title: WT 1h E2 RNA polymerase II ChIP-seq

description: WT E2 Pol2

data_processing:
Sequences (36 nt reads) were aligned to the mouse genome (NCBI Build 37.1/mm9) using Eland (Illumina pipeline) software. Only unique genomic hits with no more than 2 mismatches were retained. The Partek Genomics Suite (Partek Inc, St Louis, MO) was used for detection of ERα peaks. Peaks were then filtered using intra- and inter- sample statistics, with a binomial test between sample and control, a Mann-Whitney U test for the separation of forward and reserve reads, and application of FDR cut off of  0.05.  For coverage files, mapped reads were extended to the average fragment length for the given sample and converted to bedGraph format.
Genome Build:
WT_Pol2_E2.fragsize137.bedGraph.gz: mm9

value: RNA polymerase II (ab5095, lot# GR32890-1, Abcam)


title: input chromatin (WT V and WT 1hE2 mixed)

status: Public on Apr 09 2012

type: SRA

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

country: USA

institute: NIEHS

description: input

library_source: genomic

data_processing:
Sequences (36 nt reads) were aligned to the mouse genome (NCBI Build 37.1/mm9) using Eland (Illumina pipeline) software. Only unique genomic hits with no more than 2 mismatches were retained. The Partek Genomics Suite (Partek Inc, St Louis, MO) was used for detection of ERα peaks. Peaks were then filtered using intra- and inter- sample statistics, with a binomial test between sample and control, a Mann-Whitney U test for the separation of forward and reserve reads, and application of FDR cut off of  0.05.  For coverage files, mapped reads were extended to the average fragment length for the given sample and converted to bedGraph format.
Genome Build:
mouse_uterus_input.fragsize120.bedGraph.gz: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: uterus

growth_protocol: mice were maintained on NIH-31 chow, standard light/dark cycle, 1-5 mice per cage

extract_protocol: Uteri were submersed in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearor (Biospec Products, Bartlesville, OK) and finally spun down and washed 2x in PBS. Chromatin was isolated from the sample by adding 5-10 ml lysis buffer containing PIPES, Igepal, PMSF and Protease Inhibitor Cocktail, followed by disruption with a Dounce homogenizer. Samples were pelleted by centrifugation and resuspended in buffer containing Na deoxycholate, SDS, and Triton X-100. Lysates were sonicated using a Misonix Sonicator 3000 (Misonix, Farmingdale, NY) equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and the chromatin suspensions were transferred to new tubes and stored at -80 C. To prepare Input DNA (genomic DNA), two aliquots of 10-25 µl each (approximately 1/50 of each chromatin preparation) were removed and treated with RNase for 1-2 h at 37 C, proteinase K for 3 h at 37 C, and 65 C heat for at least 6 h to overnight for de-crosslinking. DNAs were purified by phenol-chloroform extraction and ethanol precipitated. Pellets were resuspended in 1/5 TE. Resulting DNAs were quantified on a Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE). Extrapolation to the original chromatin volume allowed determination of the yield for each chromatin preparation, as measured by the DNA content.  Prior to use in ChIP, protein A agarose beads (Invitrogen Technologies, Carlsbad, CA) were preblocked using blocking proteins and nucleic acids for 3 h. For each ChIP reaction, an aliquot of chromatin (20-30 µg) was precleared with 30 µl preblocked protein A agarose beads for 1-2 h. ChIP reactions were set up using precleared chromatin and antibody to ERα (sc-542, Santa Cruz Inc, Santa Cruz CA) or PolII phospho Ser5 (ab5095, Abcam, Cambridge, MA) in a buffer containing Na deoxycholate and incubated overnight at 4 C. Preblocked protein A agarose beads were added and incubation at 4 C was continued for another 3 h. Agarose beads containing the immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. An SDS-containing buffer was added to elute the immune complexes from the beads, and the eluates were subjected to RNase treatment at 37 C for 20 min and proteinase K treatment at 37 C for 3 h. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNAs were purified by phenol/chloroform extraction and ethanol precipitation. Quality of ERα ChIP enrichment was assayed by qPCR using primers against candidate EREs in the Igf1 and Stat5a promoters (9). Quality of PolII ChIP enrichment was assayed by qPCR using primers against region in Intron 1 of the housekeeping genes Actin B and  Gapdh. Input DNA was queried at the same sites in parallel. ChIP DNA was amplified by following the Illumina ChIP-Seq DNA Sample Prep Kit (Illumina, Inc.  San Diego, California)  protocol. In brief, DNA ends were polished and 5’-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. After addition of 3’-A to the ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size fractionated (200-250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles, Phusion polymerase, New England Bioloabs, Ipswich, MA), the resulting DNA libraries were quantified and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions. DNA libraries were sequenced on a Genome Analyzer II (Illumina).

treatment_protocol: mice were ovariectomized and injected intraperitoneally 10-14 days later with saline vehicle or estradiol (250 ng/mouse). Uterine tissue was collected one hour later

tag: strain

tag: tissue

value: uterus

tag: agent

value: vehicle and estradiol

tag: chip antibody


title: Control 2

status: Public on Apr 10 2012

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

description: Primary polyps at 380 ppm

library_source: transcriptomic

data_processing: Data were mapped to the Acropora millepora transcriptome using bowtie v0.12.7, allowing up to 2 mismatches. Reads mapping to more than 10 references were discarded. GSM*.counts.txt supplementary files list TSA assembly accession numbers and counts.

molecule: polyA RNA

organism: Acropora millepora

source_name: Primary polyps at 380 ppm

growth_protocol: Fifteen adult colonies of Acropora millepora were collected off the coast of Orpheus Island, Queensland, Australia (GBRMPA Permit No G10/33232.1), prior to the spawning event in November, 2009 and transported to the aquaculture facilities at James Cook University in Townsville where they were maintained in outdoor flow-through aquaria filled with 5 μm filtered seawater.

extract_protocol: Total RNA was extracted from the samples using Trizol Reagent (Invitrogen) and dissolved in RNAse free water. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrometer and denaturing gel electrophoresis. Before being shipped on dry ice to the Macrogen sequencing facilities in Seoul, South Korea, each RNA sample was precipitated in ethanol and sodium-acetate (2x and 0.1x sample volume respectively), and stored at -80°C.

treatment_protocol: Larvae were cultivated and settled under ambient conditions (380 ppm pCO2(air), pH 8.16 ± 0.01, 27.5°C). Five days after fertilization, settlement was induced by placing autoclaved unglazed terracotta tiles treated with crustose coralline algae into the container holding the larvae.  Twenty-four hours after the induction of settlement, tiles on which Acropora millepora primary polyps settled were transferred to the experimental tanks, where they were exposed for 3 days to seawater that had been equilibrated with air containing 380 ppm (pH~8.16), 750 ppm (pH~7.96), or 1000 ppm CO2 (pH~7.86)

tag: developmental stage

value: primary polyp

tag: treatment

value: 380 ppm (control)

value: whole polyps


title: RenLab-HiC-IMR90, replicate one

city: La Jolla

first: Feng

last: Yue

state: CA

address: 9500 Gilman Dr.

institute: Ludwig Institue for Cancer Research

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
IMR90_HindIII_HiC.nodup.summary.txt: hg18

organism: Homo sapiens

source_name: Human IMR90

growth_protocol: mESC line J1 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments. H1 and IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91

extract_protocol: Hi-C experiment were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).

tag: cell line

value: IMR90 fetal lung fibroblast cell line

tag: restriction enzyme

value: HindIII


title: D. willistoni male thorax rep1

status: Public on Apr 08 2012

city: Houston

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: GAII pipeline 1.3.2 CASAVA 1.0, 37bp

data_processing: GAII pipeline 1.3.2 CASAVA 1.0, 37bp

organism: Drosophila willistoni

source_name: Thorax

growth_protocol: Flies were grown at 18C on cornmeal media. Newly eclosed males and females were seperated under CO2 and aged for 5-7 days.

extract_protocol: Whole flies were placed live in Ringer's solution. Heads, thoraxes, and abdomens were dissected. Samples from each segment were flash frozen on dry ice and stored at -80C. RNA was extracted from the samples using TRIzol (Invitrogen Inc, Carlsbad, CA) following the manufacturers instructions. Poly-adenylated RNA was isolated using oligo-dT Dynabeads (Invitrogen Inc, Carlsbad, CA), mRNA was fragmented using alkaline hydrolysis, double-stranded cDNA was created using random hexamer primers, sequencing adapters were ligated to the cDNA, fragments were size selected by gel purification, and the size selected fragments were amplified by PCR.

value: Thorax

value: Adult

tag: Sex

value: Male

tag: age

value: 5-7 days post eclosion


title: WT V ER alpha ChIP-seq

description: WT_V ER

data_processing:
Sequences (36 nt reads) were aligned to the mouse genome (NCBI Build 37.1/mm9) using Eland (Illumina pipeline) software. Only unique genomic hits with no more than 2 mismatches were retained. The Partek Genomics Suite (Partek Inc, St Louis, MO) was used for detection of ERα peaks. Peaks were then filtered using intra- and inter- sample statistics, with a binomial test between sample and control, a Mann-Whitney U test for the separation of forward and reserve reads, and application of FDR cut off of  0.05.  For coverage files, mapped reads were extended to the average fragment length for the given sample and converted to bedGraph format.
Genome Build:
WT_vehicle.ER_peaks.bed: mm9
WT_vehicle.fragsize132.bedGraph.gz: mm9

value: vehicle

value: ER alpha (sc-542, lot# D1310, Santa Cruz)


title: D. willistoni female thorax rep1

description: GAII pipeline 1.3.2 CASAVA 1.0, 44bp

data_processing: GAII pipeline 1.3.2 CASAVA 1.0, 44bp

value: Female


title: D. willistoni male head rep1

description: GAII pipeline 1.3.2 CASAVA 1.0, 37bp

source_name: Head

value: Head


title: H3K4me3_MLL2_HET_LPS_4h

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin IP against H3K4me3

data_processing: Alignment: sequence reads were mapped to the mouse mm9 genome using Bowtie (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.

growth_protocol: Bone marrow cells isolated from mixed C57BL/6 (94%) and 129/Ola (6%) mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% Î²-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: ChIP lysates were generated from 2x10^8 cells. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65C. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for Solexa 2G sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturerâs instruction.

treatment_protocol: Macrophages were stimulated with lipopolysaccharide (LPS, 10 ug/ml)

tag: strain background

tag: genotype/variation

tag: cell type

value: Primary BMDM cells (7th day of differentiation)

value: Anti- Histone H3 trimethyl Lys4 (Active Motif, Catolog # 39159)

value: LPS (10 ug/ml) for 4hrs


title: H3K4me3_MLL2_HET_UT

description: Chromatin IP against H3K4me3

value: No treatment


title: D. willistoni female abdomen rep1

description: GAII SCS/RTA 2.4, pipeline 1.4, 44bp

data_processing: GAII SCS/RTA 2.4, pipeline 1.4, 44bp

source_name: Abdomen

value: Abdomen


title: D. willistoni male abdomen rep1

description: GAII SCS/RTA 2.4, pipeline 1.4, 44bp


title: D. willistoni male head rep2

description: HiSeq RTA 1.10.36.0, 50bp


title: D. willistoni female head rep2

description: HiSeq RTA 1.10.36.0, 50bp


title: D. willistoni female head rep1

description: GAII pipeline 1.3.2 CASAVA 1.0, 37bp


title: mut-16 embryo

status: Public on Apr 07 2012

city: Boston

first: Taiowa

last: Montgomery

state: MA

address: 185 Cambridge Street, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

description:
Sample 11.
~18-26 nt RNAs, TAP treated.

data_processing:
Raw datasets are fastq files generated using Illumina software. The sequence of the 3' adapter used during library preparation is 5'-TGGAATTCTCGGGTGCCAAGG or 5'-CTGTAGGCACCATCAAT for samples 1-11 and samples 12-19, respectively.  For processed datasets, small RNA sequences were parsed from fastq files using CASHX v. 2.0 with a Q value threshold of 20. Sequences were not filtered for alignment to a genome. Unique sequences and corresponding read counts were generated using custom perl scripts.

Supplementary_files_format_and_content: Tab-delimited text file containing unique sequences and corresponding read counts.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: mut-16 embryos, TAP treated

growth_protocol: C. elegans were grown at 20˚C on E. coli strain OP50 or on strain HT115 containing RNAi plasmids.

extract_protocol: Total RNA was isolated from synchronized worms and small RNAs were size selected, either untreated or tobacco acid pyrophosphatase (TAP) treated to remove 5' di- and triphosphate groups, ligated to 5' and 3' adapters and subjected to reverse transcription and PCR. PCR amplicons were PAGE purified prior to sequencing.

treatment_protocol: For RNAi treatment, animals were dropped as L1 stage larvae on E. coli strain HT115 containing the indicated control or pos-1 RNAi plasmids and harvested as day one adults for RNA isolation.

value: embryo

tag: rna treatment

value: tobacco acid pyrophosphatase (TAP)


title: WT V RNA polymerase II ChIP-seq

description: WT V Pol2

data_processing:
Sequences (36 nt reads) were aligned to the mouse genome (NCBI Build 37.1/mm9) using Eland (Illumina pipeline) software. Only unique genomic hits with no more than 2 mismatches were retained. The Partek Genomics Suite (Partek Inc, St Louis, MO) was used for detection of ERα peaks. Peaks were then filtered using intra- and inter- sample statistics, with a binomial test between sample and control, a Mann-Whitney U test for the separation of forward and reserve reads, and application of FDR cut off of  0.05.  For coverage files, mapped reads were extended to the average fragment length for the given sample and converted to bedGraph format.
Genome Build:
WT_Pol2_vehicle.fragsize141.bedGraph.gz: mm9

value: uterus

value: RNA polymerase II (ab5095, lot# GR32890-1, Abcam)


title: rde-11 adult

description:
Sample 9
~18-26 nt RNAs, TAP treated.

source_name: rde-11 adult animals, TAP treated

value: adult


title: rde-11 embryo

description:
Sample 10.
~18-26 nt RNAs, TAP treated.

source_name: rde-11 embryos, TAP treated


title: rde-10 embryo

description:
Sample 8.
~18-26 nt RNAs, TAP treated.

source_name: rde-10 embryos, TAP treated


title: H3K4me3_MLL2_KO_UT

description: Chromatin IP against H3K4me3


title: wild type pos-1 RNAi untreated

description:
Sample 17.
~18-26 nt RNAs, untreated.

source_name: wild type adult animals, pos-1 RNAi, untreated

value: wild type

tag: RNAi


title: wild type embryo

description:
Sample 6.
~18-26 nt RNAs, TAP treated.

source_name: wild type embryos, TAP treated


title: rde-10 adult 2

description:
Sample 7.
~18-26 nt RNAs, TAP treated.

source_name: rde-10 adult animals, TAP treated


title: rde-11 control RNAi untreated

description:
Sample 18.
~18-26 nt RNAs, untreated.

source_name: rde-11 adult animals, control RNAi, untreated

value: control


title: rde-11 pos-1 RNAi untreated

description:
Sample 19.
~18-26 nt RNAs, untreated.

source_name: rde-11 adult animals, pos-1 RNAi, untreated


title: wild type control RNAi untreated

description:
Sample 16.
~18-26 nt RNAs, untreated.

source_name: wild type adult animals, control RNAi, untreated


title: rde-10 adult

description:
Sample 3.
~18-26 nt RNAs, TAP treated.


title: wild type adult 2

description:
Sample 5.
~18-26 nt RNAs, TAP treated.

source_name: wild type adult animals, TAP treated


title: wt pos-1 RNAi TAP treated

description:
Sample 13.
~18-26 nt RNAs, TAP treated.

source_name: wild type adult animals, pos-1 RNAi, TAP treated


title: rde-11 pos-1 RNAi TAP treated

description:
Sample 15.
~18-26 nt RNAs, TAP treated.

source_name: rde-11 adult animals, pos-1 RNAi, TAP treated


title: rde-11 control RNAi TAP treated

description:
Sample 14.
~18-26 nt RNAs, TAP treated.

source_name: rde-11 adult animals, control RNAi, TAP treated


title: wild type adult

description:
Sample 2.
~18-26 nt RNAs, TAP treated.


title: rsd-2 adult

description:
Sample 4.
~18-26 nt RNAs, TAP treated.

source_name: rsd-2 adult animals, TAP treated


title: wild type control RNAi TAP treated

description:
Sample 12.
~18-26 nt RNAs, TAP treated.

source_name: wild type adult animals, control RNAi, TAP treated


title: miR-125b NB4 Rep 2

status: Public on Apr 06 2012

city: Oxford

first: Diu

last: Nguyen

address: Headley way

department: Clinical Laboratory Sciences

country: United Kingdom

institute: University of Oxford

description: promyelocytic leukemic cell line

data_processing:
ELAND was used for mapping reads to the human hg18 genome
Gene expression values were calculated as Reads Per Kilobase of Exon Model Per Million Mapped Reads (RPKM)
Genome_build: hg18
Supplementary_files_format_and_content: Text (genecount) files include RPKM values for each Sample.

source_name: miR-125b NB4

growth_protocol: NB4 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% L-Glutamine and 1% penicillin and streptomycin (GIBCO)

extract_protocol: Total RNA was extracted using an RNeasy kit (Qiagen). The library preparation was performed using polyA enriched RNA according to the manufacturer's instructions (Illumina) and then sequenced on a Solexa sequencing cell.

treatment_protocol: NB4 cells were transiently transfected with pre-miR negative control or pre-miR-125b (Ambion). Two independent transfections were performed for each condition.

value: promyelocytic leukemia

tag: transfected with


title: Control NB4 Rep 2

description: promyelocytic leukemic cell line

source_name: Control NB4

value: pre-miR control


title: miR-125b NB4 Rep 1

description: promyelocytic leukemic cell line


title: rsd-6 adult

description:
Sample 1.
~18-26 nt RNAs, TAP treated.

source_name: rsd-6 adult animals, TAP treated


title: Wild-type small RNAs Sample 2

status: Public on Apr 05 2012

city: Salt Lake City

first: Michael

middle: Bryan

last: Warf

state: UT

address: 15 N Medical Dr East, room 4800

department: Biochemistry

institute: University of Utah

description: small RNA (18-30 nts) with 5' monophosphate

data_processing:
Sequence reads were obtained using the Illumina Genome Analyzer Pipeline version 1.6 (OLB 1.6, CASAVA 1.6.0)
Alingment: Sequnces were aligned to the genome (May 2008) using Novoalign, with an r-value of 0.2 and a q-value of 5. Sequences were filtered using the USeq. software package component NovoalignParser, using a posterior probability of 0.1. Output is a bed file for each chromosome, with separate files for plus and minus strands.

source_name: Whole worm

growth_protocol: Worms were grown on OP50 lawn at 20 degrees Celsius

extract_protocol: Total RNA was isolating using TRIzol reagent (Invitrogen), small RNAs were isolated by gel purication and cDNA was prepared using the small RNA v1.5 illumina kit

value: Wild-type (N2)

value: mixed stage

value: Whole worm


title: adr-2 mutant small RNAs


title: Wild-type small RNAs Sample 1


title: adr-1 mutant small RNAs


title: adr-1;adr-2 mutant small RNAs


title: miR-125b 32Dclone3 Rep 2

city: Cambridge

first: Marina

last: Bousquet

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
ELAND was used for mapping reads to the mouse mm9 genome
Gene expression values were calculated as Reads Per Kilobase of Exon Model Per Million Mapped Reads (RPKM)
Genome_build: mm9
Supplementary_files_format_and_content: excel files include RPKM values for each Sample.

source_name: myeloid cell line

growth_protocol: 32Dclone3 were grown in 10% fetal bovine serum, 10% IL3 (WEHI media) and 1% penicillin and streptomycin (GIBCO)

treatment_protocol: 32Dclone3 was stably infected with XZ (control) or XZ-miR-125b. Infection was performed twice with two different virus supernatants for each condition.

tag: infection status

value: XZ-miR-125b virus

value: myeloid cell line


title: miR-125b 32Dclone3 Rep 1


title: Smarcal1+/+ liver at 39.5oC- lane 1

city: Vancouver

first: Alireza

last: Baradaran-Heravi

state: BC

address: 950 West 28th Avenue, Room 218

department: Medical Genetics

country: Canada

institute: UBC

data_processing: Image analysis and base calling were done by the GA pipeline v1.0 (Illumina, Hayward, CA) using phasing and matrix values calculated from a control phiX174 library run on each flow cell. Raw quality scores were calibrated by alignment to the reference mouse genome (NCBI build 37, mm9) using ELAND (Illumina, Hayward, CA). Short read sequences obtained from the Illumina Genome Analyzer for each sample were mapped to the reference mouse genome (NBCI build 37, mm9) plus a database of known exon junctions using MAQ in paired end mode. The exon junction sequences consisted of N-1 nucleotides of the donor exon ‘spliced’ to N-1 nucleotides of the acceptor exon for every known pair of exons in the mouse transcriptome, where N is the read length. This was designed to rescue reads that would not map to the mouse reference genome due to their spanning a splice site. The maximum insert size (-a parameter) to MAQ was 500. Mouse sequence summary count data were log2 scaled. All genes with a count per kilobase summary greater than 4 (log2 >2) in either temperature condition in wt samples were identified as well enough represented to be considered in our analysis.

source_name: Smarcal1+/+ (39.5oC)-liver

growth_protocol: Smarcal1+/+ and Smarcal1del/del mice were housed according to standard protocols.

extract_protocol: RNA was extracted from the mouse liver using the RNeasy Mini Kit (Qiagen) and elimination of genomic DNA was performed using  on-column DNAase (Qiagen). For each sample, double-stranded cDNA was synthesized from purified polyadenylated RNA, sheared, and paired-end sequencing library was prepared following the Illumina paired-end library preparation protocol for the Genome Analyzer II (Illumina).

treatment_protocol: Smarcal1+/+ and Smarcal1del/del mice were either housed at 20oC or heat stressed at 39.5oC for 1 hour.

value: Liver

value: Female

tag: strain

value: Mixed 129SvEv and C57BL/6

value: 3-4 months

tag: temperature


title: Smarcal1del/del liver at 20oC- lane 2

source_name: Smarcal1del/del (20oC)-liver

tag: tissue


title: Smarcal1del/del liver at 39.5oC- lane 2

source_name: Smarcal1del/del (39.5oC)-liver


title: Smarcal1del/del liver at 39.5oC- lane 1


title: Smarcal1+/+ liver at 39.5oC- lane 2


title: Smarcal1del/del liver at 20oC- lane 1


title: Smarcal1+/+ liver at 20oC- lane 2

source_name: Smarcal1+/+ (20oC)-liver


title: Smarcal1+/+ liver at 20oC- lane 1


title: Control NB4 Rep 1

description: promyelocytic leukemic cell line


title: WT_Sucrose_3_4h

city: Berkeley

first: N

middle: Louise

last: Glass

address: 341 Koshland Hall, Univerisity of California

department: Plant and Microbial Biology

institute: UC Berkeley

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864241.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_3.expr.txt: N. crassa OR74A (NC10)

organism: Neurospora crassa OR74A

growth_protocol: Innoculated at 10^6 conidia/mL and grown 16 hours in sucrose media.

extract_protocol: mRNA was purified with Dynabeads® Oligo dT magnetic beads (Illumina).   Purified mRNA was fragmented with buffered zinc solution from Ambion (Cat # AM8740).  First and second strand cDNA synthesis was carried out using Superscript II Reverse Transcriptase (Invitrogen) and DNA pol I (Invitrogen) and random primers.    Illumina sequencing adapters were then ligated to the cDNA, 200bp fragments were purified by gel electrophoresis, and PCR enriched with Pfx DNA polymerase (Invitrogen).

treatment_protocol: Washed and transferred to fresh media with sucrose, cellulose (Avicel PH101), cellobiose or no carbon source

value: Wild Type Reference Strain (FGSC 2489)

tag: carbon source

value: Sucrose

tag: time after media shift

value: 4 hours


title: WT_No_Carbon_3_4h

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864235.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_No_Carbon_3.expr.txt: N. crassa OR74A (NC10)


title: WT_Avicel_1_4h

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864229.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_1.expr.txt: N. crassa OR74A (NC10)

value: Avicel


title: TBGK_Cellobiose_4h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
TBGK_Cellobiose.expr.txt: N. crassa OR74A (NC10)

value: Deletion mutant (NCU04952, NCU00130, NCU08755)

value: Cellobiose


title: TBGK_Avicel_4h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
TBGK_Avicel.expr.txt: N. crassa OR74A (NC10)


title: TBGK_Sucrose_4h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
TBGK_Sucrose.expr.txt: N. crassa OR74A (NC10)


title: WT_No_Carbon_2_4h

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864234.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_No_Carbon_2.expr.txt: N. crassa OR74A (NC10)


title: WT_Avicel_3_4h

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864231.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_3.expr.txt: N. crassa OR74A (NC10)


title: WT_Sucrose_1_4h

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864239.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_1.expr.txt: N. crassa OR74A (NC10)


title: WT_Avicel_2_4h

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864230.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_2.expr.txt: N. crassa OR74A (NC10)


title: WT_No_Carbon_1_4h

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864233.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_No_Carbon_1.expr.txt: N. crassa OR74A (NC10)


title: control 32Dclone3 Rep 2

value: XZ control virus


title: control 32Dclone3 Rep 1


title: WT_Cellobiose_4h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Cellobiose.expr.txt: N. crassa OR74A (NC10)


title: Digital Genomic Footprinting assay of H1 BMP4 Derived Mesendoderm Cultured Cells; DGF.DS19310

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19310
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12039
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM909313_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Digital_Genomic_Footprinting.DGF.DS19310.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS19310.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DGF.DS19310 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13110
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 323,679,569
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4331
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4824
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5191
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM909313_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Digital_Genomic_Footprinting.DGF.DS19310.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS19310.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DGF.DS19310 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13115
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDM DGF 10
BROWSER_TRACK_DESCRIPTION: UW H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Library DGF.DS19310 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 323,679,569
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4331
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4824
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5191
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; DGF.DS19310

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

tag: passage

value: Between 20 and 30

tag: medium

value: Male

tag: batch

value: Digital Genomic Footprinting

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Digital Genomic Footprinting assay of H1 Derived Mesenchymal Stem Cells; DGF.DS21042

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS21042
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11978
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM909314_UW.H1_Derived_Mesenchymal_Stem_Cells.Digital_Genomic_Footprinting.DGF.DS21042.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS21042.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on H1 Derived Mesenchymal Stem Cells, Library DGF.DS21042 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13109
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 243,488,451
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.5147
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.5507
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5834
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM909314_UW.H1_Derived_Mesenchymal_Stem_Cells.Digital_Genomic_Footprinting.DGF.DS21042.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS21042.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  H1 Derived Mesenchymal Stem Cells, Library DGF.DS21042 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13114
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HDMSC DGF 42
BROWSER_TRACK_DESCRIPTION: UW H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Library DGF.DS21042 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 243,488,451
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.5147
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.5507
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5834
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; DGF.DS21042

value: H1 Derived Mesenchymal Stem Cells

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

tag: Sex


title: Digital Genomic Footprinting assay of Penis Foreskin Fibroblast Primary Cells; DGF.DS18224

description:
sample_term_id: CL_1001608
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS18224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12000
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.7320
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM909312_UW.Penis_Foreskin_Fibroblast_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18224.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18224.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Penis Foreskin Fibroblast Primary Cells, Donor skin01, Library DGF.DS18224 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13112
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 433,775,987
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6769
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6776
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9983
IROC_PERCENTILE: 40
POISSON_SCORE: 0.7024
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM909312_UW.Penis_Foreskin_Fibroblast_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18224.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18224.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  Penis Foreskin Fibroblast Primary Cells, Donor skin01, Library DGF.DS18224 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13117
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFF DGF 01 24
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18224 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 433,775,987
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6769
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6776
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9983
IROC_PERCENTILE: 40
POISSON_SCORE: 0.7024
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Penis, Foreskin, Fibroblast Primary Cells skin01; DGF.DS18224

value: Penis, Foreskin, Fibroblast skin01

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Fibroblast

tag: markers

value: Invitrogen 154CF + HKGS + .07mM Ca

value: Neonate

value: Disease Free

tag: karyotype

tag: parity


title: Digital Genomic Footprinting assay of Induced pluripotent stem cell; DGF.DS15153

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS15153
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11957
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM909311_UW.iPS_DF_19.11.Digital_Genomic_Footprinting.DGF.DS15153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS15153.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on the iPS DF 19.11 Cell Line, Library DGF.DS15153 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13113
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 217,450,671
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.309
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3498
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9916
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4068
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM909311_UW.iPS_DF_19.11.Digital_Genomic_Footprinting.DGF.DS15153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS15153.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  the iPS DF 19.11 Cell Line, Library DGF.DS15153 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13118
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: iD19.11 DGF 53
BROWSER_TRACK_DESCRIPTION: UW iPS DF 19.11 Cell Line Digital Genomic Footprinting Library DGF.DS15153 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 217,450,671
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.309
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3498
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9916
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4068
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; DGF.DS15153

value: iPS DF 19.11 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: Between 30 and 40

value: mTeSR


title: RNA-Seq (Total RNA) Moblized CD34 Primary Cells; RNA.RS18745

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Moblized CD34 Primary Cells
Library name: lib-RNA.RS18745
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12162
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM909310_UW.Mobilized_CD34_Primary_Cells.mRNA-Seq.RO_01549.lib-RNA.RS18745.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18745.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Mobilized CD34 Primary Cells, Donor RO 01549 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13741
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 346,073,864
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.3
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM909310_UW.Mobilized_CD34_Primary_Cells.mRNA-Seq.RO_01549.lib-RNA.RS18745.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18745.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13742
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: MCD34 mRNA 49 45
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells mRNA-Seq Donor RO 01549 Library lib-RNA.RS18745 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 346,073,864
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.3
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: flow sorted CD34+ cells from cord blood; RNA.RS18745

extract_protocol: Library construction protocol: Illumina TruSeq RNA PART# 15008136 REVISION A

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: 33 years

value: Female

value: Caucasian

value: mRNA-Seq

value: Ambion Ribopure

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: Reference Epigenome: ChIP-Seq Analysis of H4K12ac in BMP4 Trophoblast Cells; renlab.H4K12ac.BMP4T.02.01

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K12ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY203
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12168
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM908963_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K12ac.AY203.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K12ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H4K12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H4K12ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY203, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13481
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,679,101
NUMBER_OF_H4K12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.3961
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4634
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9556
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5772
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM908963_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K12ac.AY203.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K12ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H4K12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H4K12ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY203, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13601
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H4K12ac 03
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY203 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,679,101
NUMBER_OF_H4K12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.3961
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4634
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9556
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5772
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H4K12ac.BMP4T.02.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: Male

value: Histone H4K12ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H4K12ac in BMP4 Trophoblast Cells; renlab.H4K12ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K12ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY231
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12156
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM908962_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K12ac.AY231.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K12ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H4K12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H4K12ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY231, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13512
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,227,161
NUMBER_OF_H4K12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.167
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2931
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9274
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3926
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM908962_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K12ac.AY231.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K12ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H4K12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H4K12ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY231, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13632
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H4K12ac 31
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY231 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,227,161
NUMBER_OF_H4K12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.167
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2931
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9274
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3926
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H4K12ac.BMP4T.01.01


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in hESC H1 Cells; renlab.H4K8ac.hESC.H1.02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY18
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12106
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM908966_UCSD.H1.H4K8ac.AY18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.hESC.H1.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Cell Line H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H4K8ac ChIP-Seq on H1 Cell Line, Library AY18, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13483
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,685,315
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0532
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.3227
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.7751
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5179
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.65

**********************************************************************

ANALYSIS FILE NAME: GSM908966_UCSD.H1.H4K8ac.AY18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.hESC.H1.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H4K8ac ChIP-Seq read mappings from the H1 Cell Line, Library AY18, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13603
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: H1 H4K8ac 18
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H4K8ac Library AY18 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,685,315
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0532
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.3227
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.7751
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5179
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.65

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H4K8ac.hESC.H1.02.01

value: H1 Cell Line

value: James Thompson Laboratory

value: mTeSER

value: Histone H4K8ac

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in BMP4 Trophoblast Cells; renlab.H4K8ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY233
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12158
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM908964_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K8ac.AY233.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H4K8ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY233, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13498
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,615,943
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.2191
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3226
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9573
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4466
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM908964_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K8ac.AY233.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H4K8ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY233, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13618
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H4K8ac 33
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY233 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,615,943
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.2191
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3226
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9573
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4466
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H4K8ac.BMP4T.01.01

value: genomic DNA

value: James Thomson Laboratory


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in BMP4 Trophoblast Cells; renlab.H4K91ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY206
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12170
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM908967_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K91ac.AY206.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H4K91ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY206, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13462
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,019,377
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.556
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5822
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9961
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6433
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM908967_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K91ac.AY206.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H4K91ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY206, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13582
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H4K91ac 06
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K91ac Library AY206 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,019,377
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.556
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5822
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9961
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6433
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H4K91ac.BMP4T.01.01

value: Cell Line

value: Embryonic Stem Cell

value: Histone H4K91ac

value: Abcam


title: WT_Sucrose_2_4h

description: In order to allow efficient download of related data from both GEO and SRA, this entry duplicates what has been submitted previously in GSM864240.

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_2.expr.txt: N. crassa OR74A (NC10)

tag: strain

value: Wild Type Reference Strain (FGSC 2489)

value: Sucrose

value: 4 hours


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in BMP4 Trophoblast Cells; renlab.H3K79me1.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY229
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12131
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM908958_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K79me1.AY229.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K79me1 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY229, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13441
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,133,086
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.3369
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4065
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9861
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5211
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM908958_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K79me1.AY229.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K79me1 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY229, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13561
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H3K79me1 29
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY229 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,133,086
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.3369
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4065
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9861
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5211
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K79me1.BMP4T.01.01

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: Male

value: Histone H3K79me1

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in BMP4 Trophoblast Cells; renlab.H3K79me1.BMP4T.02.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY201
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12152
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM908959_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K79me1.AY201.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K79me1 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY201, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13457
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,261,776
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.3036
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3934
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9575
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5121
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM908959_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K79me1.AY201.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K79me1 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY201, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13577
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H3K79me1 01
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY201 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,261,776
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.3036
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3934
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9575
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5121
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K79me1.BMP4T.02.01

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in BMP4 Trophoblast Cells; renlab.H3K4ac.BMP4T.02.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY200
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12150
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM908955_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4ac.AY200.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY200, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13505
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,233,440
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4235
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4837
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9893
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5618
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

ANALYSIS FILE NAME: GSM908955_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4ac.AY200.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY200, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13625
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H3K4ac 00
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY200 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,233,440
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4235
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4837
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9893
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5618
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K4ac.BMP4T.02.01

value: genomic DNA

value: Histone H3K4ac

value: Upstate