title: Long_treated

description: Endogenous RNA

data_processing:
Long_treated.txt; genome build: chromosome built 07/25/2008, plasmid pTT27 built 05/01/2009
Read mapping was done using an algorithm described previously (Yassour et al., http://www.ncbi.nlm.nih.gov/pubmed/20796282).The algorithm was applied with the following parameters: 1. A minimum match length of 17 nt between read and genome was required. 2. For the medium and long libraries a sequence at the 5’ or 3’ read end was only considered part of the adapter if it had at least seven matches to the corresponding A5 (starting from its 3’ end) or A3 adapter (starting from its 5’ end) sequence. For the short library we were less restrictive requiring a minimum of only three nt match. 3. A maximum of two mismatches and/or insertions/deletions were allowed for the whole read. 4. Read length was adapted to the Illumina output and was defined as 36 nt for the short library and 100 nt for the medium and long libraries. The Illumina software applied in the mapping of the medium and long libraries adds to the short read sequences that have a full A3 adapter random nucleotides at their 3’ ends up to the fixed read length. Thus to map such reads we first used cutadapt-0.9.3 (http://code.google.com/p/cutadapt) to identify the A3 adapter. We then replaced the random nucleotides stretches with polyA and allowed the SolexaMatch to identify polyA matches 3’ to the full adapter length in the analysis of the medium and long libraries. This was not required for the short library as the combination of the length of the A3 adapter (21 nt) and the minimal genomic match length (17 nt) exceeds the maximal read length (36 nt). In analyses that regarded reads that were mapped to multiple genomic locations we divided the read count by the corresponding number of genomic locations. Each one of the multiple genomic location was assigned this normalized value.

The Read annotation supplementary file (*.txt) lists all the reads that were mapped to the genome. The annotation of tRNA, mRNA, ncRNA, and rRNA follows the NCBI annotation. For rRNA however we expanded slightly the genes' boundaries based on the reads in the region.

The supplementary .txt file is tab-delimited and includes the following information:
Field 1 read  sequence
Field 2 read sequence with no adapter
Field 3 read length
Field 4 normalized copy number (divided by the number of genomic locations) (Field 5/Field 11)
Field 5 the copy number of the read
Field 6 chromosome
Field 7 start
Field 8 strand
Field 9 mismatch (0-no mismatch -1 one mismatch -2 two mismatches)
Field 10 adapter
Field 11 number of genomic locations
Field 12 annotation  (reads might have multiple annotations even within a specific genomic location); reads with no annotation are assigned 'None'.

value: treated


title: Endogenous mRNA from MEF wildtype cells 2

status: Public on Feb 25 2012

type: SRA

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

description: polyA RNA purification followed be chemical fragmentation and reverse transcription using random hexamers (all describes in the manufacturer’s instruction)

library_source: transcriptomic

data_processing: Mapping of reads with Bowtie to the respective genome (ce6 for C.elegans; mm9 for M.musculus samples) and to a splice site data set created using UCSC's RefSeq annotation. Counting of uniquely mapped reads and assignemt to RefSeq genes using R Statistical Language and Bioconductor.

molecule: total RNA

organism: Mus musculus

source_name: murine embryonic fibroblasts (MEF), wildtype

growth_protocol: C. elegans: Synchronisation with egg laying period, Worms were maintained on NGM agar plates and fed with E. coli OP50 , Worms were harvested for RNA isolation at the age of 5 days after L4 larvae stage; MEF: Cells were cultured in DMEM containing 25 mM Glucose and 10% FBS

extract_protocol: library was prepared using Illumina RNA sample prep kit (RS-100-0801), following the instructions

tag: genetic background

tag: genotype

value: wild type

tag: cell type

value: murine embryonic fibroblasts (MEF)

tag: passage


title: Endogenous mRNA from MEF insr+/- knockout cells 1

source_name: murine embryonic fibroblasts (MEF), insr+/- knockout

value: insr+/-


title: Medium_treated

city: Bonn

first: Stefan

middle: Andreas

last: Juranek

state: NRW

address: Venusber-Campus 1

department: Medizinische Klinik III

institute: UK Bonn

description: Endogenous RNA

data_processing:
Medium_treated.txt; genome build: chromosome built 07/25/2008, plasmid pTT27 built 05/01/2009
Read mapping was done using an algorithm described previously (Yassour et al., http://www.ncbi.nlm.nih.gov/pubmed/20796282).The algorithm was applied with the following parameters: 1. A minimum match length of 17 nt between read and genome was required. 2. For the medium and long libraries a sequence at the 5’ or 3’ read end was only considered part of the adapter if it had at least seven matches to the corresponding A5 (starting from its 3’ end) or A3 adapter (starting from its 5’ end) sequence. For the short library we were less restrictive requiring a minimum of only three nt match. 3. A maximum of two mismatches and/or insertions/deletions were allowed for the whole read. 4. Read length was adapted to the Illumina output and was defined as 36 nt for the short library and 100 nt for the medium and long libraries. The Illumina software applied in the mapping of the medium and long libraries adds to the short read sequences that have a full A3 adapter random nucleotides at their 3’ ends up to the fixed read length. Thus to map such reads we first used cutadapt-0.9.3 (http://code.google.com/p/cutadapt) to identify the A3 adapter. We then replaced the random nucleotides stretches with polyA and allowed the SolexaMatch to identify polyA matches 3’ to the full adapter length in the analysis of the medium and long libraries. This was not required for the short library as the combination of the length of the A3 adapter (21 nt) and the minimal genomic match length (17 nt) exceeds the maximal read length (36 nt). In analyses that regarded reads that were mapped to multiple genomic locations we divided the read count by the corresponding number of genomic locations. Each one of the multiple genomic location was assigned this normalized value.

The Read annotation supplementary file (*.txt) lists all the reads that were mapped to the genome. The annotation of tRNA, mRNA, ncRNA, and rRNA follows the NCBI annotation. For rRNA however we expanded slightly the genes' boundaries based on the reads in the region.

The supplementary .txt file is tab-delimited and includes the following information:
Field 1 read  sequence
Field 2 read sequence with no adapter
Field 3 read length
Field 4 normalized copy number (divided by the number of genomic locations) (Field 5/Field 11)
Field 5 the copy number of the read
Field 6 chromosome
Field 7 start
Field 8 strand
Field 9 mismatch (0-no mismatch -1 one mismatch -2 two mismatches)
Field 10 adapter
Field 11 number of genomic locations
Field 12 annotation  (reads might have multiple annotations even within a specific genomic location); reads with no annotation are assigned 'None'.

organism: Thermus thermophilus

source_name: Thermus thermophilus HB8

growth_protocol: T. thermophilus HB8 cells were grown in LB media supplemented with 1 mM magnesium chloride and 1 mM calcium chloride shaking at 220 rpm at 75˚C

extract_protocol:
RNA was extracted using the guanidiniumisothiocyanate/phenol method, according to Chomczynski and Sacchi, Analytical Biochemistry, 1987.
Briefly, 200 µg of total RNA were separated on a 15% 15x17x0.08 cm denaturing polyacrylamide (19:1) gel. RNA size marker cocktail (20 µg, composed of 4 µg each of a 19, 24, 35, 50, and 100 nt (nucleotide) long oligoribonucleotides) was loaded in separate lanes with empty lanes between marker and sample loading. After electrophoresis (0.5x TBE, 30 W, 45 min), the size markers were visualized by 260 nm UV shadowing. The portion of the gel that represented the RNA size region between 19-35, 35-50, and 50-100 nt was cut out and the gel pieces were eluted for 12 h with 3 volumes (v/w) 0.3 M sodium chloride at 4ºC in a thermomixer shaking at 800 rpm. The RNA was precipitated using 3 volumes absolute ethanol and resuspended in water. The yield of fractionated RNA was approximately 1% relative to the total RNA input. Each of the three RNA size fractions was divided in two aliquots. One was directly used as input for the 3’ adapter ligation, whereas the second was treated with alkaline phosphatase (NEB) for 1 h at 37ºC in 1 x reaction buffer (NEB) to remove all 5’ or 3’ phosphoryl groups. Alkaline phosphatase was removed by phenol/chloroform extraction and the small RNAs were subsequently completely phosphorylated at the 5’ end by T4 polynucleotide kinase (NEB) for 1 h at 37ºC in 1x reaction buffer (NEB) with 2 mM ATP. Preadenylated 3’ adapter was ligated to the small RNAs in 20 µl reaction volume using 1 µg RNA, 2.5 µM 3’ adapter A3 rAppTCGTATGCCGTCTTCTGCTTG and 1 µg T4 Rnl2(1-249)K227Q (NEB) in RNA ligation buffer (50 mM Tris-HCl, pH 7.6, 10 mM magnesium chloride, 10 mM 2-mercaptoethanol, 0.1 mg/ml acetylated BSA (Sigma, B-8894), and 15% aqueous DMSO) at 4ºC for 12 h and subsequently separated by denaturing PAA gel electrophoresis. Ligated products (indicated by adapter-ligated size markers loaded in separate lanes, with one empty lane distance to the samples) were cut out and eluted as described above. After ethanol precipitation, the 5’ adapter was ligated to the small RNAs in a total reaction volume of 20 µl using 1 µg T4 Rnl1 (Fermentas), 5 µM 5’ adapter A5 r(GUUCAGAGUUCUACAGUCCGACGAUC), r indicating ribonucleotide, in RNA ligation buffer containing 0.2 mM ATP for 1 h at 37ºC. The ligated product was purified on a 12% denaturing PAA gel. The final product was reverse transcribed by SuperScript III reverse transcriptase according to manufacturer’s instructions (Invitrogen). 100 pmol of the reverse transcription primer (CAAGCAGAAGACGGCATACGA) was added to the purified RNAs taken up in 6.5 µl H2O and the mixture was denatured for 30 s at 90ºC and transferred directly to 50ºC. 7.5 µl of a reaction mixture containing 100 mM Tris-HCl (pH 8.3), 150 mM potassium chloride, 6 mM magnesium chloride, 20 mM DTT, and 1 mM dNTPs, was added and the samples were incubated for 3 min at 50ºC. 150 U reverse transcriptase was added and the reaction mixture was incubated at 42ºC for 60 min. To hydrolyze the RNA 100 mM potassium hydroxide was added, and the mixture was incubated for 10 min at 90ºC. The solution was neutralized by adding hydrochloric acid to 100 mM. The pH of the solution was checked by spotting 1 µl on pH paper. The cDNA was used for PCR amplification using a standard PCR protocol and primers compatible with Solexa sequencing (CAAGCAGAAGACGGCATACGA and AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA). The libraries were deep sequenced using the Solexa technology at the Rockefeller University Genomic Resource Center using standard protocol by Illumina.

tag: strain

tag: size

tag: od 600 nm at harvest

tag: treatment group


title: Endogenous mRNA from MEF irs1-/- knockout cells 1

source_name: murine embryonic fibroblasts (MEF), irs1-/- knockout

value: irs1 KO


title: Short_treated

description: Endogenous RNA

data_processing:
Short_treated.txt; genome build: chromosome built 07/25/2008, plasmid pTT27 built 05/01/2009
Read mapping was done using an algorithm described previously (Yassour et al.,  http://www.ncbi.nlm.nih.gov/pubmed/20796282).The algorithm was applied with the following parameters: 1. A minimum match length of 17 nt between read and genome was required. 2. For the medium and long libraries a sequence at the 5’ or 3’ read end was only considered part of the adapter if it had at least seven matches to the corresponding A5 (starting from its 3’ end) or A3 adapter (starting from its 5’ end) sequence. For the short library we were less restrictive requiring a minimum of only three nt match. 3. A maximum of two mismatches and/or insertions/deletions were allowed for the whole read. 4. Read length was adapted to the Illumina output and was defined as 36 nt for the short library and 100 nt for the medium and long libraries. The Illumina software applied in the mapping of the medium and long libraries adds to the short read sequences that have a full A3 adapter random nucleotides at their 3’ ends up to the fixed read length. Thus to map such reads we first used cutadapt-0.9.3 (http://code.google.com/p/cutadapt) to identify the A3 adapter. We then replaced the random nucleotides stretches with polyA and allowed the SolexaMatch to identify polyA matches 3’ to the full adapter length in the analysis of the medium and long libraries. This was not required for the short library as the combination of the length of the A3 adapter (21 nt) and the minimal genomic match length (17 nt) exceeds the maximal read length (36 nt). In analyses that regarded reads that were mapped to multiple genomic locations we divided the read count by the corresponding number of genomic locations. Each one of the multiple genomic location was assigned this normalized value.

The Read annotation supplementary file (*.txt) lists all the reads that were mapped to the genome. The annotation of tRNA, mRNA, ncRNA, and rRNA follows the NCBI annotation. For rRNA however we expanded slightly the genes' boundaries based on the reads in the region.

The supplementary .txt file is tab-delimited and includes the following information:
Field 1 read  sequence
Field 2 read sequence with no adapter
Field 3 read length
Field 4 normalized copy number (divided by the number of genomic locations) (Field 5/Field 11)
Field 5 the copy number of the read
Field 6 chromosome
Field 7 start
Field 8 strand
Field 9 mismatch (0-no mismatch -1 one mismatch -2 two mismatches)
Field 10 adapter
Field 11 number of genomic locations
Field 12 annotation  (reads might have multiple annotations even within a specific genomic location); reads with no annotation are assigned 'None'.


title: Medium_untreated

description: Endogenous RNA

data_processing:
Medium_untreated.txt; genome build: chromosome built 07/25/2008, plasmid pTT27 built 05/01/2009
Read mapping was done using an algorithm described previously (Yassour et al., http://www.ncbi.nlm.nih.gov/pubmed/20796282).The algorithm was applied with the following parameters: 1. A minimum match length of 17 nt between read and genome was required. 2. For the medium and long libraries a sequence at the 5’ or 3’ read end was only considered part of the adapter if it had at least seven matches to the corresponding A5 (starting from its 3’ end) or A3 adapter (starting from its 5’ end) sequence. For the short library we were less restrictive requiring a minimum of only three nt match. 3. A maximum of two mismatches and/or insertions/deletions were allowed for the whole read. 4. Read length was adapted to the Illumina output and was defined as 36 nt for the short library and 100 nt for the medium and long libraries. The Illumina software applied in the mapping of the medium and long libraries adds to the short read sequences that have a full A3 adapter random nucleotides at their 3’ ends up to the fixed read length. Thus to map such reads we first used cutadapt-0.9.3 (http://code.google.com/p/cutadapt) to identify the A3 adapter. We then replaced the random nucleotides stretches with polyA and allowed the SolexaMatch to identify polyA matches 3’ to the full adapter length in the analysis of the medium and long libraries. This was not required for the short library as the combination of the length of the A3 adapter (21 nt) and the minimal genomic match length (17 nt) exceeds the maximal read length (36 nt). In analyses that regarded reads that were mapped to multiple genomic locations we divided the read count by the corresponding number of genomic locations. Each one of the multiple genomic location was assigned this normalized value.

The Read annotation supplementary file (*.txt) lists all the reads that were mapped to the genome. The annotation of tRNA, mRNA, ncRNA, and rRNA follows the NCBI annotation. For rRNA however we expanded slightly the genes' boundaries based on the reads in the region.

The supplementary .txt file is tab-delimited and includes the following information:
Field 1 read  sequence
Field 2 read sequence with no adapter
Field 3 read length
Field 4 normalized copy number (divided by the number of genomic locations) (Field 5/Field 11)
Field 5 the copy number of the read
Field 6 chromosome
Field 7 start
Field 8 strand
Field 9 mismatch (0-no mismatch -1 one mismatch -2 two mismatches)
Field 10 adapter
Field 11 number of genomic locations
Field 12 annotation  (reads might have multiple annotations even within a specific genomic location); reads with no annotation are assigned 'None'.

value: untreated


title: Endogenous mRNA from MEF wildtype cells 1


title: Short_untreated

description: Endogenous RNA

data_processing:
Short_untreated.txt; genome build: chromosome built 07/25/2008, plasmid pTT27 built 05/01/2009
Read mapping was done using an algorithm described previously (Yassour et al., http://www.ncbi.nlm.nih.gov/pubmed/20796282).The algorithm was applied with the following parameters: 1. A minimum match length of 17 nt between read and genome was required. 2. For the medium and long libraries a sequence at the 5’ or 3’ read end was only considered part of the adapter if it had at least seven matches to the corresponding A5 (starting from its 3’ end) or A3 adapter (starting from its 5’ end) sequence. For the short library we were less restrictive requiring a minimum of only three nt match. 3. A maximum of two mismatches and/or insertions/deletions were allowed for the whole read. 4. Read length was adapted to the Illumina output and was defined as 36 nt for the short library and 100 nt for the medium and long libraries. The Illumina software applied in the mapping of the medium and long libraries adds to the short read sequences that have a full A3 adapter random nucleotides at their 3’ ends up to the fixed read length. Thus to map such reads we first used cutadapt-0.9.3 (http://code.google.com/p/cutadapt) to identify the A3 adapter. We then replaced the random nucleotides stretches with polyA and allowed the SolexaMatch to identify polyA matches 3’ to the full adapter length in the analysis of the medium and long libraries. This was not required for the short library as the combination of the length of the A3 adapter (21 nt) and the minimal genomic match length (17 nt) exceeds the maximal read length (36 nt). In analyses that regarded reads that were mapped to multiple genomic locations we divided the read count by the corresponding number of genomic locations. Each one of the multiple genomic location was assigned this normalized value.

The Read annotation supplementary file (*.txt) lists all the reads that were mapped to the genome. The annotation of tRNA, mRNA, ncRNA, and rRNA follows the NCBI annotation. For rRNA however we expanded slightly the genes' boundaries based on the reads in the region.

The supplementary .txt file is tab-delimited and includes the following information:
Field 1 read  sequence
Field 2 read sequence with no adapter
Field 3 read length
Field 4 normalized copy number (divided by the number of genomic locations) (Field 5/Field 11)
Field 5 the copy number of the read
Field 6 chromosome
Field 7 start
Field 8 strand
Field 9 mismatch (0-no mismatch -1 one mismatch -2 two mismatches)
Field 10 adapter
Field 11 number of genomic locations
Field 12 annotation  (reads might have multiple annotations even within a specific genomic location); reads with no annotation are assigned 'None'.


title: Goat_Skin_1

city: Huhehot

first: Liu

last: Zhihong

address: Zhaowuda Road 306

country: China

institute: Inner Mongolia Agriculture University

data_processing: A perl scripts was wrote to remove the the adapters, low quality reads and short reads from raw sequences, the clean distinct reads were mapped onto the sheep genome of International Sheep Genomics Consortium(http://www.sheephapmap.org/) using the program SOAP (Li et al. 2008), and the perfectly mapped reads were further analyzed to detect known sheep microRNA and novo microRNA.

organism: Capra hircus

source_name: Cashmere Goat

growth_protocol: we collect the skin of the body of Inner Mongolia Cashmere goat

extract_protocol: According to the manufacturer's instruction, total RNA was isolated from skin of Capra hircus by the RNAiso kit (TakaRa). Small RNA cDNA libraries were constructed following the protocol of Morin et al. (2008). In brief, small RNA (18 ~ 30 nt) of each samples were purified and enriched from total RNA by polyacrylamide gel electrophoresis (PAGE), and ten microgram of small RNA of each were ligated with proprietary adapters used for cDNA synthesis and libraries construction; then Solexa sequencing-by-synthesis method were performed (Illumina).

treatment_protocol: Tissues of skin in hibernating and aroused states, which were collected and stored at -80 ºC, were used for RNA extraction and small RNA cDNA library preparation.

tag: tissue

value: Skin

tag: developmental stage

value: Adult


title: H3K27me3_ChIPSeq

status: Public on Feb 24 2012

city: Chicago

first: Joseph

middle: M

last: Zullo

state: IL

address: 929 E 57th Street

department: MGCB

country: USA

institute: University of Chicago

library_source: genomic

data_processing:
Sequence reads were mapped to the mouse genome assembly mm8 using MAQ v 0.7.1, and these alignments were converted to BED format.  Read density maps were produced using IGVTools v 1.5.10 to generate a WIG file, which was then converted to BigWig format using the UCSC WigToBigWig conversion utility v 4.
Genome Build:
314G6AAXX.3.bed: mm8
314G6AAXX.3.bw: mm8

molecule: genomic DNA

growth_protocol: Standard 3T3 growth conditions:  37C, .05% CO2.  Medium was DMEM (Gibco) with 10% FCS (Hyclone).  Cells were split 1:8 every 2-3 days.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared as follows: DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Cells were cross-linked with 1% formaldehyde in cell culture medium for 10 min at 37C. After quenching with the addition of 125 mM glycine for 5 min at 37C, the cells were washed twice with ice-cold PBS containing proteinase inhibitor. Cells were collected after each wash by centrifugation at 2,500g for 3 min. Finally cells were aliquoted, frozen and kept at -80C.

tag: cell line

value: Mouse embryonic fibroblast cell

tag: chip antibody

tag: chip antibody vendor

value: Upstate

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: H3K4me3_ChIPSeq

data_processing:
Sequence reads were mapped to the mouse genome assembly mm8 using MAQ v 0.7.1, and these alignments were converted to BED format.  Read density maps were produced using IGVTools v 1.5.10 to generate a WIG file, which was then converted to BigWig format using the UCSC WigToBigWig conversion utility v 4.
Genome Build:
315BDAAXX.6.bed: mm8
315BDAAXX.6.bw: mm8

value: Millipore


title: h3k36me3 sictrl ChIP-Seq

city: Shanghai

first: yan

last: huang

address: Yueyang Road 320

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing: All single-read sequencing reads were aligned by Bowtie program (http://bowtie-bio.sourceforge.net/index.shtml) and parameters are followings: -v1, --best, --strata, -k2, -m1. Peak calling was performed using MACS (http://liulab.dfci.harvard.edu/MACS/) with the following settings for aligned data: bw=300, tsize=75 and a p-value threshold of 10−5. All ChIP-sequencing analysis were conducted based on the human genome March 2006 build (NCBI36.1/hg18).

organism: Homo sapiens

source_name: Hela cells knockdown control

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle’s medium containing 10% FBS (Hyclone)

extract_protocol: Purified DNA of multiple samples was prepared for sequencing according to  the ChIP procedure. About 12 ng ChIP’ ed DNA were used for DNA library construction using Preparing Samples for ChIP-seq Sample Prep Kit (Illumina) following the manufacture’s recommendation. Adapter-modified DNA between 200 and 350 bp were isolated by agarose gel electrophoresis and purified. Then, DNA was enriched by 18 cycles of linker-mediated-PCR using primers from Illumina. 7 pmol linker-ligated DNA were applied to the flow-cell using the cBOT (Illumina) device. Samples were the subjected to 76 bases of sequencing on Genome analyzer IIx (Illumina) according to Illumina’s standard protocols.

tag: treatment

value: knockdown control

value: HeLa

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: h3k36me3 si23 ChIP-Seq

source_name: Hela cells knockdown Med23

value: knockdown Med23


title: Input control

data_processing:
Sequence reads were mapped to the mouse genome assembly mm8 using MAQ v 0.7.1, and these alignments were converted to BED format.  Read density maps were produced using IGVTools v 1.5.10 to generate a WIG file, which was then converted to BigWig format using the UCSC WigToBigWig conversion utility v 4.
Genome Build:
315BDAAXX.5.bed: mm8
315BDAAXX.5.bw: mm8

source_name: NIH-3T3_Input control


title: CTCF_ChIPSeq

data_processing:
Sequence reads were mapped to the mouse genome assembly mm8 using MAQ v 0.7.1, and these alignments were converted to BED format.  Read density maps were produced using IGVTools v 1.5.10 to generate a WIG file, which was then converted to BigWig format using the UCSC WigToBigWig conversion utility v 4.
Genome Build:
314G6AAXX.2.bed: mm8
314G6AAXX.2.bw: mm8

value: CTCF


title: H3K36me3_ChIPSeq

data_processing:
Sequence reads were mapped to the mouse genome assembly mm8 using MAQ v 0.7.1, and these alignments were converted to BED format.  Read density maps were produced using IGVTools v 1.5.10 to generate a WIG file, which was then converted to BigWig format using the UCSC WigToBigWig conversion utility v 4.
Genome Build:
314G6AAXX.1.bed: mm8
3158LAAXX.5.bed: mm8
3158LAAXX.8.bed: mm8
314G6AAXX.1.bw: mm8
3158LAAXX.5.bw: mm8
3158LAAXX.8.bw: mm8


title: eyedisc_mb_wce

status: Public on Feb 23 2012

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

data_processing: Filtered reads were then aligned to the fly genome (UCSC dm3) using the bowtie (Langmead et al., 2009) alignment tool, version 0.12.7.  Only those sequences that matched uniquely to the genome with up to two mismatches were retained for subsequent analysis.  Enriched regions of ChIP-seq signal for Jarid2 and Su(z)12 were determined by the ‘MACS’ (Zhang et al., 2008) peak-finding program, version 1.4.0rc2.  Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively.  The effective genome size was configured appropriately for the fly datasets, and the p-value cutoff was set to 1.00e-08 or FDR < 1%, and a fold-change greater than four.  All other MACS parameters were left default.

organism: Drosophila melanogaster

source_name: eye-antenna imaginal disc

extract_protocol: 1g of larvae were homogenized (TISSUE TEAROR, model 985370-395, BIOSPEC PRODUCTS, INC.) on low speed for 2 min in 10 ml of buffer A1 (15 mM HEPES pH7.5, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 0.5% Triton X-100, 0.5 mM DTT, protease inhibitors (Roche, complete, EDTA-free, Cat No. 1873 580)) plus 1.3 ml of 16% paraformaldehyde (1.8% final) following further homogenization with a dounce tissue grinder 15 times with a loose pestle (Wheaton, 15 ml dounce). The sample was incubated on a nutator at room temperature until 15 min after the first homogenization step and then quenched with 1130 μl of 2.5 M glycine (225 mM glycine final) for 5 min at room temperature. The homogenate was passed through a 70 μm cell strainer (FALCON, 2350) and centrifuged for 5 min at 2000g, 4ºC. The supernatant was aspirated, resuspended in 5 ml of buffer A1 and centrifuged for 5 min at 2000g, 4ºC. The supernatant was aspirated again, resuspended in 5 ml of buffer A2 (10 mM Tris HCl pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, 0.5 mM DTT, protease inhibitors (Roche, complete, EDTA-free, Cat No. 1873 580)) and centrifuged for 5 min at 2000g, 4ºC. The previous step was repeated one more time and the pellet resuspended in 4 ml RIPA buffer (25 mM Tris pH 7.5, 140 mM NaCl, 1% Triton X-100, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 0.5 mM DTT, protease inhibitors (Roche, complete, EDTA-free, Cat No. 1873 580)) with 0.5% N-lauroylsarcosine. 1.3 ml samples were biorupted (Diagenode, Bioruptor) two times for 15 min (50% on/off) in 15 ml hard plastic tubes (Corning, 430055) following centrifugation for 20 min at 14 krpm, 4ºC. The supernatant was kept and 10 μl of biorupted chromatin reserved for gel analysis (to check sizing) and 150 μl as input control. The sizing sample was reverse cross-linked at 65ºC over night with 90 μl TE and 3 μl proteinase K (30 mg/μl) and the input sample with 5 μl proteinase K. The remaining chromatin was diluted five fold with RIPA buffer and incubated over night with the respective antibody on a nutator at 4ºC. 60 μl of protein A agarose (Invitrogen, 15918-014) was washed in 5 ml RIPA buffer, centrifuged for 2 min at 1000 rpm, 4ºC. The supernatant was aspirated, the chromatin sample added and incubated for 2 h on a nutator at 4ºC. After centrifugation for 2 min at 1000 rpm, 4ºC the protein A agarose was transferred into a 1.5 ml tube, washed with 1 ml RIPA buffer, incubated for 5 min on a nutator at room temperature and centrifuged for 2 min at 2500 rpm, 4ºC. The supernatant was aspirated and the previous washing steps repeated another seven times. Elution was performed on a nutator at room temperature for 20 min with 300 μl elution buffer (0.1 M NaHCO3, 1% SDS) containing proteinase K (1 ml elution buffer and 5 μl proteinase K (30 mg/μl) and the sample centrifuged for 2 min at 2500 rpm at room temperature. The supernatant was kept and the elution step repeated. Elution fractions were pooled and reverse cross-linked at 65ºC over night. DNA was isolated with the Qiagen PCR purification kit and eluted in 50 μl H2O and DNA concentration determined by Pico Green Assay. 20 ng of DNA was amplified (Single end primers, Illumina) and analyzed on a 2100 Bioanalyzer (Agilent Technologies) before submitted to sequencing (Genome Analyzer, Illumina).  ChIP-sequencing of eye-antenna imaginal discs was performed following (Papp and Muller 2006). Samples were biorupted and processed as described above.

value: eye-antanna imaginal discs

tag: antibody

tag: ChIP

tag: genotype/variation

value: Jarid2 mutant


title: eyedisc_mb_suz12

value: rb-α-Su(z)12 full length (Jürg Müller)


title: eyedisc_wt_suz12

value: wild type


title: hnrnpl si23 ChIP-Seq

value: hnRNP L

value: Sigma-Aldrich


title: larvae_mb_h3

source_name: whole larvae

value: 3rd instar larvae

value: m-α-HA (Covance, MMS-101P)


title: larvae_e0_h3k27me3

value: rb-α-H3K27me3 (Active Motif, 39155)


title: larvae_e0_wce


title: larvae_e0_h3


title: larvae_mb_jarid2

value: rb-α-Jarid2 (Masamitsu Yamaguchi)


title: larvae_e0_jarid2


title: larvae_wt2_h3


title: eyedisc_wt_wce


title: hnrnpl sictrl ChIP-Seq


title: larvae_wt2_h3k27me3


title: larvae_e0_suz12


title: larvae_wt1_h3


title: larvae_wt1_h3k27me3


title: larvae_mb_h3k27me3


title: larvae_wt2_wce


title: larvae_wt1_wce


title: larvae_wt2_suz12


title: larvae_wt1_suz12


title: Chromatin accessibility assay of Fetal Renal Cortex; DS20568

status: Public on Feb 22 2012

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20568
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11583
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11582
****************
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: GSM878667_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24493.DS20568.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20568.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-24493, Library DS20568 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.12760
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,055,205
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4877
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4829
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.995
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5319
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM878667_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24493.DS20568.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20568.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-24493, Library DS20568 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.12818
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FRC DNase 93 68
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24493 Library DS20568 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,055,205
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4877
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4829
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.995
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5319
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, renal, cortex primary tissue, day 89; DS20568

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Renal Cortex

tag: molecule

value: genomic DNA

tag: disease

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 89

value: Female

value: Chromatin Accessibility

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Kidney; DS20564

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20564
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11595
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11594
****************
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: GSM878666_UW.Fetal_Kidney.ChromatinAccessibility.H-24507.DS20564.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20564.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-24507, Library DS20564 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.12789
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,760,462
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3685
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3651
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9931
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4265
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM878666_UW.Fetal_Kidney.ChromatinAccessibility.H-24507.DS20564.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20564.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney, Donor H-24507, Library DS20564 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.12847
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FK DNase 07 64
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-24507 Library DS20564 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,760,462
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3685
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3651
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9931
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4265
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney primary tissue, day 121; DS20564

value: Fetal Kidney

value: day 121


title: larvae_wt2_jarid2

tag: tissue

value: wild type


title: larvae_mb_suz12

value: 3rd instar larvae

value: rb-α-Su(z)12 full length (Jürg Müller)

value: Jarid2 mutant


title: larvae_wt1_jarid2

value: rb-α-Jarid2 (Masamitsu Yamaguchi)


title: Chromatin accessibility assay of Fetal Stomach; DS20546

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20546
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11294
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11293
****************
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: GSM878665_UW.Fetal_Stomach.ChromatinAccessibility.H-24507.DS20546.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20546.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24507, Library DS20546 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.12733
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,924,782
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3759
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.3697
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9931
IROC_PERCENTILE: 38
POISSON_SCORE: 0.429
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM878665_UW.Fetal_Stomach.ChromatinAccessibility.H-24507.DS20546.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20546.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-24507, Library DS20546 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.12791
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FS DNase 07 46
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24507 Library DS20546 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,924,782
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3759
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.3697
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9931
IROC_PERCENTILE: 38
POISSON_SCORE: 0.429
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fetal Stomach primary tissue, day 121; DS20546

value: Fetal Stomach


title: Chromatin accessibility assay of Fetal Placenta; DS20346

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20346
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11434
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11433
****************
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: GSM878659_UW.Fetal_Placenta.ChromatinAccessibility.H-24409.DS20346.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20346.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Placenta, Donor H-24409, Library DS20346 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.12747
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,566,125
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4505
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4341
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9969
IROC_PERCENTILE: 78
POISSON_SCORE: 0.4936
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878659_UW.Fetal_Placenta.ChromatinAccessibility.H-24409.DS20346.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20346.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Placenta, Donor H-24409, Library DS20346 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.12805
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FP DNase 09 46
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta DNase Hypersensitivity Donor H-24409 Library DS20346 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,566,125
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4505
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4341
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9969
IROC_PERCENTILE: 78
POISSON_SCORE: 0.4936
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Placenta primary tissue, day 113; DS20346

value: Fetal Placenta

value: genomic DNA

value: day 113


title: Chromatin accessibility assay of Fetal Thymus; DS20335

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20335
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11276
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11275
****************
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: GSM878656_UW.Fetal_Thymus.ChromatinAccessibility.H-24401.DS20335.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20335.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-24401, Library DS20335 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.12776
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,220,507
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3546
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3522
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.998
IROC_PERCENTILE: 95
POISSON_SCORE: 0.3718
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878656_UW.Fetal_Thymus.ChromatinAccessibility.H-24401.DS20335.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20335.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-24401, Library DS20335 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.12834
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FT DNase 01 35
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-24401 Library DS20335 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,220,507
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3546
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3522
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.998
IROC_PERCENTILE: 95
POISSON_SCORE: 0.3718
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Thymus primary tissue, day 108; DS20335

value: Fetal Thymus

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: day 108

value: Male


title: Chromatin accessibility assay of Fetal Adrenal Gland; DS20343

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20343
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11626
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11631
****************
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: GSM878658_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24409.DS20343.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20343.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Adrenal Gland, Donor H-24409, Library DS20343 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.12734
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,016,826
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3408
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3389
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9931
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4152
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM878658_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24409.DS20343.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20343.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Adrenal Gland, Donor H-24409, Library DS20343 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.12792
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FAG DNase 09 43
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-24409 Library DS20343 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,016,826
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3408
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3389
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9931
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4152
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Adrenal Gland primary tissue, day 113; DS20343

value: Fetal Adrenal Gland

value: fetal

value: Female

value: Chromatin Accessibility

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Spinal Cord; DS20530

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20530
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11306
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11305
****************
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: GSM878663_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24493.DS20530.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20530.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Spinal Cord, Donor H-24493, Library DS20530 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.12779
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,763,064
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3502
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3435
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9888
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4106
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM878663_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24493.DS20530.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20530.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Spinal Cord, Donor H-24493, Library DS20530 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.12837
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FSC DNase 93 30
BROWSER_TRACK_DESCRIPTION: UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24493 Library DS20530 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,763,064
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3502
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3435
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9888
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4106
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Fetal Spinal, Cord primary tissue, day 89; DS20530

value: Fetal Spinal Cord

value: day 89


title: kdrl:egfp-pos microRNA

status: Public on Feb 28 2012

city: Worcester

first: Abirami

last: Lakshmanan

state: Massachusetts

address: 55 Lake Avenue North

department: PGFE

institute: Umass Medical School

description:
GFPplus
microRNA

data_processing: The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR-Deep2.

organism: Danio rerio

source_name: FACS-isolated kdrl:egfp-positive cells

extract_protocol: Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters, followed by cDNA synthesis and amplification with Illumina primers.

treatment_protocol: Tg(kdrl:egfp) embryos were dissociated at 24 hours post fertilization (hpf), followed by fluorescence-activated cell sorting to isolate GFP-positive and -negative cells.

tag: genotype

tag: age

value: 24 hpf

tag: developmental stage

value: embryo

tag: cell type

value: endothelial cells


title: Chromatin accessibility assay of Fetal Muscle, Trunk; DS20242

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20242
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11447
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11446
****************
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: GSM878654_UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24409.DS20242.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20242.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Trunk, Donor H-24409, Library DS20242 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.12737
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,977,886
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4924
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4739
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9939
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5254
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM878654_UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24409.DS20242.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20242.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Trunk, Donor H-24409, Library DS20242 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.12795
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FMT DNase 09 42
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24409 Library DS20242 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,977,886
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4924
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4739
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9939
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5254
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Muscle, Trunk primary tissue, day 113; DS20242

value: Fetal Muscle, Trunk

value: genomic DNA

value: day 113


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS20239

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20239
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11454
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11453
****************
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: GSM878653_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24409.DS20239.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20239.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24409, Library DS20239 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.12783
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,071,646
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.5743
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5575
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9943
IROC_PERCENTILE: 57
POISSON_SCORE: 0.6049
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM878653_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24409.DS20239.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20239.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24409, Library DS20239 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.12841
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FML DNase 09 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24409 Library DS20239 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,071,646
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.5743
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5575
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9943
IROC_PERCENTILE: 57
POISSON_SCORE: 0.6049
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Muscle, Leg primary tissue, day 113; DS20239

value: Fetal Muscle, Leg

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue


title: Chromatin accessibility assay of Fetal Brain; DS20226

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20226
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11613
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11612
****************
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: GSM878651_UW.Fetal_Brain.ChromatinAccessibility.H-24297.DS20226.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20226.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-24297, Library DS20226 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.12767
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,241,895
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.5644
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5538
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9966
IROC_PERCENTILE: 74
POISSON_SCORE: 0.5717
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM878651_UW.Fetal_Brain.ChromatinAccessibility.H-24297.DS20226.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20226.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Brain, Donor H-24297, Library DS20226 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.12825
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FB DNase 97 26
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-24297 Library DS20226 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,241,895
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.5644
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5538
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9966
IROC_PERCENTILE: 74
POISSON_SCORE: 0.5717
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Fetal Brain primary tissue, day 104; DS20226

value: Fetal Brain

value: UW

value: day 104

value: Male


title: Chromatin accessibility assay of Fetal Muscle, Trunk; DS20544

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20544
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11440
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11439
****************
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: GSM878664_UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24507.DS20544.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20544.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Trunk, Donor H-24507, Library DS20544 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.12740
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,919,608
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3626
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3445
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9935
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4057
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM878664_UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24507.DS20544.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20544.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Trunk, Donor H-24507, Library DS20544 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.12798
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FMT DNase 07 44
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24507 Library DS20544 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,919,608
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3626
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3445
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9935
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4057
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Muscle, Trunk primary tissue, day 121; DS20544

value: fetal

value: day 121

value: Female

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Renal Pelvis; DS20448

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20448
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11575
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11574
****************
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: GSM878662_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24477.DS20448.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20448.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-24477, Library DS20448 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.12735
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 57,849,885
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4365
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4249
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9914
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4852
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878662_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24477.DS20448.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20448.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-24477, Library DS20448 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.12793
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FRP DNase 77 48
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24477 Library DS20448 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 57,849,885
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4365
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4249
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9914
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4852
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Kidney, renal, pelvis primary tissue, day 103; DS20448

value: Fetal Renal Pelvis

value: day 103

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Spinal Cord; DS20351

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20351
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11312
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11311
****************
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: GSM878661_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24409.DS20351.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20351.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Spinal Cord, Donor H-24409, Library DS20351 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.12778
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,435,119
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3963
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.3851
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9917
IROC_PERCENTILE: 22
POISSON_SCORE: 0.4452
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM878661_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24409.DS20351.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20351.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Spinal Cord, Donor H-24409, Library DS20351 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.12836
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FSC DNase 09 51
BROWSER_TRACK_DESCRIPTION: UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24409 Library DS20351 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,435,119
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3963
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.3851
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9917
IROC_PERCENTILE: 22
POISSON_SCORE: 0.4452
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Spinal, Cord primary tissue, day 113; DS20351

value: Fetal Spinal Cord


title: Chromatin accessibility assay of Fetal Stomach; DS20349

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20349
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11300
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11299
****************
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: GSM878660_UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20349.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24401, Library DS20349 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.12742
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,089,889
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3466
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.3382
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9908
IROC_PERCENTILE: 12
POISSON_SCORE: 0.4111
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878660_UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20349.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-24401, Library DS20349 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.12800
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FS DNase 01 49
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24401 Library DS20349 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,089,889
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3466
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.3382
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9908
IROC_PERCENTILE: 12
POISSON_SCORE: 0.4111
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Stomach primary tissue, day 108; DS20349

value: Fetal Stomach

value: genomic DNA

value: day 108


title: Chromatin accessibility assay of Fetal Brain; DS20231

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20231
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11607
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11606
****************
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: GSM878652_UW.Fetal_Brain.ChromatinAccessibility.H-24381.DS20231.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20231.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-24381, Library DS20231 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.12749
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,413,041
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4208
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.4124
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9937
IROC_PERCENTILE: 45
POISSON_SCORE: 0.4527
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM878652_UW.Fetal_Brain.ChromatinAccessibility.H-24381.DS20231.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20231.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Brain, Donor H-24381, Library DS20231 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.12807
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FB DNase 81 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-24381 Library DS20231 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,413,041
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4208
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.4124
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9937
IROC_PERCENTILE: 45
POISSON_SCORE: 0.4527
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Brain primary tissue, day 109; DS20231

value: University of Washington, Congenital Defects Lab. Ian Glass

value: day 109


title: larvae_mb_wce

data_processing: Filtered reads were then aligned to the fly genome (UCSC dm3) using the bowtie (Langmead et al., 2009) alignment tool, version 0.12.7.  Only those sequences that matched uniquely to the genome with up to two mismatches were retained for subsequent analysis.  Enriched regions of ChIP-seq signal for Jarid2 and Su(z)12 were determined by the ‘MACS’ (Zhang et al., 2008) peak-finding program, version 1.4.0rc2.  Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively.  The effective genome size was configured appropriately for the fly datasets, and the p-value cutoff was set to 1.00e-08 or FDR < 1%, and a fold-change greater than four.  All other MACS parameters were left default.

source_name: whole larvae

value: 3rd instar larvae

value: Jarid2 mutant


title: Chromatin accessibility assay of Fetal Thymus; DS20341

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20341
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11270
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11269
****************
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: GSM878657_UW.Fetal_Thymus.ChromatinAccessibility.H-24409.DS20341.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20341.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-24409, Library DS20341 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.12750
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,969,268
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3818
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3765
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9974
IROC_PERCENTILE: 86
POISSON_SCORE: 0.4052
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878657_UW.Fetal_Thymus.ChromatinAccessibility.H-24409.DS20341.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20341.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-24409, Library DS20341 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.12808
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
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 7
BROWSER_TRACK_NAME: FT DNase 09 41
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-24409 Library DS20341 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,969,268
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3818
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3765
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9974
IROC_PERCENTILE: 86
POISSON_SCORE: 0.4052
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Thymus primary tissue, day 113; DS20341

value: Fetal Thymus

value: Primary Tissue

value: UW

value: day 113


title: kdrl:egfp-min microRNA

description:
GFPminus
microRNA

source_name: FACS-isolated egfp-negative cells

value: 24 hpf

value: embryo

value: non-endothelial cells