title: Snyder_ZAG-1_GFP_L4_rep2 extraction2_seq1 aliquote 1

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220


title: SunyAlbany_RipSeq_K562_T7Tag

status: Public on Jun 06 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

extract_protocol:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSunyRipSeq
library_strategy: RIP-Seq
library_selection: RNA binding protein antibody

tag: lab

value: SunyAlbany

tag: lab description

value: Tenenbaum - SUNY at Albany

tag: datatype

value: RipSeq

tag: datatype description

value: RNA IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: antibody

tag: antibody antibodydescription

value: 1) Mil AB3790 Anti-t7 Epitope tag, T7 (MASMTGGQQMG) 2) Novagen 69522 Negative Control Ab (T7 Tag Mouse Monoclonal). Antibody Target:T7Tag

tag: antibody targetdescription

tag: antibody vendorname

value: 1)Millipore; 2)Novagen

tag: antibody vendorid

tag: labversion

value: Nov_69522 antibody

tag: replicate


title: Stat3 (LIF)

status: Public on Jun 07 2012

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 36bp reads were mapped to the mm9 mouse genome build using Bowtie with the following parameter: --solexa1.3-qual --best --trim5 1 mm9
To identify binding peaks, we processed the mapped sequence reads with MACS version 1.3.7.1 using matching number of IgG control reads to Stat3 or GR samples. We used the following setting in MACS: --format BOWTIE --wig --tsize 35 --bw 250 --mfold 7 --pvalue 1e-8 --gsize 1870000000
Genome_build: mm9
Supplementary_files_format_and_content: wig files generated by MACS 1.3.7.1 and bed files scores reprensent the Cluster number.

molecule: genomic DNA

organism: Mus musculus

source_name: AtT-20 corticotroph cells treated with Stat3 (LIF)

growth_protocol: AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.

extract_protocol: Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific polyclonal antibodies.  Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina GAIIx sequencer following the manufacturer's protocols to obtain 36bp reads.

treatment_protocol: The third day after plating, the treatment agents were added directly into the culture medium (DMEM + 10% FBS) and left for 20min.

tag: cell line

tag: cell type

value: pituitary corticotroph cell

tag: treatment

value: LIF

tag: chip antibody

value: p-STAT3 (sc-7993) and STAT3 (sc-482x) from SantaCruz


title: MCF7 siTCF7L2

status: Public on Jun 05 2012

city: Columbus

first: rui

last: wang

state: OHIO

address: 212 Biomedical Research Tower,460 West 12th Ave

institute: Ohio State University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol as described in Trapnell et al, Nature Protocols  7, 562–578 (2012). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human breast adenocarcinoma cell-line MCF7

growth_protocol: Thawing Cells:  1. Thaw vial immediately in 37º C water bath. Keep O ring above the water surface to prevent contamination. Thaw content with slight  shake until only small ice is left in vial. It usually takes 1 min. Spray vial with 70% ethanol all over and wipe its surface with clean tissue in the hood.  2. Open the vial and transfer the content to a 15 ml Falcon tube already containing 5 ml of fresh medium.  3. Spin down at 1000 rpm or 200g for 3 to 5 mins at 4º C. Aspirate supernatant.  4. Resuspend cells in fresh medium and transfer to 150mm x 25mm tissue culture dish.  5. Check the cells under microscope.  6. Cells are cultured in CO2 incubator and medium is changed about every 3 days.  7. It usually takes 3 days or more for cells to recovery from freezing. After cell culture reaches  80-85%  confluence, subculture is conducted. Subculture ratio is about 1:3 or 1:4.  Passaging Cells:  1. Observe cells to see how confluent they are, whether the cells are alive, whether the cells are contaminated, and whether the cells have the correct morphology. After cell culture reaches 80 to 85% confluence, subculture is conducted  2. Remove media from dish  3. Wash 1x with 10 ml of PBS  4. Add 5 ml of Trypsin and trypsinize for 3 min at 37C. Whack hard – you should see the cells coming down. (Important: never overtrypsinize the cells, so work quickly)  5. Add 5 ml of media and use it to rinse the dish to detach the cells off (4 to 5 times)  6. Spin down at 1000rpm for 3 to 5 min at room temperature. Aspirate supernatant  7. Add 15 ml of media to 15ml tube containing cell pellet, and pipette up and down to mix  8. Add 15 ml of media to each new 150mm x 25mm tissue culture dish (we split 1 dish into 3 to 4 dishes)  9. Add 5mls of cell culturecontaining media to each tissue culture dish. Make sure the media covers the entire area of the dish. Put the cells into 37C with 5% CO2.

extract_protocol: RNA was extracted using Trizol Reagent (Life Technologies) following the suggested protocol; 2ug of each RNA sample was used with the Illumina TruSeq RNA Sample Prep Kit (Cat # RS-122-2001) to make RNA libraries following the Illumina TruSeq RNA Sample preparation Low-Throughput protocol. Briefly, RNA was fragmented, then first-strand cDNA was prepared using the kit supplied 1st Strand Master Mix and user-supplied Superscript III (Life Technologies, cat # 18080-051) followed by second strand cDNA synthesis. The Illumina protocol and reagents were used to complete the library preparation, with 12 cycles of PCR amplification.

treatment_protocol: 1. Low passage MCF7 cells were grown in DMEM supplemented with 10% FBS (no Pen/Step) to 85% confluency and passaged into 6-well dish at approximately 50% confluency  2. Cells were transfected with final concentration 50nM siRNA using Lipofectamine2000 according to the manufacturer's instructions (Invitrogen)  3. The media was replaced 12 hours post transfection and cells were grown for an additional 36 hours (hours posttransfection)

tag: passage

tag: sirna

value: ON-TARGETplus Non-Targeting siRNA against TCF7L2

value: TCF7L2 KD


title: Snyder_UNC-62_GFP_D4YA_rep2 extraction2_seq1 aliquote 1

status: Public on Jun 04 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

organism: Caenorhabditis elegans

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

tag: strain

value: OP600(official name :OP600 genotype :unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by :S Kim )

tag: developmental stage

value: Day Four Young Adult

tag: genotype

tag: Sex

value: Hermaphrodite


title: Snyder_UNC-62_GFP_D4YA_rep1 extraction1_seq1 aliquote 1


title: SunyAlbany_RipSeq_GM12878_T7Tag

tag: lab

value: SunyAlbany

tag: lab description

value: Tenenbaum - SUNY at Albany

tag: datatype

value: RipSeq

tag: datatype description

value: RNA IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: cell karyotype

value: normal

tag: cell lineage

tag: cell sex

tag: antibody

value: Negative Control Ab (T7 Tag Mouse Monoclonal).


title: MCF7 siCONTROL

tag: cell line

tag: passage

value: ON-TARGETplus Non-Targeting siRNA Control (Dharmacon, D-001810-01)

tag: treatment

value: control


title: Snyder_UNC-62_Input_D4YA_rep1 extraction1_seq1 aliquote 1

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

tag: strain

tag: developmental stage


title: Snyder_UNC-62_Input_D4YA_rep2 extraction2_seq1 aliquote 1

description: input DNA

tag: genotype

tag: Sex


title: UW_ChipSeq_AG04450_Input

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwHistone

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: fetal lung fibroblast

value: endoderm

value: M

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: 5hmC in DC-treated 3T3-L1 cells

city: Rennes

first: Aurelien

last: Serandour

address: Bâtiment 13, Campus de Beaulieu

department: UMR CNRS 6290

country: France

institute: Université de Rennes 1

data_processing:
Reads were mapped onto the reference genome (mm8 for P19.6 cells and mm9 for 3T3-L1 cells) by Bowtie (Langmead et al. Genome Biol. 2009) using parameters -l 28 -n 1 -m 1 --best --strata.
Mapped reads were processed by MACS algorithm (Model-based Analysis of ChIP-Seq) (Zhang Y. et al. Genome Biol. 2008).
Genome_build: mm8 for P19.6 cells and mm9 for 3T3-L1 cells.
Supplementary_files_format_and_content: wig files were generated using macs 1.4.

source_name: DC-treated 3T3-L1_MeDIP-Seq

growth_protocol: P19.6 mouse embryonal carcinoma cells were grown in high glucose Dulbeccos’ Modified Eagle’s Medium (DMEM) containing 10% fetal calf serum (GIBCO). 3T3-L1 cells were grown in high glucose DMEM supplemented with 10% bovine calf serum (GIBCO).

extract_protocol: Libraries were prepared according to Illumina's instructions at IBL sequencing facility (Lille, France)

treatment_protocol: P19.6 cells were differentiated with 1 µM all-trans retinoic acid (RA) for 48 hours. Confluent 3T3-L1 cells were treated with DC (0.5 mM IBMX, 1 µM dexamethasone, 10 µg/ml insulin) for 2 days. Medium was then replaced with DMEM supplemented with 10% bovine serum and 10 µg/ml insulin). After 2 days, cells were maintained in DMEM supplemented with 10% bovine serum for 4 additional days.

tag: cell line

tag: treated with

value: differentiation cocktail (DC) for 2 days

tag: antibody

tag: antibody vendor

value: Diagenode

tag: antibody cat. #

value: CS-HMC

tag: antibody lot #


title: 5hmC in 3T3-L1 cells


title: 5hmC in P19.6 cells

tag: cell type

value: embryonal carcinoma cells


title: Tet1 ChIP-seq in P19.6 cells

data_processing:
Reads were mapped to the reference genome (mouse mm8) by Bowtie (Langmead et al. Genome Biol. 2009) using parameters -l 28 -n 1 -m 1 --best --strata.
Mapped reads were processed by MACS algorithm (Model-based Analysis of ChIP-Seq) (Zhang Y. et al. Genome Biol. 2008).
Genome_build: mm8
Supplementary_files_format_and_content: wig files were generated using macs 1.4.

source_name: P19.6_Tet1 ChIP-seq

growth_protocol: P19.6 mouse embryonal carcinoma cells were grown in high glucose Dulbeccos’ Modified Eagle’s Medium (DMEM) containing 10% fetal calf serum (GIBCO).

extract_protocol: Libraries were prepared according to Illumina's instructions by IGBMC sequencing facility (Strasbourg, France)

treatment_protocol: P19.6 cells were differentiated with 1 µM all-trans retinoic acid (RA) for 48 hours.

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: Tet1 ChIP-seq in RA-treated P19.6 cells

source_name: RA-treated P19.6_Tet1 ChIP-seq

value: 1µM all-trans retinoic acid for 48hr


title: H3K4me2 ChIP-seq in RA-treated cells

source_name: RA-treated P19.6_H3K4me2 ChIP-seq


title: 5hmC in RA-treated P19.6 cells

source_name: RA-treated P19.6_MeDIP-Seq

value: 1µM all-trans retinoic acid (RA) for 48hr


title: Snyder_ZAG-1_Input_L4_rep1 extraction1_seq1 aliquote 1

description: input DNA

tag: strain

value: OP83(official name :OP83 genotype :unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by :R Waterston )

tag: developmental stage

tag: genotype

tag: Sex

value: Hermaphrodite


title: H3K27ac ChIP-seq in RA-treated P19.6 cells

description: P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).

data_processing: Reads were mapped to the reference genome (mouse mm8) by Bowtie (Langmead et al. Genome Biol. 2009 (PMID 19261174)). Mapped reads were processed by the MACS algorithm (Model-based Analysis of ChIP-Seq) (Zhang Y et al. Genome Biol. 2008 (PMID 18798982)).

source_name: RA-treated P19.6 cells, H3K27ac ChIP

growth_protocol: P19.6 mouse embryonal carcinoma cells were grown in high glucose Dulbeccos' Modified Eagle's Medium (DMEM) containing 10% fetal calf serum (GIBCO).

extract_protocol: Libraries were prepared according to Illumina's instructions by the IGBMC sequencing facility (Strasbourg, France). P19.6 cells were cross-linked with 1.5% formaldehyde for 10 min at room temperature. The cells were rinsed with cold PBS, harvested and lysed with 1% SDS, 10 mM EDTA, and 50 mM Tris-HCl (pH 8.1) containing a protease inhibitor cocktail (Roche). Chromatin fragmentation was subsequently obtained by sonicating samples for 14 min (30 sec on/off cycles) using a Bioruptor (Diagenode) set up at the highest intensity. The soluble chromatin was diluted 10 times in a buffer containing 1% Triton, 2 mM EDTA, 150 mM NaCl, and 20 mM Tris-HCl (pH 8.1), and incubated overnight with antibodies. Sepharose beads (Amersham Pharmacia Biosciences) were then added to the samples together with yeast tRNA as non-specific competitors. After 4 h, beads were serially washed using 1mL of washing buffer I (2mM EDTA, 20mM Tris-HCl (pH8.1), 0.1% SDS, 1% Triton X-100, 150mM NaCl), washing buffer II (2mM EDTA, 20mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 500 mM NaCl), washing buffer III (1mM EDTA, 10mM Tris-HCl (pH8.1), 1% NP-40, 1% deoxycholate, 0.25M LiCl) and then twice with 1mM EDTA, 10mM Tris-HCl (pH8.1), and immune complexes were eluted using 100 mL of 1% SDS and 0.1 M NaHCO3. Samples were incubated overnight at 65C to reverse cross-linking. DNA was finally purified using the NucleoSpin Extract II kit (Macherey-Nagel). Each ChIP was performed 10 times. The 10 samples were pooled and concentrated by DNA precipitation.

tag: background strain

tag: treatment

value: all-trans retinoic acid (RA)

tag: treatment dosage

tag: treatment duration

value: 48 hours

tag: ip antibody

value: Abcam

tag: antibody catalog #

tag: antibody lot


title: Input-seq in RA-treated P19.6 cells

source_name: RA-treated P19.6 cells, input

tag: cell line


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: RNA-Seq analysis of foreskin keratinocyte from skin02 (A07121) using Illumina HiSeq 2000
library name: A07121
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.3
RNA_PREPARATION_INITIAL_RNA_QNTY: 10 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 280-400 bp
****************
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: GSM941745_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.mRNA-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A07121-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12930
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 313,156,699
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.63
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM941745_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.mRNA-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A07121-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12933
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFK mRNA 02 21
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin02 Library A07121 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 313,156,699
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.63
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

extract_protocol: library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: male

tag: body site

value: Penis

tag: histological type

value: Keratinocyte

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: foreskin keratinocyte


title: WT-0

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

data_processing:
base-calling, Illumina sequencing control software
filtering, FASTX-Toolkit, quality cut-off: 20, clipping adapter: TGGAATTCTCGGGTGCCAAGG
Supplementary_files_format_and_content: fasta

organism: Gossypium hirsutum

source_name: upland cotton ovule

growth_protocol: Cotton plants (Gossypium hirsutum cv. Xuzhou 142) were grown in a soil mixture in fully automated walk-in growth rooms with 300 µmol m–2 s–1 average light intensity, 60% relative humidity and temperatures set to 30C during the light period and 28C during the dark (12-h light/dark cycle). These conditions were consistent throughout the year.

extract_protocol: Briefly, after PAGE purification of small RNA molecules under 30 bases and ligation of a pair of adaptors to their 5' and 3' ends, the small RNA molecules were amplified using the adaptor primers for 17 cycles and the fragments around 90 bp (small RNA+adaptors) were isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina GA according to the manufacturer's instructions.

tag: tissue

value: ovule

value: 0 DPA


title: WT-7

source_name: upland cotton fiber

value: upland cotton fiber

tag: developmental stage

value: 7 DPA


title: WT-3

value: 3 DPA


description:
design description: ChIP-Seq input analysis of foreskin keratinocyte from skin02 (A11925) using Illumina HiSeq 2000
library name: A11925
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 74-336 bp
****************
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: GSM941742_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11925-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12888
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,932,878
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0022
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0318
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0549
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.52

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

ANALYSIS FILE NAME: GSM941742_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11925-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12912
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFK Input 02 25
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin02 Library A11925 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,932,878
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0022
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0318
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0549
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.52

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

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)


description:
design description: RNA-Seq analysis of foreskin fibroblast from skin02 (A07120) using Illumina HiSeq 2000
library name: A07120
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.6
RNA_PREPARATION_INITIAL_RNA_QNTY: 10 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 280-400 bp
****************
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: GSM941744_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.mRNA-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A07120-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12929
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 320,925,979
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.29
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM941744_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.mRNA-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A07120-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12932
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFF mRNA 02 20
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin02 Library A07120 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 320,925,979
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.29
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

value: Fibroblast

value: foreskin fibroblast


description:
design description: ChIP-Seq input analysis of foreskin melanocyte from skin02 (A08748) using Illumina HiSeq 2000
library name: A08748
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 87-297 bp
****************
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: GSM941741_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08748-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12870
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,644,201
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.002
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0107
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0339
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM941741_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08748-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12894
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFM Input 02 48
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin02 Library A08748 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,644,201
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.002
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0107
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0339
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

value: Melanocyte

value: foreskin melanocyte


title: WT-15

value: 15 DPA


title: H3K27ac ChIP-seq in P19.6 cells

source_name: Untreated P19.6 cells, H3K27ac ChIP

value: embryonal carcinoma cells

tag: antibody vendor

value: Abcam


title: H3K4me2 ChIP-seq in P19.6 cells

source_name: P19.6_H3K4me2 ChIP-seq

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


description:
design description: H3K9me3 ChIP-Seq analysis of foreskin keratinocyte from skin02 (A11922) using Illumina HiSeq 2000
library name: A11922
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 91-373 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
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: GSM941737_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K9me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11922-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12884
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,639,202
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2498
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2914
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9299
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4745
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM941737_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K9me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11922-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12908
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFK H3K9me3 02 22
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin02 Library A11922 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,639,202
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2498
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2914
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9299
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4745
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

tag: Sex

value: male

value: Penis

value: Keratinocyte


description:
design description: RNA-Seq analysis of foreskin melanocyte from skin02 (A07119) using Illumina HiSeq 2000
library name: A07119
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9
RNA_PREPARATION_INITIAL_RNA_QNTY: 10 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 280-400 bp
****************
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: GSM941743_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.mRNA-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A07119-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12928
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 318,299,784
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.85
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM941743_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.mRNA-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A07119-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12931
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFM mRNA 02 19
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin02 Library A07119 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 318,299,784
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.85
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: No

value: primary cell culture


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin keratinocyte from skin02 (A11923) using Illumina HiSeq 2000
library name: A11923
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 86-374 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
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: GSM941738_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11923-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12881
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,709,160
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.1237
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.1952
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9254
IROC_PERCENTILE: 86
POISSON_SCORE: 0.3696
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.79

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

ANALYSIS FILE NAME: GSM941738_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11923-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12905
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFK H3K27me3 02 23
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin02 Library A11923 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,709,160
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.1237
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.1952
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9254
IROC_PERCENTILE: 86
POISSON_SCORE: 0.3696
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.79

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

value: foreskin keratinocyte


description:
design description: H3K4me1 ChIP-Seq analysis of foreskin keratinocyte from skin02 (A11920) using Illumina HiSeq 2000
library name: A11920
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 93-341 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM941736_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me1.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11920-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12880
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,029,353
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.2981
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3505
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9779
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5001
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

ANALYSIS FILE NAME: GSM941736_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me1.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11920-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12904
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFK H3K4me1 02 20
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin02 Library A11920 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,029,353
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.2981
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3505
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9779
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5001
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.71

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


title: Input-seq in P19.6 cells

source_name: Untreated P19.6 cells, input

tag: background strain

tag: treatment

tag: ip antibody


description:
design description: H3K36me3 ChIP-Seq analysis of foreskin keratinocyte from skin02 (A11924) using Illumina HiSeq 2000
library name: A11924
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 77-106 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM941739_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K36me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11924-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12890
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,723,145
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4049
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3489
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9903
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6027
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM941739_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K36me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11924-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12914
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFK H3K36me3 02 24
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin02 Library A11924 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,723,145
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4049
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3489
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9903
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6027
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: ChIP-Seq input analysis of foreskin melanocyte from skin01 (A08388) using Illumina HiSeq 2000
library name: A08388
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 76-240 bp
****************
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: GSM941740_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08388-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.12869
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,917,132
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0019
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0414
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8699
IROC_PERCENTILE: 83
POISSON_SCORE: 0.0565
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM941740_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08388-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.12893
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFM Input 01 88
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin01 Library A08388 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,917,132
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0019
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0414
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8699
IROC_PERCENTILE: 83
POISSON_SCORE: 0.0565
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.91

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


title: MEIS1 ChIP-seq in RA-treated P19.6 cells

source_name: RA-treated P19.6 cells, MEIS1 ChIP

tag: cell line

value: all-trans retinoic acid (RA)

tag: treatment dosage

tag: treatment duration

value: 48 hours

tag: antibody catalog #

tag: antibody lot


description:
design description: H3K4me3 ChIP-Seq analysis of foreskin keratinocyte from skin02 (A11921) using Illumina HiSeq 2000
library name: A11921
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 84-336 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM941735_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11921-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12874
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,943,476
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.6613
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6631
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9993
IROC_PERCENTILE: 75
POISSON_SCORE: 0.67
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM941735_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11921-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12898
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFK H3K4me3 02 21
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin02 Library A11921 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,943,476
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.6613
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6631
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9993
IROC_PERCENTILE: 75
POISSON_SCORE: 0.67
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

tag: submitted sample id

tag: body site

tag: histological type

tag: is tumor

tag: cell type


description:
design description: H3K36me3 ChIP-Seq analysis of foreskin melanocyte from skin01 (A08387) using Illumina HiSeq 2000
library name: A08387
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 99-355 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM941729_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K36me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08387-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.12883
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,943,114
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.0141
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1097
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.8434
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3029
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM941729_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K36me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08387-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.12907
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFM H3K36me3 01 87
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin01 Library A08387 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,943,114
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.0141
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1097
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.8434
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3029
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.94

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


description:
design description: H3K36me3 ChIP-Seq analysis of foreskin melanocyte from skin02 (A08747) using Illumina HiSeq 2000
library name: A08747
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 20 ug
SIZE_FRACTION: 119-366 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM941734_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K36me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08747-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12885
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,040,031
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.2257
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2366
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9754
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4696
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM941734_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K36me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08747-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12909
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFM H3K36me3 02 47
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin02 Library A08747 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,040,031
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.2257
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2366
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9754
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4696
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.94

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


description:
design description: H3K4me3 ChIP-Seq analysis of foreskin melanocyte from skin02 (A08744) using Illumina HiSeq 2000
library name: A08744
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 20 ug
SIZE_FRACTION: 106-341 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM941731_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08744-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12879
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,957,396
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.6339
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.6336
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9987
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6448
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM941731_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08744-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12903
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFM H3K4me3 02 44
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin02 Library A08744 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,957,396
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.6339
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.6336
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9987
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6448
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.99

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


description:
design description: MeDIP-Seq analysis of foreskin melanocyte from skin02 (A09693) using Illumina HiSeq 2000
library name: A09693
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.972 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
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: GSM941727_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A09693-1-A08304-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12916
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 115,654,127
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4984
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5187
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9861
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5848
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM941727_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A09693-1-A08304-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12919
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFM MeDIP 02 93
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin02 Library A09693 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 115,654,127
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4984
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5187
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9861
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5848
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

extract_protocol: library construction protocol: Refer to document 'MeDIP-seq library construction protocol v2' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin melanocyte from skin02 (A08746) using Illumina HiSeq 2000
library name: A08746
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 20 ug
SIZE_FRACTION: 113-408 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
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: GSM941733_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08746-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12872
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,766,122
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.0463
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1154
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8424
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3579
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM941733_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08746-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12896
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: PFM H3K27me3 02 46
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin02 Library A08746 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,766,122
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.0463
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1154
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8424
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3579
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.92

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