_optimal_narrowPeak_p16.bed

value: 10 uM abscisic acid, 4 hours


title: polyA mRNA RNA-seq from olfactory bulb (ENCLB043XBK)

description:
https://www.encodeproject.org/experiments/ENCSR000CHL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse olfactory bulb
experiment encode accession: ENCSR000CHL
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB043XBK
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl olfactory bulb tissue male adult (8 weeks)

value: olfactory bulb

value: tissue

value: Olfactory Bulb from an individual mouse

value: adult

value: 8 week

value: male

value: Bing Ren, UCSD

value: ENCBS050NOP at ENCODE; https://www.encodeproject.org/ENCBS050NOP/

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

value: ENCODE dbxrefs OlfactBulb; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=OlfactBulb


title: polyA mRNA RNA-seq from small intestine (ENCLB972TNU)

description:
https://www.encodeproject.org/experiments/ENCSR170SVO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of mouse small intestine tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR170SVO
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB972TNU
size range: 350-450

source_name: Mus musculus strain C57BL/6J small intestine tissue female adult (10 weeks)

value: small intestine

value: 10 week

value: female

value: Michael Snyder, Stanford

value: ENCBS443BDC at ENCODE; https://www.encodeproject.org/ENCBS443BDC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: AT1G22640_MYB3_ABA_ChIP_rep3

description: AT1G22640_MYB3_ABA_optimal_narrowPeak_p16.bed

source_name: whole seedlings

value: 3 day

value: dark

value: 10 uM abscisic acid, 4 hours

value: GFP (ThermoFisher #A11122)


title: AT1G22640_MYB3_ABA_ChIP_rep2


title: AT4G37790_HAT22_EtOH_ChIP_rep1

value: EtOH mock treatment, 4 hours


title: AT1G22640_MYB3_ABA_ChIP_rep1


title: polyA mRNA RNA-seq from limb (ENCLB341DPI)

description:
https://www.encodeproject.org/experiments/ENCSR000CHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 14.5 day embryonic mouse limb
experiment encode accession: ENCSR000CHJ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB341DPI
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (14.5 days)

value: limb

value: tissue

value: Limb from an individual mouse

value: embryonic

value: pooled male and female

value: unknown

value: ENCBS146ENC at ENCODE; https://www.encodeproject.org/ENCBS146ENC/


title: polyA mRNA RNA-seq from MEL cell line (ENCLB131SUF)

description:
https://www.encodeproject.org/experiments/ENCSR000CID/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse erythroleukemia cells cell (single end)
experiment encode accession: ENCSR000CID
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB131SUF
size range: >175

source_name: Mus musculus strain MEL MEL immortalized cell line

value: MEL cell line

value: immortalized cell line

value: Leukemia

value: not collected

value: Ross Hardison, PennState

value: ENCBS706GHU at ENCODE; https://www.encodeproject.org/ENCBS706GHU/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: AT1G51140_FBH3_ABA_ChIP_rep2

value: 3 day

value: dark

value: 10 uM abscisic acid, 4 hours

value: GFP (ThermoFisher #A11122)


title: polyA mRNA RNA-seq from brown adipose tissue (ENCLB589BAO)

description:
https://www.encodeproject.org/experiments/ENCSR000CHN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 24 week adult mouse brown adipose tissue
experiment encode accession: ENCSR000CHN
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB589BAO
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl brown adipose tissue male adult (24 weeks)

value: brown adipose tissue

value: tissue

value: Brown adipocytes tissue from an individual mouse

value: adult

value: 24 week

value: male

value: Bing Ren, UCSD

value: ENCBS498WSA at ENCODE; https://www.encodeproject.org/ENCBS498WSA/

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

value: ENCODE dbxrefs BAT; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=BAT


title: AT1G51140_FBH3_ABA_ChIP_rep1


title: polyA mRNA RNA-seq from brown adipose tissue (ENCLB305OAY)

description:
https://www.encodeproject.org/experiments/ENCSR000CHN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 24 week adult mouse brown adipose tissue
experiment encode accession: ENCSR000CHN
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB305OAY
size range: >200
spikeins used: /references/ENCSR866KGS/

value: unknown

value: ENCBS183ENC at ENCODE; https://www.encodeproject.org/ENCBS183ENC/