title: Col_RNASeq_SOLiD

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

country: China

institute: Institute of Genetics and Developmental Biology

data_processing: The reads sequences from SOLiD system were aligned to Arabidopisis TAIR9 genome sequence using color space alignment software Bowtie (Langmead et al., 2009), allowing up to two mismatches. Then all unmapped reads were aligned to splicing junction sequences which were extracted from TAIR9 gene annotation.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: wild-type

growth_protocol: The wild-type Col and atprmt5 mutants were grown on Murashige and Skoog plates with 3% Suc for 12 days at 23°C under 16 h of light followed by 8 h of darkness

extract_protocol: Total RNA extracted from wild-type Col and atprmt5 mutants were selected for polyadenylated RNA using the Oligotex mRNA mini kit (Qiagen). The libraries were prepared according to SOLiDTM Whole Transcriptome Analysis Kit Protocol (PN 4409491). In brief, poly(A) RNA was firstly treated with RNase III and ~50-150 nt of fragmented RNA was isolated using Ambion flashPAGETM Fractionator System and flashPAGE Reaction Clean-Up Kit. The size-selected RNA was then hybridized with Adaptor Mix A, a set of RNA/DNA oligonucleotides with single-stranded degenerate sequence at one end and a defined sequence required for SOLiD sequencing at the other end. Then using RNA ligase, the adaptors were ligated to the fragmented RNA molecules. Next, reverse transcription was performed to generate cDNA. Treatment with RNase H follows, to digest the RNA from RNA/cDNA duplexes. The generated cDNA library was PCR amplified with the supplied primer sets for 15-18 cycles. PCR products ~140-200bp in length were isolated by PAGE. The purified cDNA library was attached to beads at the emulsion PCR step of the SOLiD sample preparation workflow, and was sequenced on the AB SOLiD System 2.0.

treatment_protocol: The seedlings were ground into a fine power in liquid nitrogen and processed using Trizol reagent (Invitrogen).

tag: ecotype

value: Col-O

tag: genotype/variation

value: wild-type

value: seedlings


title: prmt5_RNASeq_SOLiD

status: Public on Oct 07 2010

type: SRA

library_source: transcriptomic

source_name: atprmt5 mutant

value: atprmt5 mutant

tag: tissue


title: h_Tumour9_MBD_M

status: Public on Oct 05 2010

city: Edinburgh

first: Adrian

middle: P

last: Bird

state: Midlothian

address: Mayfield Road

department: WTCCB

country: United Kingdom

institute: The University of Edinburgh

description: MBD affinity chromatography

library_source: genomic

data_processing: Alignment: Single-end sequence reads were mapped to the mouse genome (NCBIm37) using MAQ (http://maq.sourceforge.net/). Reads with a mapping score greater or equal to 30 where retained. Alignment was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.

molecule: genomic DNA

organism: Homo sapiens

source_name: Colorectal Tumour

extract_protocol:
DNA was extracted using phenol/chloroform and sheared to approximately 400 bp using sonication. Methylated DNA was purified by two step MBD Affinity Purification as described in Skene et al., 2010.
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.

value: Colorectal Tumour

tag: age

tag: chip antibody/mbd affinity column

value: MBD Affinity Purifcation (MAP)-seq (recombinant human MBD domain)


title: h_Escell_PolII_M

description: Chromatin IP against RNA Polymerase II

source_name: ES cells

extract_protocol:
ES cells were crosslinked using 1% formaldehyde. Chromatin was sheared using sonication. Protein-DNA complexes were immunoprecipitated with an RNA Ploymerase II antibody and the DNA was subsequently extracted using the genomic tip 500/G kit from Qiagen (cat no. 10262).
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.

tag: cell type

value: ES cells

tag: cell line

value: Shef 4 cells

value: anti-RNA Polymerase II (ab817; Abcam)


title: h_Tumour6_MBD_F

description: MBD affinity chromatography


title: h_Escell_H3K4me3_M

description: Chromatin IP against H3K4me3

extract_protocol:
ES cells were crosslinked using 1% formaldehyde. Chromatin was sheared using sonication. Protein-DNA complexes were immunoprecipitated with an H3K4me3 antibody and the DNA was subsequently extracted using the genomic tip 500/G kit from Qiagen (cat no. 10262).
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.

value: anti-H3K4me3 (ab8580; Abcam)


title: h_Tumour10_MBD_F

description: MBD affinity chromatography


title: h_Tumour5_MBD_M

description: MBD affinity chromatography


title: m_Escell_PolII_M

description: Chromatin IP against RNA Polymerase II

organism: Mus musculus

value: E14 TG2a


title: h_Colon10_MBD_F

description: MBD affinity chromatography

source_name: Colon Mucosa

value: Colon Mucosa


title: h_Colon9_MBD_M

description: MBD affinity chromatography


title: m_Cerebellum_MBD_F

description: MBD affinity chromatography

source_name: Cerebellum

value: Cerebellum

value: 15 weeks


title: m_Escell_H3K4me3_M

description: Chromatin IP against H3K4me3


title: h_Colon6_MBD_F

description: MBD affinity chromatography


title: m_Blood_MBD_F

description: MBD affinity chromatography

source_name: Blood

value: Blood


title: h_Colon3_MBD_F

description: MBD affinity chromatography


title: h_Colon5_MBD_M

description: MBD affinity chromatography


title: m_Blood_MBD_M

description: MBD affinity chromatography

value: 30 weeks


title: h_Cerebellum_MBD_F

description: MBD affinity chromatography

value: pooled:44,49 and 51


title: m_Sperm_MBD_M

description: MBD affinity chromatography

source_name: Sperm

value: Sperm


title: h_Blood_MBD_M

description: MBD affinity chromatography

value: pooled:24,26 and 61


title: epitheliumbreast-normal-N1

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: Sage-Seq

data_processing: Sequencing was carried out at the Wistar Institute. The first 17bps of each read is used as a tag. The number of each unique tag is counted.   Processed data file includes tag sequences (17bps) in the first column and counts (frequencies) in the second column. Illumina software pipeline OLB version 1.6, 1.7, 1.8 with CASAVA 1.5 was used for generation  of sequence: frequency processed files.

molecule: total RNA

source_name: reduction mammoplasty

extract_protocol:
cDNA made from polyA RNA isolated from purified cells using antibody attached to beads were fragmented with NlaIII/MmeI restriction enzyme with subsequent adapter ligation.
Details of antibodies used in study:
CD24-Antibody: Vendor: BD-Pharmingen, Cat.#: 555426
CD44-Antibody: Vendor: BD-Pharmingen, Cat.#: 550988
CD201(EPCR)-Antibody: Vendor: BD-Pharmingen, Cat.#: 552500

value: breast

value: epithelial cell

tag: disease state

value: normal

tag: cell marker


title: h_Cerebellum_MBD_M

description: MBD affinity chromatography

value: pooled:41,50 and 54

value: MBD Affinity Purifcation (MAP)-seq (recombinant human MBD domain)


title: m_Cerebellum_CXXC_M

description: CXXC affinity chromatography

extract_protocol:
DNA was extracted using phenol/chloroform and sheared to approximately 400 bp using sonication. Non-methylated DNA was purified by single step CXXC Affinity Purification at 600mM NaCl as described in Illingworth et al., 2010.
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.

tag: strain

value: CXXC Affinity Purifcation (CAP)-seq (recombinant mouse CXXC domain)


title: ActivatedBCell_PolII

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
fastq: ***Raw data*** Image analysis, base calling, quality filtering:  Standard settings of GAPipeline 1.3+ using PhiX control; Fastq files contain full length reads (36nts) that passed the chastity filter. If necessary, quality scales were adjusted to phred64.
bedGraph: ***Peak finder results***.  Density of non-redundant alignments was determined in 100nt bins along the genome.  SICER 1.03 was used to detect regions of enrichment over a theoretical background model (e=0.00001).  BedGraph files show density in enriched regions only.

growth_protocol: CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech).  Following isolation, resting B cells were stimulated with LPS (50 mcg/ml) and IL-4 (2.5 ng/ml) for 72 hrs.

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37°C for 10 minutes followed by quenching with glycine and sonication. Chromatin fragments were then immunoprecipitated with the antibodies shown in the sample characteristics following standard protocols. Immunoprecipitates were processed following Illumina’s protocol and sequenced on a Genome Analyzer II.

value: in vitro activated B cells

tag: chip target

value: PolII

tag: chip antibody

value: Abcam (4H8) ab5408


title: m_CerebellumLowNaCl_CXXC_M

description: CXXC affinity chromatography

extract_protocol:
DNA was extracted using phenol/chloroform and sheared to approximately 400 bp using sonication. Non-methylated DNA was purified by single step CXXC Affinity Purification at 550mM NaCl as described in Illingworth et al., 2010.
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.


title: m_BloodLowNaCl_CXXC_M

description: CXXC affinity chromatography


title: h_Blood_MBD_F

description: MBD affinity chromatography


title: m_Blood_CXXC_M

description: CXXC affinity chromatography


title: h_Sperm_MBD_M

description: MBD affinity chromatography


title: h_Cerebellum_CXXC_M

description: CXXC affinity chromatography


title: h_Tumour3_MBD_F

description: MBD affinity chromatography

value: Colorectal Tumour


title: m_SpermLowNaCl_CXXC_M

description: CXXC affinity chromatography


title: h_Sperm_CXXC_M

description: CXXC affinity chromatography


title: h_Blood_CXXC_M

description: CXXC affinity chromatography


title: m_Sperm_CXXC_M

description: CXXC affinity chromatography


title: ActivatedBCell_Spt5_rep1

value: Santa Cruz Biotechnology anti-Spt5 (H300)


title: ActivatedBCell_Spt5_rep2


title: Ath_rdr6_smRNA

status: Public on Oct 04 2010

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

description:
rdr6_smRNA
small RNA

3' adaptor sequence: TCGTATGCCGTCTTCTGCTTG

data_processing:
Abundance info of NR-seq (*info.txt file): All reads are reduced to non-redundant (NR) sequences at first to minimize the computational requirement for subsequent analysis steps. Only NR-seq that can map to the Arabidopsis thaliana genome (TAIR9 assembly) are shown (either trimmed or untrimmed).

NR-seq after trimming of 3'-adapters (*seq.fasta file): In order to detect 3’-adapter sequences, all NR-sequences are aligned to the Illumina 3'-adapter version 1.5 sequence using the “cross-match” program. The alignment parameters for cross-match are carefully tuned to maintain all alignments with less than 6% mis-matches. The cross-match alignment results are parsed using in-house Perl scripts. All NR-sequences that align to ≥ 6 bp of the 3’-adapter sequence at their 3’ end are defined as short and are subsequently trimmed at the adapter-sequence boundary. The remaining NR-sequences (without detectable 3’-adapters) remain “untrimmed”. Only NR-seq that can map to the Arabidopsis thaliana genome (TAIR9 assembly) are shown.

Alignment (*loc.txt file): All trimmed and untrimmed NR-sequences are aligned to the Arabidopsis genome (TAIR9 assembly) using cross-match, with the program parameters set to guarantee all sequences that align with ≤ 6% mis-matches to the Arabidopsis genome. Alignment results for trimmed or untrimmed inputs are then parsed independently using in-house Perl scripts. More specifically, alignments for trimmed sequences are required to extend to the ends of the query sequences, whereas alignments for untrimmed sequences are only required to extend to the imaginary positions of undetectable 3’-adapters (< 6 bp from the 3’ end of the sequence). The true lengths of the untrimmed sequences are also determined in this step by the most-frequent aligned length of all possible alignments to the Arabidopsis genome. At last, trimmed and untrimmed NR-sequences, as well as their genome loci information, are combined to form the final dataset using in-house Perl scripts. The smRNA libraries are pre-processed by this balanced pipeline as well.

source_name: unopened flower buds, rdr6, smRNA

extract_protocol: Total RNA is subjected to one (1X Ribominus) or two (2X Ribominus) rounds of rRNA depletion as per manufacturer’s instructions (Ribominus, Invitrogen (Carlsbad, CA)). Next, these rRNA-depleted RNA samples are treated with a single-strand specific ribonuclease as per manufacturer’s instructions (RNase One, Promega (Madison, WI)). The RNA sample is then used as the substrate for sequencing library construction using the Small RNA Sample Prep v1.5 kit (Illumina, San Diego, CA) as per manufacturer’s instructions.

tag: ecotype background

tag: genotype

value: rdr6 mutant

value: unopened flower buds

tag: target-molecules

value: small RNAs (smRNAs)


title: ActivatedBCell_AID

value: AID

value: Rabbit polyclonal described in Chaudhuri et al., Nature (2003)


title: Ath_rdr6_dsRNA

description:
rdr6_dsRNA
dsRNA

3' adaptor sequence: TCGTATGCCGTCTTCTGCTTG

source_name: unopened flower buds, rdr6, dsRNA

value: double-stranded RNAs (dsRNAs)

tag: rrna depletion

value: 1-round rRNA depletion (1X Ribominus)

tag: rna-treatment

value: ssRNase (Rnase One)


title: Ath_col0_smRNA

description:
col0_smRNA
small RNA

3' adaptor sequence: TCGTATGCCGTCTTCTGCTTG

source_name: unopened flower buds, wild-type, smRNA

tag: ecotype

value: wild-type


title: Ath_col0_dsRNA_1Xribominus

description:
col0_dsRNA_1Xribo
dsRNA

3' adaptor sequence: TCGTATGCCGTCTTCTGCTTG

source_name: unopened flower buds, wild-type, dsRNA


title: Piwi bound piRNAs from tj GAL4 > RNAi-zuc ovaries

city: Vienna

first: Julius

last: Brennecke

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

description: small RNAs from Piwi immuno-precipitation

data_processing: raw reads start at their 5'end with the first base of the small RNA; at the 3' end, reads contain the 3' linker used for library generation (sequence: TCGTATGCCGTCTTCTGCTTG); this linker was trimmed bioinformatically and resulting reads matching the release5 genome sequence of D. melanogaster were the basis for the processed data file.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: flies were grown at 25 degrees on standard medium

extract_protocol: ovary lysate was cleared by centrifugation and Piwi-piRNA complexes were isolated using polyclonal rabbit antibodies directed against the Piwi N-terminus. piRNAs were isolated from beads using Phenol-Chloroform; piRNAs were cloned as described in Brennecke et al. 2007.

tag: developmental stage

value: 4d old flies

tag: genotype/variation


title: Piwi bound piRNAs from tj GAL4 > RNAi-piwi ovaries


title: Piwi bound piRNAs from tj GAL4 > RNAi-fs(1)Yb ovaries


title: Piwi bound piRNAs from tj GAL4 > RNAi-armi ovaries


title: H3K79me2 ChipSeq in human ES cells

status: Public on Oct 01 2010

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against H3K79me2 in human ES cells

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Embyonic stem cells

growth_protocol: hES cells were grown in mTESR media (Stem Cell Technologies) on plates coated with matrigel (BD Biosciences) in the absence of feeder cells.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: Abcam AB3594

value: BGO3 (feeder free)


title: H3K27me3 ChIPseq in human ES cells

description: Chromatin IP against H3K27me3 in human ES cells

value: Abcam AB6002


title: Suz12 ChipSeq in human ES cells

description: Chromatin IP against Suz12 in human ES cells

value: Abcam AB12073


title: ChIP-Seq for E2F4 in 2nd MEF

description: Chromatin IP against E2F4

source_name: Mouse Embryonic Fibroblasts with Dox-inducible Klf4, Sox2 and Oct4 (KSO)

growth_protocol: Oct4/Klf4/Sox2-inducible iPS cells with Oct4-selectable cassette were derived in the presence of Wnt3a-conditioned medium and were injected into BDF2 blastocysts. Secondary fibroblasts were harvested from the resulting chimeric embryos at 13.5dpc. Fibroblasts derived from the injected iPS cells were selected for with 2µg/ml puromycin for 48 hours. Cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% cosmic calf serum, β-mercaptoethanol, nonessential amino acids, L glutamine and penicillin/streptomycin.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Santa Cruz SC-1082

value: Secondary


title: WCE in 2nd MEF 1

description: WCE in 2nd MEF


title: ChIP-Seq for RNA Pol II in 2nd MEF

description: Chromatin IP against RNA Pol II

value: RNA Pol II (8WG16)

value: Covance MMS-126R


title: ChIP-Seq for H3K27me3 in 2nd MEF

description: Chromatin IP against H3K27me3


title: 3T3L1_t4_CTCF

status: Public on Sep 30 2010

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

description: Chromatin IP against CTCF

data_processing:
Alignments: Reads were aligned to the mouse reference genome (mm9) using MAQ v0.6.8 with default parameters, except '-C 10' (discard reads that match to more than 10 locations). Redundant reads (alinign to the same starting position and orientation) were discarded.
Densities: Aligned reads were extended to an assumed fragment length of 200 bp. The number of fragments overlapping nucleotide x in the reference sequnece were counted at 25bp resolution. The counts were then normalized to 'fragments per 10 million aligned reads'.
Peak calling (histones): The numbers of aligned ChIP and input reads were counted in sliding windows of 500 bp for H3K4me3/me2/me1/K27ac and 5000bp H3K27me3/K36me3 and a step size of 25bp. The likelihood of the null hypothesis (no ChIP enrichment) was calculated as the probability of observing at least the number of ChIP reads, given a Poisson distribution with a mean equal to the expected number of ChIP reads (given the window size, the genome size and the total number of aligned reads) multiplied by the ratio of observed over expected input reads in the same window. Windows with p < 0.0001 after Benjamini correction for multiple-hypothesis testing were kept and merged into non-overlapping intervals of arbitrary size.
Peak calling (CTCF and PPARG): Binding sites and ChIP enrichment intervals were inferred using QuEST v2.3 (Valouev et al. Nat Methods 2008; 5(9):829-834; PMID: 19160518) in the 'transcription factor' mode.

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

extract_protocol: ChIP-Seq libraries were prepared as described by Mikkelsen et al. (Nature 2007; 448(7153):553-60; PMID: 17603471)

value: 3T3-L1 adipocytes

tag: time (relative to induction)

value: day 7

tag: chip epitope

value: CTCF


title: 3T3L1_t4_PpargAb2

description: Chromatin IP against PPARG (81B8)

tag: cell type

value: PPARG (81B1)

value: Call Signaling Technologies, Cat# 2443, Lot# 5/29/2007


title: 3T3L1_t4_H3K4me1

description: Chromatin IP against H3K4me1


title: 3T3L1_t4_H3K4me2

description: Chromatin IP against H3K4me2

value: Abcam, Cat# ab7766, Lot# 56293


title: 3T3L1_t4_PpargAb1

description: Chromatin IP against PPARG (H-100)

value: PPARG (H-100)

value: SCBT, Cat# SC-7196X, Lot# A0380


title: 3T3L1_t4_H3K27me3

description: Chromatin IP against H3K27me3


title: 3T3L1_t3_CTCF

description: Chromatin IP against CTCF

value: day 2


title: Ath_col0_dsRNA_2Xribominus

description:
col0_dsRNA_2Xribo
dsRNA

3' adaptor sequence: ATCTCGTATGCCGTCTTCTGCTTG

value: wild-type

tag: tissue

value: unopened flower buds

value: double-stranded RNAs (dsRNAs)

value: 2-round rRNA depletion (2X Ribominus)

value: ssRNase (Rnase One)


title: 3T3L1_t4_H3K4me3

description: Chromatin IP against H3K4me3


title: 3T3L1_t3_H3K36me3

description: Chromatin IP against H3K36me3


title: Piwi bound piRNAs from tj GAL4 > RNAi-aub ovaries

value: 4d old flies


title: 3T3L1_t3_H3K27ac

description: Chromatin IP against H3K27ac

value: Abcam, Cat# ab4729, Lot# 31456


title: 3T3L1_t3_H3K4me1

description: Chromatin IP against H3K4me1


title: WCE in 2nd MEF B2

description: WCE in 2nd MEF

value: Secondary


title: 3T3L1_t3_H3K4me2

description: Chromatin IP against H3K4me2

value: 3T3-L1 adipocytes


title: 3T3L1_t2_H3K36me3

description: Chromatin IP against H3K36me3

value: 3T3-L1 pre-adipocytes

value: day 0


title: 3T3L1_t3_H3K4me3

description: Chromatin IP against H3K4me3


title: 3T3L1_t2_H3K27me3

description: Chromatin IP against H3K27me3


title: 3T3L1_t2_H3K27ac

description: Chromatin IP against H3K27ac


title: 3T3L1_t2_CTCF

description: Chromatin IP against CTCF

value: CTCF


title: 3T3L1_t2_H3K4me1

description: Chromatin IP against H3K4me1


title: 3T3L1_t4_H3K36me3

description: Chromatin IP against H3K36me3

value: day 7


title: 3T3L1_t4_H3K27ac

description: Chromatin IP against H3K27ac


title: 3T3L1_t2_H3K4me3

description: Chromatin IP against H3K4me3


title: 3T3L1_t3_H3K27me3

description: Chromatin IP against H3K27me3


title: 3T3L1_t1_H3K4me2

description: Chromatin IP against H3K4me2

value: day -2

value: Abcam, Cat# ab7766, Lot# 56293


title: 3T3L1_t1_H3K27me3

description: Chromatin IP against H3K27me3


title: 3T3L1_t1_H3K4me1

description: Chromatin IP against H3K4me1


title: KO2_litter2_8wk

city: Los Angeles

first: Yi

last: Sun

state: CA

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

data_processing: Analysis of small RNA raw datasets (csfasta files) was done with ABI SOLiD’s small RNA Analysis Tool V0.50 (RNA2MAP). All raw reads are aligned to filter sequences that include rRNA, tRNA, adaptor, polyA, polyG, polyT and polyC sequences. Alignment is based only on the first 25 bases of the read with 2 mismatches allowed. The remaining reads that have no alignment to the filter sequences are subsequently mapped to annotated mouse miRNA precursor sequences (miRBASE version 15, retrieved from ftp://mirbase.org/pub/mirbase/).  Alignment is based on first 18 bases of the read with 3 mismatches allowed. Once an alignment is found, the algorithm attempts to find the adaptor location. A test read is created by combining bases from the genome and adaptor sequence and compared against the full length read, a step that tries all possible starting points of the adaptor. The one that minimizes the number of mismatches is used and the small RNA size is determined.

growth_protocol: WT and KO littermate mice were maintained under standard conditions.

extract_protocol: Small RNA species (<200bp) were isolated and purified using the Invitrogen PureLink™ miRNA Isolation Kit. We subsequently prepared small RNA libraries for each animal and sequenced individual library separately according to small RNA sequencing procedures of the SOLiD total RNA-seq kit protocol (Applied Biosystems).

tag: age

value: Postnatal 8-week

value: Cerebellum

value: Mecp2tm1.1Jae/+, mix background (129, C57BL/6 and BALB/c) backcrossed with BALB/c for >6 generations


title: WT_litter2_8wk

tag: strain


title: KO1_litter2_8wk


title: 3T3L1_t1_H3K27ac

description: Chromatin IP against H3K27ac


title: 3T3L1_t1_H3K36me3

description: Chromatin IP against H3K36me3


title: 3T3L1_t1_CTCF

description: Chromatin IP against CTCF


title: 3T3L1_t1_H3K4me3

description: Chromatin IP against H3K4me3


title: WT_litter1_8wk


title: KO1_litter1_8wk


title: 3T3L1_WCE

description: Whole cell extract (input control)

source_name: 3T3-L1, Whole Cell Extract (input control)

value: 3T3-L1 pre-adipocytes and adipocytes


title: WT_pooled_6wk

data_processing: Sequencing results were obtained as ‘good’ and ‘best’ beads in colorspace by the SOLiD sequence analysis software.  WT and KO samples were distinguished by adding unique barcode-attached amplification primers (provided by the SOLiD SREK kit).  After the usual sequencing reactions, a second set of reactions decoded the barcode sequence. The sequencing reads were aligned to all 590 annotated mouse miRNA precursor sequences (miRBASE version 15, retrieved from ftp://mirbase.org/pub/mirbase/) by the SHRiMP program (version 1.1.0) with default parameters. The sequencing reads were also mapped to sequences of other small non-coding RNAs that were retrieved from the Rfam database release 10 (rRNAs, snRNAs and snoRNAs, ftp://ftp.sanger.ac.uk/pub/databases/Rfam/) and the genomic transfer RNA database (tRNA, http://lowelab.ucsc.edu/GtRNAdb/download.html).  Mapped reads were loaded into a MySQL database and overlapping alignments were analyzed for read counting using custom Python scripts.

extract_protocol: Total RNA samples were extracted using Trizol and ethanol precipitation. 100 ng total RNA were processed into sequencing libraries using the Small RNA Expression Kit (SREK, Applied Biosystems). Briefly, RNA was ligated overnight with the “A” adapters from the kit, reverse transcribed, RNAse H-treated, and PCR-amplified before size selection on polyacrylamide gels to contain 18–30 nt of inserted sequences. After quantification by qPCR, libraries were amplified onto beads using emulsion PCR, deposited on slides, and sequenced.

value: Postnatal 6-week


title: KO_pooled_6wk


title: 3T3L1_t2_H3K4me2

description: Chromatin IP against H3K4me2


title: hASC_t4_H3K36me3

description: Chromatin IP against H3K36me3

data_processing:
Alignments: Reads were aligned to the mouse reference genome (hg18) using MAQ v0.6.8 with default parameters, except '-C 10' (discard reads that match to more than 10 locations). Redundant reads (alinign to the same starting position and orientation) were discarded.
Densities: Aligned reads were extended to an assumed fragment length of 200 bp. The number of fragments overlapping nucleotide x in the reference sequnece were counted at 25bp resolution. The counts were then normalized to 'fragments per 10 million aligned reads'.
Peak calling (histones): The numbers of aligned ChIP and input reads were counted in sliding windows of 500 bp for H3K4me3/me2/me1/K27ac and 5000bp H3K27me3/K36me3 and a step size of 25bp. The likelihood of the null hypothesis (no ChIP enrichment) was calculated as the probability of observing at least the number of ChIP reads, given a Poisson distribution with a mean equal to the expected number of ChIP reads (given the window size, the genome size and the total number of aligned reads) multiplied by the ratio of observed over expected input reads in the same window. Windows with p < 0.0001 after Benjamini correction for multiple-hypothesis testing were kept and merged into non-overlapping intervals of arbitrary size.
Peak calling (CTCF and PPARG): Binding sites and ChIP enrichment intervals were inferred using QuEST v2.3 (Valouev et al. Nat Methods 2008; 5(9):829-834; PMID: 19160518) in the 'transcription factor' mode.

source_name: hASC, ChIP

growth_protocol: hASCs were grown in MesenPRO RS medium (Invitrogen) plus 4ng/ml FGF-2 on plates coated with 10ug/cm2 collagen I (Invitrogen). Two days after confluence, the cells were placed in induction medium (DMEM/F12 supplemented with 10% FBS plus 1uM dexamethasone, 1.7uM insulin, 0.5mM IBMX, 5uM rosiglitazone, 40ng/ml BMP4, 17uM pantothenic acid, and 33uM biotin). 72h later, the medium was replaced with maintenance medium (DMEM/F12 with 10% FBS plus 1uM dexamethasone, 1.7uM insulin, 17uM pantothenic acid, and 33uM biotin) and media was replaced every two days thereafter.

value: Adipose stromal cell (ASC) adipocyte

value: day 9


title: hASC_t4_PpargAb1

description: Chromatin IP against PPARG

value: PPARG (H-100)

value: SCBT, Cat# SC-7196X, Lot# A0380


title: hASC_t4_H3K4me3

description: Chromatin IP against H3K4me3


title: hASC_t4_CTCF

description: Chromatin IP against CTCF


title: hASC_t4_H3K27ac

description: Chromatin IP against H3K27ac

value: Abcam, Cat# ab4729, Lot# 31456


title: hASC_t4_PpargAb2

description: Chromatin IP against PPARG

value: PPARG (81B1)

value: Cell Signaling Technologies, Cat# 2443, Lot# 5/29/2007


title: KO2_litter1_8wk


title: Kc167, untreated, replicate 2 [RNA tag]

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
TAG COUNTS: Adaptor sequences were removed and all identical sequences collated.  See data table below.
GENE COUNTS:  BLAST (Altschul, Stephen F., Gish, Warren, Miller, Webb, Myers, Eugene W., and Lipman, David J. (1990). Basic local alignment search tool. J. Mol. Biol. 215; 403-410) was used to compare all 16/17+4mers sequences to a library of expected tags obtained by extracting the last GATC sequence and the following 19 bases of each transcript annotated in FlyBase 5.17. Sequences with more than 2 mis/non-aligned positions or less than 11 consecutively matching positions, and sequences that mapped to more than one expected tag were discarded. Reads for all transcripts of a gene were added up. Genes with no GATC and genes sharing an expected tag with another gene were set to NA. Finally, the reads per gene were devided by the total number of reads of the sequencing run.  See supplementary file Kc167_DGE_norm_GeneCounts.txt on Series GSE22069 record.

source_name: Embryonic Drosophila cells, Kc167 cells

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C.

extract_protocol: The Illumina protocol 'Digital Gene Expression - Tag profiling with DpnII' was followed. In short, 1 ug of total, DNaseI-digested RNA was bound to oligo(dT)-beads. First strand cDNA was synthesized, RNA was replaced by the second cDNA strand by incubation with RNaseH and DNaseI. The bead-bound cDNA was cut with DpnII to retain only the fragment corresponding to the stretch between the last DpnII site and the poly(A)-tail. A linker specific for the DpnII site was ligated that carries a site for MmeI. Bound cDNA fragments of 16-17 bp were released by digestion with MmeI, and a second linker, complementary to the oligos of the flow cell surface, was ligated to the MmeI-generated overhangs. The fragments flanked by linkers were enriched by 15 cycles of PCR, purified by gel electrophoreses and ethanol precipitation, and used for cluster generation.

tag: cell line

tag: treatment protocol

value: untreated


title: hASC_t4_H3K4me2

description: Chromatin IP against H3K4me2

tag: chip antibody


title: Kc167, untreated, replicate 1 [RNA tag]


title: hASC_t4_H3K4me1

description: Chromatin IP against H3K4me1


title: hASC_t4_H3K27me3

description: Chromatin IP against H3K27me3


title: hASC_t2_H3K36me3

description: Chromatin IP against H3K36me3

value: Adipose stromal cell (ASC) pre-adipocyte

value: day 0


title: hASC_t3_H3K36me3

description: Chromatin IP against H3K36me3

value: day 3


title: hASC_t3_H3K4me3

description: Chromatin IP against H3K4me3


title: hASC_t2_CTCF

description: Chromatin IP against CTCF

value: CTCF


title: hASC_t2_H3K27me3

description: Chromatin IP against H3K27me3


title: hASC_t3_CTCF

description: Chromatin IP against CTCF


title: hASC_t1_CTCF

description: Chromatin IP against CTCF

value: day -2


title: hASC_t3_H3K4me1

description: Chromatin IP against H3K4me1


title: hASC_t3_H3K27me3

description: Chromatin IP against H3K27me3


title: hASC_t3_H3K27ac

description: Chromatin IP against H3K27ac


title: hASC_t3_H3K4me2

description: Chromatin IP against H3K4me2

value: Abcam, Cat# ab7766, Lot# 56293


title: hASC_t2_H3K27ac

description: Chromatin IP against H3K27ac


title: hASC_t1_H3K36me3

description: Chromatin IP against H3K36me3


title: hASC_t2_H3K4me1

description: Chromatin IP against H3K4me1


title: hASC_t2_H3K4me3

description: Chromatin IP against H3K4me3


title: hASC_t1_H3K27me3

description: Chromatin IP against H3K27me3


title: hASC_t1_H3K27ac

description: Chromatin IP against H3K27ac


title: hASC_t1_H3K4me2

description: Chromatin IP against H3K4me2


title: hASC_t1_H3K4me3

description: Chromatin IP against H3K4me3


title: hASC_t1_H3K4me1

description: Chromatin IP against H3K4me1


title: hASC_WCE

description: Whole cell extract (input control)

source_name: hASC, Whole Cell Extract (input control)

value: Adipose stromal cell (ASC) pre-adipocytes and adipocytes


title: Female_DNase_control

status: Public on Sep 28 2010

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (July 2007) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the PeakSeq algorithm (Rozowsky et al, Nature Biotechnol 2009)

source_name: Liver tissue

growth_protocol: Adult male and female ICR mice were purchased from Taconic, Inc. or Charles River Laboratories, and were housed in the Boston University Laboratory of Animal Care Facility in accordance with approved protocols.  Livers were collected from 8-wk old mice euthanized by CO2 asphyxiation followed by cervical dislocation.

extract_protocol: Sucrose step gradient ultracentrifugation was performed to isolate small DNA fragments (< 1.5 kb) from both digested nuclei and control samples.  Fractions that primarily contain fragments <1.5 kb (typically fraction 7) were purified on Qiagen columns (Cat. No. 28704) and assayed by qPCR using primers designed to amplify known hypersensitive regions (non-sex specific or sex-specific).  Samples that showed strong enrichment of DNase I hypersensitive fragments and that showed strong sex differences were used for Illumina sequencing.  For each biological replicate of pooled nuclei, sequencing was carried out using a total of ~ 30 ng DNA, pooled from at least 3 independent batches of DNase digested nuclei, to minimize the impact of inter-sample variability in DNase digestion. Sequences of DNase I-released DNA fragments were generated by an Illumina Genome Analyzer platform.  Briefly, about 20 ng of DNA was subjected to end repair, adaptor ligation, and PCR enrichment using an Illumina sample preparation kit following manufacturer’s recommendation.  A DNA library in the range of 200 to 300 bp was size-purified by gel electrophoresis.  The concentration of properly ligated samples was estimated by qPCR, followed by cluster generation and sequencing.  The sequencing reads were aligned to mouse genome mm9 by Eland extended with a maximum of 2 mismatch allowed in the first 25 bp.

treatment_protocol: Continuous GH treatment of 7-week male mice was achieved using Alzet model 1007D micro-osmotic pumps (Durect Corporation, Cupertino, CA) implanted s.c. under ketamine and xylazine anesthesia delivering recombinant rat GH (obtained from Dr. Arieh Gertler, Protein Laboratories Rehovot, Ltd, Rehovot, Israel) at 20 ng rat GH/hr/gram body weight for 7 days (Holloway et al. 2006).  RNA was then extracted from individual livers using Trizol reagent (Invitrogen) followed by reverse transcription using 1 ug total RNA and a High Capacity Reverse Transcription Kit (Applied Biosystems).

value: ICR

tag: sex

value: Female

value: liver

tag: animal treatment

tag: sample treatment

value: DNase digestion

tag: average size (bp)

tag: size distribution in cv (%)

tag: assayed molecule

value: naked genomic DNA


title: hASC_t2_H3K4me2

description: Chromatin IP against H3K4me2


title: MaleGH_DNase_rep1

value: Male

value: continuous growth hormone treatment

value: chromatin


title: Female_DNase_rep2


title: MaleGH_DNase_rep2


title: Female_sonicated_control

value: sonication


title: Male_sonicated_control


title: Female_DNase_rep1


title: Chlamy_N_RNA_seq_2

status: Public on Sep 25 2010

city: East Lansing

first: Guangxi

last: Wu

state: MI

address: S308 Plant Bio Bld

institute: Michigan State University

description: RNA-seq under N-deprived conditions.

data_processing: Default parameters were used to pass reads using Illumina quality control tools. The Illumina reads were mapped with Bowtie (Langmead et al., 2009) to the C. reinhardtii v4.0 assembly from the Joint Genome Institute with GMAP (Wu and Watanabe, 2005) using parameters as follow: ≤ 2 mismatches, sum of Phred quality values at all mismatched positions ≤ 70, and excluding reads mapped to > 1 locations.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas culture, N-deprived

growth_protocol: The cells were grown in liquid cultures under continuous light (~80 µmole photons m-2 s-1).

extract_protocol: To generate material for high-throughput sequencing, cells were grown in 100 TAP+N to 5x10^6 cells/mL. The cultures were split in half and cells were collected by centrifugation, with one pellet being resuspended in 50 mL TAP+N, and the other in 50 mL TAP-N. After 48 hours, the total RNA was harvested using a QIAGEN RNeasy Plant Mini kit (QIAGEN, Valencia, CA, USA). The RNA samples were treated with QIAGEN RNase-free DNase I during extraction. Total RNA was submitted directly to the MSU-RTSF for sequencing on an Illumina Genome Analyzer II (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: For N-replete growth, TAP medium (Harris, 2009a) with 10 mM NH4+ (TAP+N) was used. N-deprivation was defined as growth in TAP+N to 5x10^6 cells/mL, followed by transfer to TAP-N for 48 hours.

tag: genotype

value: cw15, nit2, mt+

tag: condition

value: N-deprivation


title: Chlamy_N_RNA_seq_3

description: RNA-seq under N-deprived conditions.


title: Chlamy_N_454

description: ESTs under N-deprived conditions.

data_processing: For 454 data, default parameters were used to pass reads using 454 quality control tools. The filtered 454 sequencing reads were mapped to the C. reinhardtii v4.0 assembly from the Joint Genome Institute with GMAP (Wu and Watanabe, 2005). In GMAP, the maximum intron length was set at 980bp, which is at the 95 percentile of annotated C. reinhardtii intron lengths.

extract_protocol: To generate material for high-throughput sequencing, cells were grown in 100 TAP+N to 5x10^6 cells/mL. The cultures were split in half and cells were collected by centrifugation, with one pellet being resuspended in 50 mL TAP+N, and the other in 50 mL TAP-N. After 48 hours, the total RNA was harvested using a QIAGEN RNeasy Plant Mini kit (QIAGEN, Valencia, CA, USA). The RNA samples were treated with QIAGEN RNase-free DNase I during extraction. Full-length cDNA pools were generated with the Clontech SMART cDNA library construction kit (Clontech, Mountain View, CA, USA). cDNA was synthesized using a modified cDNA synthesis primer (5’TAGAGACCGAGGCGGCCGACATGTTTTGTTTTTTTTTCTTTTTTTTTTVN3’). Full-length cDNAs were amplified by PCR and pooled to increase their concentration. An SfiI digest was performed, followed by size fractionation. Fractions with the highest intensity and size distribution were pooled and purified. The resulting cDNA pools were then submitted to the MSU-Research Technologies Service Facility (RTSF) for sequencing on a 454 GSFLX Titanium Sequencer (454 Life Sciences, Branford, CT, USA).


title: Male_DNase_rep2


title: Chlamy_T_RNA_seq_3

description: RNA-seq under N-replete conditions.

source_name: Chlamydomonas culture, N-replete

value: N-repletion


title: Male_DNase_rep1


title: Chlamy_T_RNA_seq_2

description: RNA-seq under N-replete conditions.


title: Chlamy_T_454

description: ESTs under N-replete conditions.


title: MFB_3_sequence

status: Public on Sep 24 2010

city: berkeley

first: henk

last: roelink

address: 16 barker hall

department: MCB

institute: UC Berkeley

description: non-adherent

data_processing:
Alignment: Sequence reads were obtained and mapped to the human and mouse genomes using the Illumina Genome Analyzer Pipeline. eland analysis file
processed data file build: mm9 and hg18
processed data file: eland analysis file

organism:
Homo sapiens
Mus musculus

source_name: C3H10T1/2 / MIA PaCa-2 coculture, control treated

growth_protocol: cells were grown for 5 days

extract_protocol: RNA was isolated using Trizol, all subsequent steps were performed using Illumina's mRNA-Seq Sample Preparation Kit

treatment_protocol: control (Isl2) or 5E1 Shh-blocking antibody producing hybridoma supernatant was added to the cells during the last 24h

value: C3H10T1/2 / MIA PaCa-2 coculture

tag: agent

value: control


title: Chlamy_T_RNA_seq_1

description: RNA-seq under N-replete conditions.


title: MFB_1_sequence

description: adherent

source_name: C3H10T1/2, control treated


title: Male Adult

city: Houston

first: Bryce

last: Daines

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Adults three days old (MA3d and FA3d) were collected when emerging and separated as males and virgin females into new vials, followed by 48 hours of aging.

data_processing: BLAT alignment

source_name: Whole body samples

growth_protocol: CS flies were reared at room temperature (23-24C) for collection.  Flies were staged to generate 12 separate collections.

extract_protocol: For each library, mRNA was purified from 20µg of total RNA using an mRNA Purification Kit (Invitrogen).  Double-stranded cDNAs were made from mRNA using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and random hexamer primers (Invitrogen, 3ug/ul).  On a 2% agrose gel, 200-400bp cDNAs were selected and used as the DNA template for the Solexa library construction. The quality and quantity of the resulting double-stranded cDNAs was assessed using the Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA).

treatment_protocol: Whole body samples were homogenized in 1ml of Trizol (Invitrogen, Carlsbad, California, USA) per 50-100 mg of tissue using a glass-Teflon homogenizer.  RNA was purified according to the suggested manufacturer’s protocol (Invitrogen).

value: cs

tag: developmental stage

value: Adults three days old (MA3d)


title: 3 day Pupa

description: For Pupa collections, 3rd instar wandering larva were collected into new vials and approximately 30 pupae were collected at 72 hours.

value: 3rd instar wandering larva were collected and approximately 30 pupae were collected at 72 hours.


title: Pupa

description: For Pupa collections, 3rd instar wandering larva were collected into new vials and approximately 30 pupae were collected at 24, 48, 72, 96, and 108 hours.

value: 3rd instar wandering larva were collected and approximately 30 pupae were collected at 24, 48, 72, 96, and 108 hours.


title: seq-WA30534819_H3K4me3_N2_MXemb_1

city: Chapel Hill

first: Everett

last: Zhou

state: NC

address: 1000 Manning Dr.

institute: UNC

data_processing:
alignment:  BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse. The input is fastq and the output is sam file.
peak_calling: ChIP-Seq MACS Peak-calling:JL:1. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters: tagSize = 25 mfold = 10,30 genomeSize = 90000000 bandwidth = 300 pvalue = 1e-5
pipeline v.1.5, Data received between Oct.29, 2009 - Jan. 31, 2010

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans_N2_MXemb

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac. For a detailed protocol see http://www.modencode.org/. || DNA was incubated with End Repair enzyme mix (NEB Klenow, T4 DNA polymerase, T4 PNK) to ensure blunt ends and with Exo(-) Klenow fragment in the presence of dATP to ass adenosine at the 3` ends. The DNA fragments were ligated with single or pair end adaptor (Illumina) and amplified by PCR. The amplicon was loaded into an agarose gel and size selected DNA was recovered from the gel.

treatment_protocol: Worm_embryo_extraction_v3. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

tag: Stage

value: MXemb

tag: antibody manufacturer

value: Wako (WA)

tag: antibody catalog #

tag: input experiment/sample

value: seq-NA_N2_MXemb_5_EE6 (GSM599723)


title: Male_DNase_control

tag: strain

value: ICR

tag: tissue

value: liver

value: DNase digestion

value: naked genomic DNA


title: seq-WA30534819_H3K4me3_N2_MXemb_2

treatment_protocol: Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

tag: chip antibody

value: seq-NA_N2_MXemb_6_EE8 (GSM599724)


title: seq-NA_N2_MXemb_5_EE6

description: Fragment size range cut from gel: 200-600 bp

data_processing:
alignment:  BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse. The input is fastq and the output is sam file.
pipeline v.1.5, Data received between Oct.29, 2009 - Jan. 31, 2010

extract_protocol: Worm_chromatin_immunoprecipitation_vMBJ5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (10 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 25 ul packed volume of protein A sepharose (GE Healthcare), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/. || Solexa_Library_Prep_vKI1. DNA was incubated with End Repair Enzyme mix (Epicentre, Madison) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3\` ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and size-selected DNA was recovered from the gel.


title: L3i100 3rd Instar Larva

description: For 3rd Instar Larva (L3i and L3i100) approximately 30 wandering larva were collected

value: 3rd Instar Larva (L3i100)


title: L3i 3rd Instar Larva

description: For 3rd Instar Larva (L3i and L3i100) approximately 30 wandering larva were collected.

value: 3rd Instar Larva (L3i)


title: E2-4hr Early Embryo

description: For Early Embryo (E2-4hr), adults were set for two hours of egg laying on grape juice plates.  Embryos were then collected and allowed to age for an additional two hours, resulting in embryos from 2-4 hours in age.

value: Embryo (E2-4hr)


title: seq-NA_N2_MXemb_6_EE8

description: Fragment size range cut from gel: 200-400 bp

extract_protocol: Worm_chromatin_immunoprecipitation_vMBJ5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (10 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 25 ul packed volume of protein A sepharose (GE Healthcare), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/. || DNA was incubated with End Repair enzyme mix (NEB Klenow, T4 DNA polymerase, T4 PNK) to ensure blunt ends and with Exo(-) Klenow fragment in the presence of dATP to ass adenosine at the 3` ends. The DNA fragments were ligated with single or pair end adaptor (Illumina) and amplified by PCR. The amplicon was loaded into an agarose gel and size selected DNA was recovered from the gel.


title: Chlamy_N_RNA_seq_1

description: RNA-seq under N-deprived conditions.

value: cw15, nit2, mt+

value: N-deprivation


title: Female Adult

value: cs

value: Adults three days old (FA3d)


title: MFB_4_sequence

description: non-adherent

source_name: C3H10T1/2 / MIA PaCa-2 coculture, 5E1 treated

tag: cell type

value: C3H10T1/2 / MIA PaCa-2 coculture

value: 5E1 blocking antibody


title: E2-16hr100 Embryo

description: The broadly staged Embryo (E2-16hr and E2-16hr100) were set for 14 hours of egg laying on grape juice plates, followed by two hours of aging resulting in embryos from 2-16 hours in age.

value: Embryo (E2-16hr100)


title: E14-16hr Late Embryo

description: Late Embryos (E14-16hr) were collected separately, allowed to age for 14 hours, and total RNA from each was combined in equimolar amounts.

value: Late Embryos (E14-16hr)


title: E2-16hr Embryo

value: Embryo (E2-16hr)


title: MFB_2_sequence

description: non-adherent

source_name: MIA PaCa-2, control treated

value: MIA PaCa-2

value: control


title: Universal reference - RNA-Seq

status: Public on Sep 23 2010

city: South San Francisco

first: Thomas

middle: D.

address: 1 DNA Way

institute: Genentech, Inc.

description: Universal reference sample

data_processing: Reads were analyzed in two ways to identify transcription-induced chimeras: (1) targeted alignment to a set of artificial exon-exon junctions between all exons of adjacent genes within 200,000 bp, and (2) spliced alignment to reference human genome build 36.1.  All alignments were performed with the program GSNAP. The most important alignments are not to a reference genome, but to a specialized database of artificial exon-exon junctions. Interested parties should refer to the 93-page Supplemental information document in related publication that contains the relevant alignment results (alignment data not submitted to GEO).

source_name: Universal reference

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions.  RNA was random primed with polyA.

tag: sampleID

value: Stratagene 740000

tag: organ

value: Multiple

tag: subtype

value: Universal reference


title: SRC112036 - RNA-Seq

description: Normal sample 2

source_name: Normal prostate

value: Prostate

value: Adjacent normal prostate


title: SRC113063 - RNA-Seq

description: Normal sample 3


title: SRC111976 - RNA-Seq

description: Normal sample 1


title: SRC113061 - RNA-Seq

description: Tumor sample 3

source_name: Prostate adenocarcinoma

value: Prostate adenocarcinoma


title: SRC112038 - RNA-Seq

description: Tumor sample 2


title: SRC111995 - RNA-Seq

description: Tumor sample 1


title: Larva

description: Larva were collected separately (1st 2nd and 3rd instar) and mixed in equimolar amounts.

value: (1st 2nd and 3rd instar) mixed in equimolar amounts.


title: Chromatin accessibility assay of Fetal lung tissue; DS14820

status: Public on Sep 21 2010

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14820
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3138
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3135
****************
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: GSM595929_fLung-DS14820.hg19.bam
ANALYSIS ALIAS: DS14820-align
ANALYSIS TITLE: Alignments DS14820
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

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

ANALYSIS FILE NAME: GSM595929_fLung-DS14820.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14820-signal
ANALYSIS TITLE: Signal DS14820
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

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

ANALYSIS FILE NAME: GSM595929_UW.Fetal_Lung.ChromatinAccessibility.H-23284.DS14820.bed
ANALYSIS ALIAS: DS14820.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23284, Library DS14820 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.4139
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5859
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.494
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9968
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5683
POISSON_PERCENTILE: 70

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

ANALYSIS FILE NAME: GSM595929_UW.Fetal_Lung.ChromatinAccessibility.H-23284.DS14820.wig
ANALYSIS ALIAS: DS14820.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung, Donor H-23284, Library DS14820 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.4099
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 2
BROWSER_TRACK_NAME: FL DNase 84 20
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23284 Library DS14820 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5859
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.494
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9968
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5683
POISSON_PERCENTILE: 70

source_name: Fetal Lung primary tissue, day 96; DS14820

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

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

value: Primary Tissue

value: fetal lung

value: UW

value: fetal

value: day 96

value: Female

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


title: Chromatin accessibility assay of Fetal lung tissue; DS15227

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15227
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3141
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3140
****************
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: GSM595930_fLung-DS15227.hg19.bam
ANALYSIS ALIAS: DS15227-align
ANALYSIS TITLE: Alignments DS15227
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

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

ANALYSIS FILE NAME: GSM595930_fLung-DS15227.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS15227-signal
ANALYSIS TITLE: Signal DS15227
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

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

ANALYSIS FILE NAME: GSM595930_UW.Fetal_Lung.ChromatinAccessibility.H-23365.DS15227.bed
ANALYSIS ALIAS: DS15227.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23365, Library DS15227 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.4122
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.498
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.3588
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9935
IROC_PERCENTILE: 7
POISSON_SCORE: 0.4979
POISSON_PERCENTILE: 42

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

ANALYSIS FILE NAME: GSM595930_UW.Fetal_Lung.ChromatinAccessibility.H-23365.DS15227.wig
ANALYSIS ALIAS: DS15227.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung, Donor H-23365, Library DS15227 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.4082
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 2
BROWSER_TRACK_NAME: FL DNase 65 27
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23365 Library DS15227 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.498
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.3588
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9935
IROC_PERCENTILE: 7
POISSON_SCORE: 0.4979
POISSON_PERCENTILE: 42

source_name: Fetal Lung primary tissue, day 108; DS15227

value: day 108

value: Male


title: Chromatin accessibility assay of Fetal brain tissue; DS14803

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: DS14803
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3116
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3113
****************
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: GSM595926_fBrain-DS14803.hg19.bam
ANALYSIS ALIAS: DS14803-align
ANALYSIS TITLE: Alignments DS14803
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

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

ANALYSIS FILE NAME: GSM595926_fBrain-DS14803.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14803-signal
ANALYSIS TITLE: Signal DS14803
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

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

ANALYSIS FILE NAME: GSM595926_UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14803.bed
ANALYSIS ALIAS: DS14803.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-23284, Library DS14803 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.4133
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5883
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.5007
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9982
IROC_PERCENTILE: 85
POISSON_SCORE: 0.5231
POISSON_PERCENTILE: 57

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

ANALYSIS FILE NAME: GSM595926_UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14803.wig
ANALYSIS ALIAS: DS14803.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain, Donor H-23284, Library DS14803 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.4093
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 2
BROWSER_TRACK_NAME: FB DNase 84 03
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-23284 Library DS14803 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5883
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.5007
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9982
IROC_PERCENTILE: 85
POISSON_SCORE: 0.5231
POISSON_PERCENTILE: 57

source_name: Fetal Brain primary tissue, day 96; DS14803

value: fetal brain


title: 17 day Adult

description: Adults 17 days old were collected separately, allowed to age for 17 days, and total RNA from each was combined in equimolar amounts.

value: cs

value: Adults 17 days old


title: Chromatin accessibility assay of Fetal brain tissue; DS14815

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14815
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3114
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3113
****************
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: GSM595928_fBrain-DS14815.hg19.bam
ANALYSIS ALIAS: DS14815-align
ANALYSIS TITLE: Alignments DS14815
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

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

ANALYSIS FILE NAME: GSM595928_fBrain-DS14815.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14815-signal
ANALYSIS TITLE: Signal DS14815
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

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

ANALYSIS FILE NAME: GSM595928_UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14815.bed
ANALYSIS ALIAS: DS14815.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-23284, Library DS14815 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.4137
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6211
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.5392
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9982
IROC_PERCENTILE: 85
POISSON_SCORE: 0.565
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM595928_UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14815.wig
ANALYSIS ALIAS: DS14815.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain, Donor H-23284, Library DS14815 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.4097
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 2
BROWSER_TRACK_NAME: FB DNase 84 15
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-23284 Library DS14815 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6211
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.5392
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9982
IROC_PERCENTILE: 85
POISSON_SCORE: 0.565
POISSON_PERCENTILE: 67

source_name: Fetal Brain primary tissue, day 96; DS14815


title: Chromatin accessibility assay of Fetal lung tissue; DS14751

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14751
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3133
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3130
****************
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: GSM595925_fLung-DS14751.hg19.bam
ANALYSIS ALIAS: DS14751-align
ANALYSIS TITLE: Alignments DS14751
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

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

ANALYSIS FILE NAME: GSM595925_fLung-DS14751.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14751-signal
ANALYSIS TITLE: Signal DS14751
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

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

ANALYSIS FILE NAME: GSM595925_UW.Fetal_Lung.ChromatinAccessibility.H-23266.DS14751.bed
ANALYSIS ALIAS: DS14751.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23266, Library DS14751 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.4110
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.614
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5007
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9984
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5859
POISSON_PERCENTILE: 80

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

ANALYSIS FILE NAME: GSM595925_UW.Fetal_Lung.ChromatinAccessibility.H-23266.DS14751.wig
ANALYSIS ALIAS: DS14751.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung, Donor H-23266, Library DS14751 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.4070
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 2
BROWSER_TRACK_NAME: FL DNase 66 51
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23266 Library DS14751 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.614
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5007
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9984
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5859
POISSON_PERCENTILE: 80

source_name: Fetal Lung primary tissue, day 85; DS14751

value: day 85


title: Chromatin accessibility assay of Fetal lung tissue; DS14809

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14809
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3136
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3135
****************
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: GSM595927_fLung-DS14809.hg19.bam
ANALYSIS ALIAS: DS14809-align
ANALYSIS TITLE: Alignments DS14809
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

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

ANALYSIS FILE NAME: GSM595927_fLung-DS14809.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14809-signal
ANALYSIS TITLE: Signal DS14809
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

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

ANALYSIS FILE NAME: GSM595927_UW.Fetal_Lung.ChromatinAccessibility.H-23284.DS14809.bed
ANALYSIS ALIAS: DS14809.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23284, Library DS14809 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.4134
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6136
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.5432
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9968
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5695
POISSON_PERCENTILE: 72

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

ANALYSIS FILE NAME: GSM595927_UW.Fetal_Lung.ChromatinAccessibility.H-23284.DS14809.wig
ANALYSIS ALIAS: DS14809.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung, Donor H-23284, Library DS14809 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.4094
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 2
BROWSER_TRACK_NAME: FL DNase 84 09
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23284 Library DS14809 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6136
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.5432
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9968
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5695
POISSON_PERCENTILE: 72

source_name: Fetal Lung primary tissue, day 96; DS14809

value: genomic DNA


title: Chromatin accessibility assay of Fetal lung tissue; DS14724

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14724
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3131
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3130
****************
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: GSM595924_fLung-DS14724.hg19.bam
ANALYSIS ALIAS: DS14724-align
ANALYSIS TITLE: Alignments DS14724
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

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

ANALYSIS FILE NAME: GSM595924_fLung-DS14724.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14724-signal
ANALYSIS TITLE: Signal DS14724
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

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

ANALYSIS FILE NAME: GSM595924_UW.Fetal_Lung.ChromatinAccessibility.H-23266.DS14724.bed
ANALYSIS ALIAS: DS14724.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23266, Library DS14724 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.4107
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.7423
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.6395
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9984
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6601
POISSON_PERCENTILE: 97

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

ANALYSIS FILE NAME: GSM595924_UW.Fetal_Lung.ChromatinAccessibility.H-23266.DS14724.wig
ANALYSIS ALIAS: DS14724.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung, Donor H-23266, Library DS14724 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.4067
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 2
BROWSER_TRACK_NAME: FL DNase 66 24
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23266 Library DS14724 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.7423
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.6395
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9984
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6601
POISSON_PERCENTILE: 97

source_name: Fetal Lung primary tissue, day 85; DS14724

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