title: polyA mRNA RNA-seq from MEL cell line (ENCLB828GHR)

description:
https://www.encodeproject.org/experiments/ENCSR000CHM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse MEL cell line
experiment encode accession: ENCSR000CHM
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB828GHR
size range: >200
spikeins used: /references/ENCSR866KGS/

value: MEL cell line

value: immortalized cell line

value: Leukemia (K562 analog)

value: not collected

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

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_EtOH_ChIP_rep2

status: Public on Feb 03 2017

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description: AT1G51140_FBH3_EtOH_optimal_narrowPeak_p16.bed

library_source: genomic

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.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: whole seedlings

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.

tag: accession

tag: age

value: 3 day

tag: light condition

value: dark

tag: treatment

value: EtOH mock treatment, 4 hours

tag: chip antibody

value: GFP (ThermoFisher #A11122)


title: AT4G01120_GBF2_ABA_ChIP_rep3

description: AT4G01120_GBF2_ABA_optimal_narrowPeak_p16.bed

value: 10 uM abscisic acid, 4 hours


title: AT1G51140_FBH3_EtOH_ChIP_rep1


title: AT4G01120_GBF2_EtOH_ChIP_rep3

description: AT4G01120_GBF2_EtOH_optimal_narrowPeak_p16.bed


title: polyA mRNA RNA-seq from MEL cell line (ENCLB050CMT)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000CHM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse MEL cell line
experiment encode accession: ENCSR000CHM
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB050CMT
size range: >200
spikeins used: /references/ENCSR866KGS/

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain MEL MEL immortalized cell line

tag: line

tag: description

tag: biosample encode accession

tag: dev stage

value: unknown

tag: Sex

tag: lab

value: Bing Ren, UCSD

tag: link

value: ENCBS425KAG at ENCODE; https://www.encodeproject.org/ENCBS425KAG/


title: polyA mRNA RNA-seq from small intestine (ENCLB460BVP)

description:
https://www.encodeproject.org/experiments/ENCSR000CHI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse small intestine
experiment encode accession: ENCSR000CHI
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB460BVP
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl small intestine 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: small intestine

value: tissue

value: Small Intestine from a single mouse

value: adult

value: 8 week

value: male

tag: health state

value: ENCBS156ENC at ENCODE; https://www.encodeproject.org/ENCBS156ENC/

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

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


title: polyA mRNA RNA-seq from testis (ENCLB869HSY)

description:
https://www.encodeproject.org/experiments/ENCSR000CHH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse testis
experiment encode accession: ENCSR000CHH
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB869HSY
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: testis

value: Testis from an individual mouse

value: ENCBS165ENC at ENCODE; https://www.encodeproject.org/ENCBS165ENC/

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


title: polyA mRNA RNA-seq from testis (ENCLB707SLR)

description:
https://www.encodeproject.org/experiments/ENCSR000CHH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse testis
experiment encode accession: ENCSR000CHH
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB707SLR
size range: >200
spikeins used: /references/ENCSR866KGS/

value: ENCBS029VDO at ENCODE; https://www.encodeproject.org/ENCBS029VDO/


title: AT1G51140_FBH3_EtOH_ChIP_rep3

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours

value: GFP (ThermoFisher #A11122)


title: AT4G37790_HAT22_EtOH_ChIP_rep2

description: AT4G37790_HAT22_EtOH_optimal_narrowPeak_p16.bed


title: polyA mRNA RNA-seq from olfactory bulb (ENCLB748FBZ)

description:
https://www.encodeproject.org/experiments/ENCSR000CHL/
***************
biological replicate number: 1
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: ENCLB748FBZ
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: Bing Ren, UCSD

value: unknown

value: ENCBS154ENC at ENCODE; https://www.encodeproject.org/ENCBS154ENC/

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


title: polyA mRNA RNA-seq from thymus (ENCLB270YOM)

description:
https://www.encodeproject.org/experiments/ENCSR000CHK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse thymus
experiment encode accession: ENCSR000CHK
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB270YOM
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: thymus

value: Thymus from an individual mouse

value: adult

value: 8 week

value: male

value: ENCBS373SAT at ENCODE; https://www.encodeproject.org/ENCBS373SAT/

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

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


title: AT4G01120_GBF2_ABA_ChIP_rep1

value: 3 day

value: dark

value: 10 uM abscisic acid, 4 hours


title: AT4G37790_HAT22_ABA_ChIP_rep2

description: AT4G37790_HAT22_ABA_optimal_narrowPeak_p16.bed

value: GFP (ThermoFisher #A11122)


title: AT1G56170_NFYC2_EtOH_ChIP_rep3

description: AT1G56170_NFYC2_EtOH_optimal_narrowPeak_p16.bed

value: EtOH mock treatment, 4 hours


title: AT1G56170_NFYC2_ABA_ChIP_rep3

description: AT1G56170_NFYC2_ABA_optimal_narrowPeak_p16.bed


title: AT4G37790_HAT22_ABA_ChIP_rep1


title: AT1G56170_NFYC2_EtOH_ChIP_rep2


title: polyA mRNA RNA-seq from heart (ENCLB330QBQ)

description:
https://www.encodeproject.org/experiments/ENCSR000CHF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 14.5 day embryonic mouse heart
experiment encode accession: ENCSR000CHF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB330QBQ
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: heart

value: tissue

value: Heart from an individual mouse

value: embryonic

value: pooled male and female

value: Bing Ren, UCSD

value: ENCBS143ENC at ENCODE; https://www.encodeproject.org/ENCBS143ENC/

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


title: polyA mRNA RNA-seq from thymus (ENCLB888YNI)

description:
https://www.encodeproject.org/experiments/ENCSR000CHK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse thymus
experiment encode accession: ENCSR000CHK
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB888YNI
size range: >200
spikeins used: /references/ENCSR866KGS/

value: thymus

value: Thymus from an individual mouse

value: adult

value: 8 week

value: male

value: unknown

value: ENCBS168ENC at ENCODE; https://www.encodeproject.org/ENCBS168ENC/


title: polyA mRNA RNA-seq from limb (ENCLB317MXI)

description:
https://www.encodeproject.org/experiments/ENCSR000CHJ/
***************
biological replicate number: 2
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: ENCLB317MXI
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: limb

value: Limb from an individual mouse

value: ENCBS456FXG at ENCODE; https://www.encodeproject.org/ENCBS456FXG/

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


title: polyA mRNA RNA-seq from MEL cell line (ENCLB966DMQ)

description:
https://www.encodeproject.org/experiments/ENCSR000CID/
***************
biological replicate number: 1
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: ENCLB966DMQ
size range: >175

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

value: MEL cell line

value: immortalized cell line

value: Leukemia

value: not collected

value: Ross Hardison, PennState

value: ENCBS671NUO at ENCODE; https://www.encodeproject.org/ENCBS671NUO/

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: AT1G56170_NFYC2_EtOH_ChIP_rep1

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours

value: GFP (ThermoFisher #A11122)


title: polyA mRNA RNA-seq from small intestine (ENCLB335ESW)

description:
https://www.encodeproject.org/experiments/ENCSR000CHI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse small intestine
experiment encode accession: ENCSR000CHI
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB335ESW
size range: >200
spikeins used: /references/ENCSR866KGS/

value: small intestine

value: tissue

value: Small Intestine from a single mouse

value: adult

value: 8 week

value: male

value: Bing Ren, UCSD

value: ENCBS914NDJ at ENCODE; https://www.encodeproject.org/ENCBS914NDJ/

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


title: polyA mRNA RNA-seq from placenta (ENCLB425SAG)

description:
https://www.encodeproject.org/experiments/ENCSR000CHD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse placenta
experiment encode accession: ENCSR000CHD
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB425SAG
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain B6NCrl placenta tissue female adult (8 weeks)

value: placenta

value: A single placenta

value: female

value: ENCBS407UZA at ENCODE; https://www.encodeproject.org/ENCBS407UZA/

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


title: polyA mRNA RNA-seq from placenta (ENCLB133YIL)

description:
https://www.encodeproject.org/experiments/ENCSR000CHD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse placenta
experiment encode accession: ENCSR000CHD
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB133YIL
size range: >200
spikeins used: /references/ENCSR866KGS/

value: unknown

value: ENCBS155ENC at ENCODE; https://www.encodeproject.org/ENCBS155ENC/


title: AT4G01120_GBF2_EtOH_ChIP_rep2

description: AT4G01120_GBF2_EtOH_optimal_narrowPeak_p16.bed

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours

value: GFP (ThermoFisher #A11122)


title: AT4G01120_GBF2_ABA_ChIP_rep2

description: AT4G01120_GBF2_ABA_optimal_narrowPeak_p16.bed

value: 10 uM abscisic acid, 4 hours


title: polyA mRNA RNA-seq from brain (ENCLB244FTZ)

description:
https://www.encodeproject.org/experiments/ENCSR000CHG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 14.5 day embryonic mouse whole brain
experiment encode accession: ENCSR000CHG
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB244FTZ
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: brain

value: tissue

value: Whole Brain from an individual mouse

value: embryonic

value: pooled male and female

value: ENCBS358ENC at ENCODE; https://www.encodeproject.org/ENCBS358ENC/

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


title: polyA mRNA RNA-seq from heart (ENCLB814UGI)

description:
https://www.encodeproject.org/experiments/ENCSR000CHF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 14.5 day embryonic mouse heart
experiment encode accession: ENCSR000CHF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB814UGI
size range: >200
spikeins used: /references/ENCSR866KGS/

value: heart

value: Heart from an individual mouse

value: Bing Ren, UCSD

value: ENCBS526PXE at ENCODE; https://www.encodeproject.org/ENCBS526PXE/

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


title: AT4G01120_GBF2_EtOH_ChIP_rep1

value: 3 day


title: polyA mRNA RNA-seq from bone marrow (ENCLB883ZDF)

description:
https://www.encodeproject.org/experiments/ENCSR000CGT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 8 week adult mouse bone marrow
experiment encode accession: ENCSR000CGT
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB883ZDF
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: bone marrow

value: Bone Marrow from an individual mouse

value: adult

value: 8 week

value: male

value: unknown

value: ENCBS129ENC at ENCODE; https://www.encodeproject.org/ENCBS129ENC/

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

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


title: polyA mRNA RNA-seq from liver (ENCLB784HFI)

description:
https://www.encodeproject.org/experiments/ENCSR000CHE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 14.5 day embryonic mouse liver
experiment encode accession: ENCSR000CHE
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB784HFI
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: liver

value: tissue

value: Liver from an individual mouse

value: embryonic

value: pooled male and female

value: ENCBS341ENC at ENCODE; https://www.encodeproject.org/ENCBS341ENC/

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


title: AT1G56170_NFYC2_ABA_ChIP_rep1

value: 3 day

value: dark

value: 10 uM abscisic acid, 4 hours

value: GFP (ThermoFisher #A11122)


title: PSC5 T5 transwell coculture

city: Cold Spring Harbor

first: David

middle: A.

last: Tuveson

state: NY

address: 1 Bungtown Rd.

department: Cancer Center

institute: Cold Spring Harbor Laboratory

description:
TA017
Pancreatic stellate cells grown as a 3D activated cocultures in a transwell with 3D pancreatic tumor organoids in the lower chamber
Sample 8

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
We mapped the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat (Trapnell et al., 2009)(version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combined them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimated the relative abundance (i.e. expression level) of genes and splice isoforms using cufflinks (Trapnell et al., 2010)(version 2.0.2) with default settings.
Genes expressed in fewer than two libraries were filtered out before differential expression testing. The principle component analysis was calculated using the ‘prcomp’ function available in R and plotted using a customized R script.
Expression normalization and differential expression testing were performed using DESeq (Anders and Huber, 2010), with dispersion estimation parameters set as: ‘method = “per-condition" , sharingMode ="maximum" , fitType="parametric"’. Genes with adjusted p-value < 0.01 were selected as significantly differentially expressed between conditions. All plots were produced using customized R scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include the raw (countTable.txt) and normalized read counts (countTable_normalized.txt) for each gene for each sample. Tab-delimited text files of the DESeq output for each gene, for each comparison. The file DESeq_2Dvs3D.txt contains the comparison of PSCs cultured as 2D monocultures (Sample 1 and Sample 2) to PSCs cultured as quiecent 3D monocultures (Sample 3 and Sample 4). The file DESeq_2DvsTranswell.txt contains the comparison of PSCs cultured as 2D monocultures (Sample 1 and Sample 2) to PSCs cultured as activated 3D transwell cultures (Sample 5, Sample 6, Sample 7, Sample 8).  The file DESeq_3DvsTranswell.txt contains the comparison of PSCs cultured  as quiecent 3D monocultures (Sample 3 and Sample 4) to to PSCs cultured as activated 3D transwell cultures (Sample 5, Sample 6, Sample 7, Sample 8). The DEseq files include the log2 fold-change and adjusted p values for the 2D vs 3D, 2D vs transwell, and 3D vs transwell PSC comparisons.

source_name: SV40 immortalized pancreatic stellate cell line cocultured with 3D pancreatic ductal organoid line

growth_protocol: For 2D culture of pancreatic stellate cells (PSCs), cells were grown to 50-70% confluency as monolayers (2D) on one 10 cm plate, in DMEM supplemented with 5% FBS and 1X Penicillin/Streptomycin (Invitrogen). For 3D quiescent or transwell cocultures, PSCs were embedded as 40k cells in 50 uL Matrigel domes (3D quiescent), or 15k cells in 50 uL Matrigel domes (transwell coculture).  For 3D quiescent or transwell cocultures, Matrigel was overlaid with 500uL of DMEM supplemented with 5% FBS and 1X Penicillin/Streptomycin (Invitrogen), and a total of 6 wells of a 24-well plate or 6 wells of transwell co-culture were used, respectively, for the experiment. Pancreatic tumor organoids were grown to confluency in a 24-well plate and split at a 1:6 ratio before being plated in 50 uL Matrigel domes in the lower chamber of 6 transwells for coculture with PSCs.

extract_protocol:
Media was removed from Matrigel domes, and 6 wells of PSCs were harvested in 1 mL total of Trizol. RNA was extracted using the Trizol Plus RNA Purification Kit (LifeTechnologies) per manufacturer’s instructions, and RNA samples were treated on column with PureLink DNase (Life Technologies).
RNA quality was assessed on a bioanalyzer using the Agilent RNA 600 Nano kit. We used poly-A pull-down to enrich for mRNAs from total RNA samples (0.2 μg - 1 μg per sample, RIN > 8) and proceeded to library preparation using Illumina TruSeq RNA prep kit.

tag: cell line

tag: background strain

tag: genotype

value: wild-type for PSC5, KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre for T5

tag: tissue origin

value: for PSC5:pancreatic from histologically confirmed normal pancreas, for T5:histologically confirmed mouse pancreatic adenocarcinoma

tag: culture method

value: 3D transwell culture in Matrigel


title: AT1G56170_NFYC2_ABA_ChIP_rep2

tag: accession

tag: age


title: AT1G77450_ANAC032_ABA_ChIP_rep1

description: AT1G77450_ANAC032_ABA_optimal_narrowPeak_p16.bed

tag: light condition

tag: treatment


title: PSC4 T5 transwell coculture

description:
TA015
Pancreatic stellate cells grown as a 3D activated cocultures in a transwell with 3D pancreatic tumor organoids in the lower chamber
Sample 6

value: wild-type for PSC4, KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre for T5

value: for PSC4:pancreatic from histologically confirmed normal pancreas, for T5:histologically confirmed mouse pancreatic adenocarcinoma


title: AT1G77450_ANAC032_EtOH_ChIP_rep3

description: AT1G77450_ANAC032_EtOH_optimal_narrowPeak_p16.bed

value: EtOH mock treatment, 4 hours

tag: chip antibody


title: polyA mRNA RNA-seq from brain (ENCLB881JVT)

description:
https://www.encodeproject.org/experiments/ENCSR000CHG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 14.5 day embryonic mouse whole brain
experiment encode accession: ENCSR000CHG
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB881JVT
size range: >200
spikeins used: /references/ENCSR866KGS/

value: brain

tag: description

value: Whole Brain from an individual mouse

value: Bing Ren, UCSD

value: ENCBS564LEX at ENCODE; https://www.encodeproject.org/ENCBS564LEX/

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

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


title: polyA mRNA RNA-seq from ES-Bruce4 (ENCLB443JOH)

description:
https://www.encodeproject.org/experiments/ENCSR000CGU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic mouse stem cell line Bruce4
experiment encode accession: ENCSR000CGU
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB443JOH
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Mus musculus strain Bruce4 ES-Bruce4 stem cell male embryo

value: stem cell

value: mouse embryonic stem cells

tag: biosample encode accession

value: embryonic

value: unknown

value: male

value: ENCBS359ENC at ENCODE; https://www.encodeproject.org/ENCBS359ENC/

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

value: ENCODE dbxrefs Cellosaurus CVCL_K037; http://web.expasy.org/cellosaurus/CVCL_K037

value: ENCODE dbxrefs ES-Bruce4; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-Bruce4


title: AT5G63790_ANAC102_ABA_ChIP_rep2

description: AT5G63790_ANAC102_ABA_optimal_narrowPeak_p16.bed

value: 3 day

value: dark

value: 10 uM abscisic acid, 4 hours

value: GFP (ThermoFisher #A11122)


title: AT1G77450_ANAC032_ABA_ChIP_rep3


title: AT5G63790_ANAC102_EtOH_ChIP_rep1

description: AT5G63790_ANAC102_EtOH_optimal_narrowPeak_p16.bed

value: EtOH mock treatment, 4 hours


title: polyA mRNA RNA-seq from ES-Bruce4 (ENCLB331QIU)

description:
https://www.encodeproject.org/experiments/ENCSR000CGU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic mouse stem cell line Bruce4
experiment encode accession: ENCSR000CGU
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB331QIU
size range: >200
spikeins used: /references/ENCSR866KGS/

tag: dev stage

value: Bing Ren, UCSD

value: ENCBS250IKX at ENCODE; https://www.encodeproject.org/ENCBS250IKX/


title: AT1G77450_ANAC032_EtOH_ChIP_rep2


title: polyA mRNA RNA-seq from bone marrow (ENCLB338PBI)

description:
https://www.encodeproject.org/experiments/ENCSR000CGT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 8 week adult mouse bone marrow
experiment encode accession: ENCSR000CGT
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2011-08-04
lab: Bing Ren, UCSD
library encode accession: ENCLB338PBI
size range: >200
spikeins used: /references/ENCSR866KGS/

value: bone marrow

value: tissue

value: Bone Marrow from an individual mouse

value: adult

value: 8 week

tag: Sex

value: ENCBS706ITR at ENCODE; https://www.encodeproject.org/ENCBS706ITR/

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

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


title: AT1G77450_ANAC032_EtOH_ChIP_rep1


title: PSC5 T4 transwell coculture

description:
TA016
Pancreatic stellate cells grown as a 3D activated cocultures in a transwell with 3D pancreatic tumor organoids in the lower chamber
Sample 7

value: wild-type for PSC5, KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre for T4

value: for PSC5:pancreatic from histologically confirmed normal pancreas, for T4:histologically confirmed mouse pancreatic adenocarcinoma

value: 3D transwell culture in Matrigel


title: AT2G46270_GBF3_EtOH_ChIP_rep3

description: AT2G46270_GBF3_EtOH_optimal_narrowPeak_p16.bed

value: 3 day

value: dark


title: AT5G63790_ANAC102_EtOH_ChIP_rep2

value: GFP (ThermoFisher #A11122)


title: PSC5 2D

description:
TA011
Pancreatic stellate cells grown as a 2D monolayer
Sample 2

source_name: SV40 immortalized pancreatic stellate cell line

value: wild-type

value: pancreatic from histologically confirmed normal pancreas

value: 2D monoculture on plastic


title: PSC4 T4 transwell coculture

description:
TA014
Pancreatic stellate cells grown as a 3D activated cocultures in a transwell with 3D pancreatic tumor organoids in the lower chamber
Sample 5

value: wild-type for PSC4, KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre for T4

value: for PSC4:pancreatic from histologically confirmed normal pancreas, for T4:histologically confirmed mouse pancreatic adenocarcinoma


title: AT2G46270_GBF3_ABA_ChIP_rep2

description: AT2G46270_GBF3_ABA_optimal_narrowPeak_p16.bed

value: 10 uM abscisic acid, 4 hours


title: AT5G63790_ANAC102_ABA_ChIP_rep1


title: PSC5 3D

description:
TA013
Pancreatic stellate cells grown as a 3D quiescent cultures (monoculture within Matrigel)
Sample 4

value: 3D monoculture in Matrigel


title: PSC4 3D

description:
TA012
Pancreatic stellate cells grown as a 3D quiescent cultures (monoculture within Matrigel)
Sample 3


title: AT2G46270_GBF3_EtOH_ChIP_rep1

value: EtOH mock treatment, 4 hours


title: AT2G46270_GBF3_ABA_ChIP_rep3


title: polyA mRNA RNA-seq from liver (ENCLB399DXG)

description:
https://www.encodeproject.org/experiments/ENCSR000CHE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 14.5 day embryonic mouse liver
experiment encode accession: ENCSR000CHE
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-04
lab: Bing Ren, UCSD
library encode accession: ENCLB399DXG
size range: >200
spikeins used: /references/ENCSR866KGS/

value: liver

value: tissue

value: Liver from an individual mouse

value: embryonic

value: pooled male and female

tag: lab

value: Bing Ren, UCSD

value: unknown

value: ENCBS918BKE at ENCODE; https://www.encodeproject.org/ENCBS918BKE/

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


title: AT1G77450_ANAC032_ABA_ChIP_rep2

description: AT1G77450_ANAC032_ABA_optimal_narrowPeak_p16.bed

value: 3 day

value: dark

value: GFP (ThermoFisher #A11122)


title: PSC4 2D

description:
TA010
Pancreatic stellate cells grown as a 2D monolayer
Sample 1

value: wild-type

value: pancreatic from histologically confirmed normal pancreas

value: 2D monoculture on plastic


title: AT1G49720_ABF1_ABA_ChIP_rep2

description: AT1G49720_ABF1_ABA_optimal_narrowPeak_p16.bed

value: 10 uM abscisic acid, 4 hours


title: AT2G46680_HB7_ABA_ChIP_rep1

description: AT2G46680_HB7_ABA_optimal_narrowPeak_p16.bed


title: Pool1_RNA

city: Cambridge

first: Sharon

last: Grossman

state: MA

address: 415 Main Street

institute: Broad Institute

description: fastq of 3' UTR barcode and residual 5' flanking sequencing

data_processing:
Perfect UTR barcode matches were assigned to their respective oligo. Counts for all barcodes assigned to an oligo were summed.
Read counts corresponding to each barcode for each oligo
Genome_build: mm9

source_name: 3T3-L1 cell line

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days after confluence, the cells were induced with DMEM supplemented with 10% FBS, 1uM dexamethasone, 1.7uM insulin, and 0.5mM 3-isobutyl-1-methylxanthine (IBMX). 48h later, the medium was replaced with DMEM supplemented with 10% FBS and the cells were fed every two days.

extract_protocol: MPRA libraries were prepared as described by Melnikov et al. (Nat Biotechnol 2012 Feb 26;30(3):271-7. PMID: 22371084)

tag: molecule subtype

value: total RNA


title: polyA mRNA RNA-seq from PFSK-1 (ENCLB016FJI)

description:
https://www.encodeproject.org/experiments/ENCSR000BYN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on PFSK-1 greater than 200bp polyA+
experiment encode accession: ENCSR000BYN
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB016FJI
size range: >200
spikeins used: /references/ENCSR466YMU/

organism: Homo sapiens

source_name: Homo sapiens PFSK-1 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0f926b2b-f4ce-402a-b936-884770ed81d1/@@download/attachment/wgEncodeHaibRnaSeq.html.pdf

tag: line

value: immortalized cell line

value: neuroectodermal cell line derived from a cerebral brain tumor, (PMID:1316433)

value: 22 month

value: male

value: Richard Myers, HAIB

tag: health state

tag: link

value: ENCBS054ENC at ENCODE; https://www.encodeproject.org/ENCBS054ENC/

value: Derived from ENCODE donor ENCDO000AAR; https://www.encodeproject.org/ENCDO000AAR/

value: ENCODE dbxrefs Cellosaurus CVCL_1642; http://web.expasy.org/cellosaurus/CVCL_1642

value: ENCODE dbxrefs PFSK-1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=PFSK-1

value: ATCC sample source; http://www.atcc.org/products/all/CRL-2060.aspx


title: AT2G46270_GBF3_EtOH_ChIP_rep2

source_name: whole seedlings

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours


title: Pool2_RNA

tag: cell line


title: polyA mRNA RNA-seq from PFSK-1 (ENCLB047DUL)

description:
https://www.encodeproject.org/experiments/ENCSR000BYN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on PFSK-1 greater than 200bp polyA+
experiment encode accession: ENCSR000BYN
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB047DUL
size range: >200
spikeins used: /references/ENCSR466YMU/

value: unknown


title: Pool6_RNA

description:
fastq of 3' UTR barcode and residual 5' flanking sequencing
processed data file: Pool6_MPRA.txt

data_processing:
Perfect UTR barcode matches were assigned to their respective oligo. Counts for all barcodes assigned to an oligo were summed.
Read counts in RNA and Plasmid libraries summed across all barcodes corresponding to each oligo
Genome_build: mm9


title: Pool5_RNA

description:
fastq of 3' UTR barcode and residual 5' flanking sequencing
processed data file: Pool5_MPRA.txt


title: Pool7_RNA

description:
fastq of 3' UTR barcode and residual 5' flanking sequencing
processed data file: Pool7_MPRA.txt


title: AT2G46270_GBF3_ABA_ChIP_rep1

value: GFP (ThermoFisher #A11122)


title: AT5G47640_NFYB2_ABA_ChIP_rep2

description: AT5G47640_NFYB2_ABA_optimal_narrowPeak_p16.bed

value: 10 uM abscisic acid, 4 hours


title: polyA mRNA RNA-seq from Panc1 (ENCLB976XGY)

description:
https://www.encodeproject.org/experiments/ENCSR000BYM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on Panc-1 greater than 200bp polyA+
experiment encode accession: ENCSR000BYM
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB976XGY
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens Panc1 immortalized cell line

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: 56 year

value: pancreatic carcinoma

value: ENCBS425ENC at ENCODE; https://www.encodeproject.org/ENCBS425ENC/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/

value: ENCODE dbxrefs Cellosaurus CVCL_0480; http://web.expasy.org/cellosaurus/CVCL_0480

value: ENCODE dbxrefs PANC-1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=PANC-1


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB193VKK)

description:
https://www.encodeproject.org/experiments/ENCSR000BYL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on SK-N-SH greater than 200bp polyA+
experiment encode accession: ENCSR000BYL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB193VKK
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens SK-N-SH immortalized cell line

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: child

value: 4 year

value: female

value: Richard Myers, HAIB

value: ENCBS428ENC at ENCODE; https://www.encodeproject.org/ENCBS428ENC/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

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


title: AT1G49720_ABF1_EtOH_ChIP_rep3

description: AT1G49720_ABF1_EtOH_optimal_narrowPeak_p16.bed

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours

value: GFP (ThermoFisher #A11122)


title: Pool4_RNA

value: total RNA


title: AT1G49720_ABF1_ABA_ChIP_rep3

value: 10 uM abscisic acid, 4 hours


title: Pool3_RNA


title: AT5G47640_NFYB2_EtOH_ChIP_rep1

description: AT5G47640_NFYB2_EtOH_optimal_narrowPeak_p16.bed


title: AT1G49720_ABF1_EtOH_ChIP_rep2


title: polyA mRNA RNA-seq from Panc1 (ENCLB122GAF)

description:
https://www.encodeproject.org/experiments/ENCSR000BYM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on Panc-1 greater than 200bp polyA+
experiment encode accession: ENCSR000BYM
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB122GAF
size range: >200
spikeins used: /references/ENCSR466YMU/

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: unknown

value: 56 year

value: male

value: pancreatic carcinoma

value: ENCBS425ENC at ENCODE; https://www.encodeproject.org/ENCBS425ENC/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/

value: ENCODE dbxrefs Cellosaurus CVCL_0480; http://web.expasy.org/cellosaurus/CVCL_0480

value: ENCODE dbxrefs PANC-1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=PANC-1


title: AT1G49720_ABF1_EtOH_ChIP_rep1


title: AT1G49720_ABF1_ABA_ChIP_rep1


title: polyA mRNA RNA-seq from A549 (ENCLB457MEV)

description:
https://www.encodeproject.org/experiments/ENCSR000BYJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 5nM
experiment encode accession: ENCSR000BYJ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB457MEV
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens A549 immortalized cell line treated with 5 nM dexamethasone for 1 hour

value: immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma. Treated with 5 nM dexamethasone (CHEBI:41879) for 1 hour

value: adult

value: 58 year

value: Richard Myers, HAIB

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_5nM;

value: ENCBS170AAA at ENCODE; https://www.encodeproject.org/ENCBS170AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549


title: AT5G47640_NFYB2_EtOH_ChIP_rep3

value: 3 day

value: dark

value: EtOH mock treatment, 4 hours

value: GFP (ThermoFisher #A11122)


title: AT5G47640_NFYB2_EtOH_ChIP_rep2


title: polyA mRNA RNA-seq from SK-N-SH (ENCLB989PZD)

description:
https://www.encodeproject.org/experiments/ENCSR000BYL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on SK-N-SH greater than 200bp polyA+
experiment encode accession: ENCSR000BYL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB989PZD
size range: >200
spikeins used: /references/ENCSR466YMU/

value: SK-N-SH

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: child

value: 4 year

value: female

value: ENCBS428ENC at ENCODE; https://www.encodeproject.org/ENCBS428ENC/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

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


title: polyA mRNA RNA-seq from A549 (ENCLB995VLB)

description:
https://www.encodeproject.org/experiments/ENCSR000BYH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 1nM
experiment encode accession: ENCSR000BYH
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB995VLB
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens A549 immortalized cell line treated with 1 nM dexamethasone for 1 hour

value: immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma. Treated with 1 nM dexamethasone (CHEBI:41879) for 1 hour

value: adult

value: 58 year

value: male

value: Richard Myers, HAIB

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_1nM;

value: ENCBS167AAA at ENCODE; https://www.encodeproject.org/ENCBS167AAA/


title: AT5G47640_NFYB2_ABA_ChIP_rep1

value: 3 day

value: dark

value: 10 uM abscisic acid, 4 hours

value: GFP (ThermoFisher #A11122)


title: polyA mRNA RNA-seq from BE2C (ENCLB297WUU)

description:
https://www.encodeproject.org/experiments/ENCSR000BYK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on BEC-C greater than 200bp polyA+
experiment encode accession: ENCSR000BYK
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB297WUU
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens BE2C immortalized cell line

value: neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy.

value: child

value: 2 year

value: unknown

value: ENCBS427ENC at ENCODE; https://www.encodeproject.org/ENCBS427ENC/

value: Derived from ENCODE donor ENCDO000ACQ; https://www.encodeproject.org/ENCDO000ACQ/

value: ENCODE dbxrefs Cellosaurus CVCL_0529; http://web.expasy.org/cellosaurus/CVCL_0529

value: ENCODE dbxrefs BE2_C; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=BE2_C


title: polyA mRNA RNA-seq from BE2C (ENCLB247MKP)

description:
https://www.encodeproject.org/experiments/ENCSR000BYK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on BEC-C greater than 200bp polyA+
experiment encode accession: ENCSR000BYK
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB247MKP
size range: >200
spikeins used: /references/ENCSR466YMU/

value: immortalized cell line


title: total RNA-seq from dendritic cell (ENCLB188VXN)

description:
https://www.encodeproject.org/experiments/ENCSR892ZUK/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR892ZUK
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB188VXN
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: dendritic cell

value: in vitro differentiated cells

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

value: not collected

value: Manuel Garber, UMass

value: ENCBS609PNX at ENCODE; https://www.encodeproject.org/ENCBS609PNX/

value: Derived from ENCODE donor ENCDO720VUI; https://www.encodeproject.org/ENCDO720VUI/


title: polyA mRNA RNA-seq from A549 (ENCLB896BPX)

description:
https://www.encodeproject.org/experiments/ENCSR000BYI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 500pM
experiment encode accession: ENCSR000BYI
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB896BPX
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens A549 immortalized cell line treated with 500 pM dexamethasone for 1 hour

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma. Treated with 500 pM dexamethasone (CHEBI:41879) for 1 hour

value: adult

value: 58 year

value: male

value: Richard Myers, HAIB

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_500pM;

value: ENCBS168AAA at ENCODE; https://www.encodeproject.org/ENCBS168AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549


title: total RNA-seq from dendritic cell (ENCLB828ADV)

description:
https://www.encodeproject.org/experiments/ENCSR707JVU/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR707JVU
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB828ADV
size range: 100-350
instrument models: Illumina NextSeq 500,Illumina HiSeq 2000

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

value: dendritic cell

value: unknown

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

value: ENCBS419IFI at ENCODE; https://www.encodeproject.org/ENCBS419IFI/


title: ChIP-seq from dendritic cell (ENCLB950CBR)

description:
https://www.encodeproject.org/experiments/ENCSR650OZF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR650OZF
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB950CBR
size range: 150-400

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

extract_protocol:
general protocol: https://www.encodeproject.org/documents/342b2d20-53cf-4698-b7db-48fefe735f56/@@download/attachment/Luban_lab_ChIP_protocol.pdf
extraction method: TruChIP chromatin shearing reagent kit Covaris cat# 520154, sonication Covaris M220, IP (home protocol), DNA isolation with QIAquick PCR Purification Kit cat# 28104.

tag: antibody

value: in vitro differentiated cells

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

value: not collected

value: Manuel Garber, UMass

value: ENCBS550GVG at ENCODE; https://www.encodeproject.org/ENCBS550GVG/

value: Derived from ENCODE donor ENCDO088XVR; https://www.encodeproject.org/ENCDO088XVR/


title: ChIP-seq from dendritic cell (ENCLB184HPY)

description:
https://www.encodeproject.org/experiments/ENCSR740ROX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR740ROX
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB184HPY
size range: 150-400

source_name: Homo sapiens dendritic in vitro differentiated cells 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: ENCBS694UTH at ENCODE; https://www.encodeproject.org/ENCBS694UTH/


title: polyA mRNA RNA-seq from A549 (ENCLB557HDM)

description:
https://www.encodeproject.org/experiments/ENCSR000BYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 5nM
experiment encode accession: ENCSR000BYJ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB557HDM
size range: >200
spikeins used: /references/ENCSR466YMU/

value: immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma. Treated with 5 nM dexamethasone (CHEBI:41879) for 1 hour

value: adult

value: 58 year

value: male

value: Richard Myers, HAIB

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_5nM;

value: ENCBS170AAA at ENCODE; https://www.encodeproject.org/ENCBS170AAA/


title: ChIP-seq from dendritic cell (ENCLB303SGY)

description:
https://www.encodeproject.org/experiments/ENCSR531MLI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR531MLI
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB303SGY
size range: 150-400

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

value: dendritic cell

value: unknown

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

value: ENCBS387MRC at ENCODE; https://www.encodeproject.org/ENCBS387MRC/


title: ChIP-seq from dendritic cell (ENCLB262KQK)

description:
https://www.encodeproject.org/experiments/ENCSR986ZZK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR986ZZK
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB262KQK
size range: 150-400

value: in vitro differentiated cells

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: ENCBS268SOT at ENCODE; https://www.encodeproject.org/ENCBS268SOT/


title: AT5G47640_NFYB2_ABA_ChIP_rep3

description: AT5G47640_NFYB2_ABA_optimal_narrowPeak_p16.bed

tag: accession

value: 3 day

value: dark

value: 10 uM abscisic acid, 4 hours

value: GFP (ThermoFisher #A11122)


title: ChIP-seq from dendritic cell (ENCLB849CIT)

description:
https://www.encodeproject.org/experiments/ENCSR482UTI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR482UTI
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB849CIT
size range: 150-400

tag: age

value: Derived from ENCODE donor ENCDO088XVR; https://www.encodeproject.org/ENCDO088XVR/


title: polyA mRNA RNA-seq from T47D (ENCLB341FID)

description:
https://www.encodeproject.org/experiments/ENCSR000BYF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on T-47D greater than 200bp polyA+ treated with estradiol at 10nM for 4 hours
experiment encode accession: ENCSR000BYF
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB341FID
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens T47D immortalized cell line treated with 10 nM estradiol for 4 hours

value: immortalized cell line

value: epithelial cell line derived from a mammary ductal carcinoma.

value: adult

value: 54 year

value: female

value: Richard Myers, HAIB

value: mammary ductal carcinoma

value: treatment_term_id:CHEBI:23965; treatment_term_name:estradiol; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:Estradiol_10nM_4hr;

value: ENCBS602ENC at ENCODE; https://www.encodeproject.org/ENCBS602ENC/

value: Derived from ENCODE donor ENCDO000ABA; https://www.encodeproject.org/ENCDO000ABA/

value: ENCODE dbxrefs Cellosaurus CVCL_0553; http://web.expasy.org/cellosaurus/CVCL_0553

value: ENCODE dbxrefs T-47D; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=T-47D

value: ATCC sample source; http://www.atcc.org/products/all/HTB-133.aspx


title: polyA mRNA RNA-seq from T47D (ENCLB039VRZ)

description:
https://www.encodeproject.org/experiments/ENCSR000BYG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on T-47D greater than 200bp polyA+ treated with genistein at 100nM for 4 hours
experiment encode accession: ENCSR000BYG
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB039VRZ
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens T47D immortalized cell line treated with 100 nM genistein for 4 hours

value: treatment_term_id:CHEBI:28088; treatment_term_name:genistein; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:Genistein_100nM_4hr;

value: ENCBS604ENC at ENCODE; https://www.encodeproject.org/ENCBS604ENC/


title: ChIP-seq from dendritic cell (ENCLB898GSK)

description:
https://www.encodeproject.org/experiments/ENCSR450JZC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR450JZC
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB898GSK
size range: 150-400

value: dendritic cell

value: in vitro differentiated cells

value: unknown

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

value: not collected

value: Manuel Garber, UMass

value: ENCBS360WKF at ENCODE; https://www.encodeproject.org/ENCBS360WKF/


title: ChIP-seq from dendritic cell (ENCLB712NKW)

description:
https://www.encodeproject.org/experiments/ENCSR945BBR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR945BBR
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB712NKW
size range: 150-400

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: ENCBS408IRE at ENCODE; https://www.encodeproject.org/ENCBS408IRE/

value: Derived from ENCODE donor ENCDO088XVR; https://www.encodeproject.org/ENCDO088XVR/


title: polyA mRNA RNA-seq from T47D (ENCLB222XID)

description:
https://www.encodeproject.org/experiments/ENCSR000BYF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on T-47D greater than 200bp polyA+ treated with estradiol at 10nM for 4 hours
experiment encode accession: ENCSR000BYF
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB222XID
size range: >200
spikeins used: /references/ENCSR466YMU/

value: immortalized cell line

value: epithelial cell line derived from a mammary ductal carcinoma.

value: adult

value: 54 year

value: female

value: Richard Myers, HAIB

value: mammary ductal carcinoma

value: treatment_term_id:CHEBI:23965; treatment_term_name:estradiol; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:Estradiol_10nM_4hr;

value: ENCBS602ENC at ENCODE; https://www.encodeproject.org/ENCBS602ENC/


title: ATAC-seq from dendritic cell (ENCLB989NXK)

description:
https://www.encodeproject.org/experiments/ENCSR904UKR/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR904UKR
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB989NXK
size range: 175-500

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

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

value: ENCBS387MRC at ENCODE; https://www.encodeproject.org/ENCBS387MRC/


title: ChIP-seq from dendritic cell (ENCLB771HUQ)

description:
https://www.encodeproject.org/experiments/ENCSR427BKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR427BKJ
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB771HUQ
size range: 150-400

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

value: not collected

value: Manuel Garber, UMass

value: ENCBS694UTH at ENCODE; https://www.encodeproject.org/ENCBS694UTH/


title: polyA mRNA RNA-seq from A549 (ENCLB241KOT)

description:
https://www.encodeproject.org/experiments/ENCSR000BYI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 500pM
experiment encode accession: ENCSR000BYI
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB241KOT
size range: >200
spikeins used: /references/ENCSR466YMU/

value: immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma. Treated with 500 pM dexamethasone (CHEBI:41879) for 1 hour

value: 58 year

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_500pM;

value: ENCBS168AAA at ENCODE; https://www.encodeproject.org/ENCBS168AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549


title: polyA mRNA RNA-seq from T47D (ENCLB209HAD)

description:
https://www.encodeproject.org/experiments/ENCSR000BYE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on T-47D greater than 200bp polyA+ treated with dimethylsulfoxide for 4 hours
experiment encode accession: ENCSR000BYE
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB209HAD
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens T47D immortalized cell line treated with 0.02% dimethyl sulfoxide for 4 hours

value: epithelial cell line derived from a mammary ductal carcinoma.

value: adult

value: 54 year

value: female

value: Richard Myers, HAIB

value: mammary ductal carcinoma

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:DMSO_4hr;

value: ENCBS624AAA at ENCODE; https://www.encodeproject.org/ENCBS624AAA/

value: Derived from ENCODE donor ENCDO000ABA; https://www.encodeproject.org/ENCDO000ABA/

value: ENCODE dbxrefs Cellosaurus CVCL_0553; http://web.expasy.org/cellosaurus/CVCL_0553

value: ENCODE dbxrefs T-47D; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=T-47D


title: ChIP-seq from dendritic cell (ENCLB479PUX)

description:
https://www.encodeproject.org/experiments/ENCSR403BAT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR403BAT
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB479PUX
size range: 150-400

value: dendritic cell

value: in vitro differentiated cells

value: unknown

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

value: not collected

value: Manuel Garber, UMass

value: ENCBS360WKF at ENCODE; https://www.encodeproject.org/ENCBS360WKF/

value: Derived from ENCODE donor ENCDO088XVR; https://www.encodeproject.org/ENCDO088XVR/


title: polyA mRNA RNA-seq from T47D (ENCLB671LPW)

description:
https://www.encodeproject.org/experiments/ENCSR000BYE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on T-47D greater than 200bp polyA+ treated with dimethylsulfoxide for 4 hours
experiment encode accession: ENCSR000BYE
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB671LPW
size range: >200
spikeins used: /references/ENCSR466YMU/

value: immortalized cell line

value: epithelial cell line derived from a mammary ductal carcinoma.

value: adult

value: 54 year


title: polyA mRNA RNA-seq from T47D (ENCLB142QEH)

description:
https://www.encodeproject.org/experiments/ENCSR000BYG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on T-47D greater than 200bp polyA+ treated with genistein at 100nM for 4 hours
experiment encode accession: ENCSR000BYG
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB142QEH
size range: >200
spikeins used: /references/ENCSR466YMU/

value: female

value: Richard Myers, HAIB

value: mammary ductal carcinoma

value: treatment_term_id:CHEBI:28088; treatment_term_name:genistein; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:Genistein_100nM_4hr;

value: ENCBS604ENC at ENCODE; https://www.encodeproject.org/ENCBS604ENC/

value: ATCC sample source; http://www.atcc.org/products/all/HTB-133.aspx


title: polyA mRNA RNA-seq from A549 (ENCLB421TSW)

description:
https://www.encodeproject.org/experiments/ENCSR000BYH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 1nM
experiment encode accession: ENCSR000BYH
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB421TSW
size range: >200
spikeins used: /references/ENCSR466YMU/

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma. Treated with 1 nM dexamethasone (CHEBI:41879) for 1 hour

value: 58 year

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_1nM;

value: ENCBS167AAA at ENCODE; https://www.encodeproject.org/ENCBS167AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549


title: total RNA-seq from dendritic cell (ENCLB551SVU)

description:
https://www.encodeproject.org/experiments/ENCSR332SRS/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR332SRS
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB551SVU
size range: 100-350

value: dendritic cell

value: in vitro differentiated cells

value: unknown

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: ENCBS026BUD at ENCODE; https://www.encodeproject.org/ENCBS026BUD/

value: Derived from ENCODE donor ENCDO467IIR; https://www.encodeproject.org/ENCDO467IIR/


title: ATAC-seq from dendritic cell (ENCLB146SIB)

description:
https://www.encodeproject.org/experiments/ENCSR329XFZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR329XFZ
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB146SIB
size range: 175-500

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

value: ENCBS580DMI at ENCODE; https://www.encodeproject.org/ENCBS580DMI/

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


title: ATAC-seq from dendritic cell (ENCLB887PKE)

description:
https://www.encodeproject.org/experiments/ENCSR237VSF/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR237VSF
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB887PKE
size range: 175-500

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

value: ENCBS408IRE at ENCODE; https://www.encodeproject.org/ENCBS408IRE/

value: Derived from ENCODE donor ENCDO088XVR; https://www.encodeproject.org/ENCDO088XVR/


title: ChIP-seq from dendritic cell (ENCLB751CXO)

description:
https://www.encodeproject.org/experiments/ENCSR075AVX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR075AVX
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB751CXO
size range: 150-400

value: ENCBS550GVG at ENCODE; https://www.encodeproject.org/ENCBS550GVG/


title: total RNA-seq from dendritic cell (ENCLB662VIT)

description:
https://www.encodeproject.org/experiments/ENCSR227MWL/
***************
biological replicate number: 1
technical replicate number: 1
description: Ovation Human FFPE RNA-Seq Multiplex System
experiment encode accession: ENCSR227MWL
assay title: total RNA-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB662VIT
size range: 100-350

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

value: ENCBS048UHR at ENCODE; https://www.encodeproject.org/ENCBS048UHR/


title: polyA mRNA RNA-seq from Ishikawa (ENCLB371LKW)

description:
https://www.encodeproject.org/experiments/ENCSR000BYC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on ECC-1 greater than 200bp polyA+ treated with genistein at 100nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.
experiment encode accession: ENCSR000BYC
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB371LKW
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens Ishikawa immortalized cell line treated with 100 nM genistein for 4 hours

value: Ishikawa

value: immortalized cell line

value: Endometrial adenocarcinoma Note:This cell line was previously mis-identified as ECC-1 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432677/).

value: adult

value: 39 year

value: female

value: Richard Myers, HAIB

value: endometrial adenocarcinoma

value: treatment_term_id:CHEBI:28088; treatment_term_name:genistein; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:Genistein_100nM_4hr;

value: ENCBS159ITB at ENCODE; https://www.encodeproject.org/ENCBS159ITB/

value: Derived from ENCODE donor ENCDO000ACV; https://www.encodeproject.org/ENCDO000ACV/

value: ENCODE dbxrefs Cellosaurus CVCL_7260; http://web.expasy.org/cellosaurus/CVCL_7260

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


title: ATAC-seq from dendritic cell (ENCLB432EGK)

description:
https://www.encodeproject.org/experiments/ENCSR208NBF/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR208NBF
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB432EGK
size range: 175-500

value: dendritic cell

value: in vitro differentiated cells

value: unknown

value: not collected

value: Manuel Garber, UMass

value: ENCBS360WKF at ENCODE; https://www.encodeproject.org/ENCBS360WKF/

value: Derived from ENCODE donor ENCDO088XVR; https://www.encodeproject.org/ENCDO088XVR/


title: polyA mRNA RNA-seq from Ishikawa (ENCLB576NZA)

description:
https://www.encodeproject.org/experiments/ENCSR000BYC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on ECC-1 greater than 200bp polyA+ treated with genistein at 100nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.
experiment encode accession: ENCSR000BYC
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB576NZA
size range: >200
spikeins used: /references/ENCSR466YMU/

value: Ishikawa

value: immortalized cell line

value: Endometrial adenocarcinoma Note:This cell line was previously mis-identified as ECC-1 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432677/).

value: adult


title: ATAC-seq from dendritic cell (ENCLB930EUP)

description:
https://www.encodeproject.org/experiments/ENCSR222SCA/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR222SCA
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB930EUP
size range: 175-500

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

value: ENCBS268SOT at ENCODE; https://www.encodeproject.org/ENCBS268SOT/


title: ATAC-seq from dendritic cell (ENCLB300DIR)

description:
https://www.encodeproject.org/experiments/ENCSR059IHA/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq
experiment encode accession: ENCSR059IHA
assay title: ATAC-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB300DIR
size range: 175-500

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

value: ENCBS550GVG at ENCODE; https://www.encodeproject.org/ENCBS550GVG/


title: polyA mRNA RNA-seq from Ishikawa (ENCLB118EHQ)

description:
https://www.encodeproject.org/experiments/ENCSR000BYA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on ECC-1 greater than 200bp polyA+ treated with dimethylsulfoxide for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.
experiment encode accession: ENCSR000BYA
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB118EHQ
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens Ishikawa immortalized cell line treated with 0.02% dimethyl sulfoxide for 4 hours

value: 39 year

value: female

value: Richard Myers, HAIB

value: endometrial adenocarcinoma

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:DMSO_4hr;

value: ENCBS743VIZ at ENCODE; https://www.encodeproject.org/ENCBS743VIZ/

value: Derived from ENCODE donor ENCDO000ACV; https://www.encodeproject.org/ENCDO000ACV/

value: ENCODE dbxrefs Cellosaurus CVCL_7260; http://web.expasy.org/cellosaurus/CVCL_7260


title: polyA mRNA RNA-seq from Ishikawa (ENCLB986QVR)

description:
https://www.encodeproject.org/experiments/ENCSR000BYA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on ECC-1 greater than 200bp polyA+ treated with dimethylsulfoxide for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.
experiment encode accession: ENCSR000BYA
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB986QVR
size range: >200
spikeins used: /references/ENCSR466YMU/

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


title: polyA mRNA RNA-seq from Ishikawa (ENCLB704HWG)

description:
https://www.encodeproject.org/experiments/ENCSR000BXZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on ECC-1 greater than 200bp polyA+ treated with bisphenol A at 100nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.
experiment encode accession: ENCSR000BXZ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB704HWG
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens Ishikawa immortalized cell line treated with 100 nM bisphenol A for 4 hours

value: Ishikawa

value: treatment_term_id:CHEBI:33216; treatment_term_name:bisphenol A; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:BPA_100nM_4hr;

value: ENCBS758FSP at ENCODE; https://www.encodeproject.org/ENCBS758FSP/


title: RPMI_8402_100nM_GSK2879552_48h_3

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

description: RNA-sequencing of RPMI8402 cells treated with 100nM GSK2879552 for 48h

data_processing:
basecalling with bcl2fastq
Alignment and gene quantification on Gencode_v23 were done with STAR v2.4.2a.
DESeq2 was used for differential expression analisis, using a multifactorial design
Genome_build: hg38
Supplementary_files_format_and_content: STAR raw count data, tdt

source_name: RPMI8402 cells

growth_protocol: Cells were seeded at 0.7 x 10^6 cells/ml. Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml kanamycin sulfate and 2 mM L-glutamine at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using the miRNeasy mini kit (Qiagen) with on-column DNase digestion. The RNA quality was checked by the Experion RNA StdSens analysis kit (Bio-Rad).
For each sample, 1µg of input material (measured with Ribogreen (Invitrogen)) was used. Libraries were constructed with the Truseq stranded mRNA protocol on the IP-star robot. During the library prep, mRNA was isolated via poly-A capture and cDNA was generated. Next, fragmentation, A-tailing, adaptor ligation and a PCR (13 cycli) were performed on them. The libraries were on average 300bp long. As quality control of the library, analysis on a bioanalyzer chip and a qPCR were done. Libraries were equimolary pooled and 2.4pM of this pool was loaded on the Nextseq500, SR75.

treatment_protocol: Cells were treated with DMSO or 100nM GSK2879552 for 48h

tag: type

value: T-ALL

tag: gender


title: polyA mRNA RNA-seq from Ishikawa (ENCLB125QNB)

description:
https://www.encodeproject.org/experiments/ENCSR000BXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on ECC-1 greater than 200bp polyA+ treated with bisphenol A at 100nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.
experiment encode accession: ENCSR000BXZ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB125QNB
size range: >200
spikeins used: /references/ENCSR466YMU/

value: immortalized cell line

value: Endometrial adenocarcinoma Note:This cell line was previously mis-identified as ECC-1 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432677/).

value: adult


title: RPMI_8402_100nM_GSK2879552_48h_2

tag: treatment


title: RPMI_8402_0nM_DMSO_GSK2879552_48h_3

description: RNA-sequencing of RPMI8402 cells treated with DMSO for 48h

value: DMSO


title: polyA mRNA RNA-seq from T47D (ENCLB624NZB)

description:
https://www.encodeproject.org/experiments/ENCSR000BYD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on T-47D greater than 200bp polyA+ treated with bisphenol A at 100nM for 4 hours
experiment encode accession: ENCSR000BYD
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB624NZB
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens T47D immortalized cell line treated with 100 nM bisphenol A for 4 hours

tag: description

value: epithelial cell line derived from a mammary ductal carcinoma.

value: 54 year

value: mammary ductal carcinoma

value: ENCBS600ENC at ENCODE; https://www.encodeproject.org/ENCBS600ENC/

value: Derived from ENCODE donor ENCDO000ABA; https://www.encodeproject.org/ENCDO000ABA/

value: ENCODE dbxrefs Cellosaurus CVCL_0553; http://web.expasy.org/cellosaurus/CVCL_0553

value: ENCODE dbxrefs T-47D; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=T-47D

value: ATCC sample source; http://www.atcc.org/products/all/HTB-133.aspx


title: polyA mRNA RNA-seq from A549 (ENCLB265UQF)

description:
https://www.encodeproject.org/experiments/ENCSR000BXY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 100pM
experiment encode accession: ENCSR000BXY
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB265UQF
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens A549 immortalized cell line treated with 100 pM dexamethasone for 1 hour

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma. Treated with 100 pM dexamethasone (CHEBI:41879) for 1 hour

tag: biosample encode accession

value: 58 year

value: male

value: Richard Myers, HAIB

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100pM;

value: ENCBS166AAA at ENCODE; https://www.encodeproject.org/ENCBS166AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549


title: polyA mRNA RNA-seq from A549 (ENCLB171BXB)

description:
https://www.encodeproject.org/experiments/ENCSR000BXY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 100pM
experiment encode accession: ENCSR000BXY
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB171BXB
size range: >200
spikeins used: /references/ENCSR466YMU/

value: immortalized cell line

tag: dev stage

value: adult


title: polyA mRNA RNA-seq from Jurkat clone E61 (ENCLB438QWV)

description:
https://www.encodeproject.org/experiments/ENCSR000BXX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on Jurkat greater than 200bp polyA+
experiment encode accession: ENCSR000BXX
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB438QWV
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens Jurkat clone E61 immortalized cell line

value: Jurkat clone E61

value: T lymphoblastoid derived from an acute T cell leukemia, The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM. - ATCC. (PMID:68013)

value: child

value: 14 year

tag: Sex

value: acute T cell leukemia

value: ENCBS429ENC at ENCODE; https://www.encodeproject.org/ENCBS429ENC/

value: Derived from ENCODE donor ENCDO000AAY; https://www.encodeproject.org/ENCDO000AAY/

value: ENCODE dbxrefs Cellosaurus CVCL_0367; http://web.expasy.org/cellosaurus/CVCL_0367

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


title: polyA mRNA RNA-seq from Ishikawa (ENCLB723FZR)

description:
https://www.encodeproject.org/experiments/ENCSR000BYB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on ECC-1 greater than 200bp polyA+ treated with estradiol at 10nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.
experiment encode accession: ENCSR000BYB
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB723FZR
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens Ishikawa immortalized cell line treated with 10 nM estradiol for 4 hours

value: Ishikawa

value: Endometrial adenocarcinoma Note:This cell line was previously mis-identified as ECC-1 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432677/).

value: 39 year

value: female

tag: lab

value: Richard Myers, HAIB

value: endometrial adenocarcinoma

value: treatment_term_id:CHEBI:23965; treatment_term_name:estradiol; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:Estradiol_10nM_4hr;

value: ENCBS222DWG at ENCODE; https://www.encodeproject.org/ENCBS222DWG/

value: Derived from ENCODE donor ENCDO000ACV; https://www.encodeproject.org/ENCDO000ACV/

value: ENCODE dbxrefs Cellosaurus CVCL_7260; http://web.expasy.org/cellosaurus/CVCL_7260

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


title: RPMI_8402_0nM_DMSO_GSK2879552_48h_1

value: T-ALL

value: DMSO


title: polyA mRNA RNA-seq from T47D (ENCLB190WRX)

description:
https://www.encodeproject.org/experiments/ENCSR000BYD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on T-47D greater than 200bp polyA+ treated with bisphenol A at 100nM for 4 hours
experiment encode accession: ENCSR000BYD
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB190WRX
size range: >200
spikeins used: /references/ENCSR466YMU/

value: immortalized cell line

value: epithelial cell line derived from a mammary ductal carcinoma.

value: adult

value: 54 year

value: mammary ductal carcinoma

value: treatment_term_id:CHEBI:33216; treatment_term_name:bisphenol A; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:BPA_100nM_4hr;

value: ENCBS600ENC at ENCODE; https://www.encodeproject.org/ENCBS600ENC/

value: Derived from ENCODE donor ENCDO000ABA; https://www.encodeproject.org/ENCDO000ABA/

value: ENCODE dbxrefs Cellosaurus CVCL_0553; http://web.expasy.org/cellosaurus/CVCL_0553

value: ENCODE dbxrefs T-47D; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=T-47D

value: ATCC sample source; http://www.atcc.org/products/all/HTB-133.aspx


title: RPMI_8402_100nM_GSK2879552_48h_1

value: female


title: RPMI_8402_0nM_DMSO_GSK2879552_48h_2


title: HSB_2_0nM_DMSO_GSK2879552_48h_3

description: RNA-sequencing of HSB2 cells treated with DMSO for 48h

source_name: HSB2 cells

value: male


title: HSB_2_100nM_GSK2879552_48h_3

description: RNA-sequencing of HSB2 cells treated with 100nM GSK2879552 for 48h


title: HSB_2_0nM_DMSO_GSK2879552_48h_2


title: HSB_2_0nM_DMSO_GSK2879552_48h_1


title: HSB_2_100nM_GSK2879552_48h_1


title: TG50_LSD1i_rep2

description: RNA-sequencing of P53/R26-Zeb2tg/tg  TG50 cells treated with 100nM GSK2879552 for 24h

data_processing:
base calling with Casava 1.8
read alignment and gene quantification on ENSG were performed with STAR v2.4.2a
DESeq2 was used for differential expression analisis using a multifactorial design
Genome_build: GRCm38
Supplementary_files_format_and_content: STAR raw count data, tdt

source_name: thymoma primary T-ALL culture

growth_protocol: mouse T-ALL cells were seeded at 0.5 x 10^6 cells/ml. Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 mM L-glutamine at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy Plus mini kit (Qiagen).
polyA Illumina Stranded Sample prep

treatment_protocol: Cells were treated with DMSO or 100nM GSK2879552 for 24h


title: TG50_LSD1i_rep3


title: PEER_100nMGSK2879552_48h_rep3

description: RNA-sequencing of PEER cells treated with 100nM GSK2879552 for 48h

source_name: PEER cells


title: PEER_100nMGSK2879552_48h_rep2


title: HSB_2_100nM_GSK2879552_48h_2


title: PEER_DMSO_48h_rep1

description: RNA-sequencing of PEER cells treated with DMSO for 48h


title: PEER_DMSO_48h_rep2


title: LOUCY_100nMGSK2879552_48h_rep2

description: RNA-sequencing of LOUCY cells treated with 100nM GSK2879552 for 48h

source_name: LOUCY cells


title: TG39_LSD1i_rep3

description: RNA-sequencing of P53/R26-Zeb2tg/tg  TG39 cells treated with 100nM GSK2879552 for 24h


title: TG50_DMSO_rep3

description: RNA-sequencing of P53/R26-Zeb2tg/tg TG50 cells treated with DMSO for 24h


title: TG50_DMSO_rep2


title: LOUCY_100nMGSK2879552_48h_rep1


title: TG50_LSD1i_rep1


title: TG50_DMSO_rep1


title: LOUCY_DMSO_48h_rep3

description: RNA-sequencing of LOUCY cells treated with DMSO for 48h


title: ChIP-seq from dendritic cell (ENCLB842UPV)

description:
https://www.encodeproject.org/experiments/ENCSR399QWL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR399QWL
assay title: ChIP-seq
encode release date: 2017-01-19
lab: Manuel Garber, UMass
library encode accession: ENCLB842UPV
size range: 150-400

value: dendritic cell

value: in vitro differentiated cells

value: unknown

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

value: not collected

value: Manuel Garber, UMass

value: ENCBS408IRE at ENCODE; https://www.encodeproject.org/ENCBS408IRE/

value: Derived from ENCODE donor ENCDO088XVR; https://www.encodeproject.org/ENCDO088XVR/


title: 62_Wang_input_BDR1841

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: Sample 62

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: *.matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices (i.e. normalized Hi-C interaction scores) with 10kb bins of B. subtilis genome.
Supplementary_files_format_and_content: *.csv: comma-separated values files of ChIP-seq results; number of reads at each genome position

organism: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-ScpA, anti-ScpB, anti-ParB or anti-GFP antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
the antibody information:
*anti-**SMC: Lindow et al., 2002: Mol Microbiol 46, 997-1009.
*anti-**ParB: Lin et al., 1997: Proc Natl Acad Sci U S A 94, 4721-4726.
*anti-GFP: Rudner et al., 1999: Proc Natl Acad Sci U S A 96, 14765-14770.
*anti-ScpA and anti-ScpB: generated in this study. Procedure described in Experimental Procedures.
Standard library construction protocol was used for Illumina Hiseq2500 sequencing platform (Hi-C) or Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

tag: sample group

value: CH, 37˚C

tag: strain info.

value: rpoC-gfp (spec)


title: LOUCY_100nMGSK2879552_48h_rep3

value: T-ALL


title: mNSp85

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Illumina Casava1.8.4 software was used for basecalling.
The reads were mapped using TopHat v.2 to the UCSC mm10 genome reference.
The gene features were counted with HTSeq v0.5.3p9 (htseq-count). Normalization and differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited text files with normalized counts and differentially expressed genes with a fold change threshold of 2 and a FDR 5% correction

source_name: Glioma

growth_protocol: GL261 and U251 GSC cells were grown in Dulbecco's modified Eagle's medium (DMEM) (Gibco) with 10% fetal bovine serum (FBS) (Gibco) and supplements (100 U/ml penicillin G (Sigma-Aldrich), 100 µg/ml streptomycin sulfate (Sigma-Aldrich), 6mM hepes (Applichem), 1.6 mM L-glutamine (Sigma-Aldrich), 50 µM β-mercaptoethanol (Biorad). NSU251 and mNS cells were cultured in neurosphere medium (DMEM/F12) medium supplemented with, 100 U/ml penicillin G, 100 µg/ml streptomycin sulfate, 6mM hepes, 1.6 mM L-glutamine, 50 µM β-mercaptoethanol, B-27 supplement (Invitrogen), 20 ng/mL recombinant basic fibroblast growth factor (basic-FGF) (Invitrogen,) and 20 ng/ml recombinant epidermal growth factor (EGF) (Invitrogen) and 50 U/ml heparin (Sigma). Cells in log phase were harvested at different passage for RNA isolation.

extract_protocol:
Total RNA were isolated from GL261 and mNS using Trizol (Invitrogen) according to the manufacturer's instructions.
The libraries were prepared with the Illumina TruSeq Stranded Total RNA kit according to the Illumina standard protocol.

tag: cell type

value: Neurospheres glioma stem like cells (GSC)

tag: passages


title: PEER_100nMGSK2879552_48h_rep1


title: 61_Wang_input_BWX3690_1mMIPTG_25m

description: Sample 61

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 25 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 25 min

value: parS∆9 no a.b., -94˚ parS no a.b., amyE::Pspank (natRBS) gfp-smc (spec)

tag: chip antibody

value: none (input)


title: mNSp77


title: 59_Wang_input_BWX3690_1mMIPTG_15m

description: Sample 59

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 15 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 15 min


title: PEER_DMSO_48h_rep3

value: female

value: DMSO


title: mNSp72


title: TG39_LSD1i_rep2


title: 58_Wang_input_BWX3690_1mMIPTG_10m

description: Sample 58

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 10 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 10 min


title: GL261p34

value: glioma differentiated cells (GDC)