title: ChIP-Seq analysis of H3K4me3 in human hippocampus middle cells; DNA_Lib 983

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 983
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9614
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
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: GSM916040_BI.Brain_Hippocampus_Middle.H3K4me3.150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 983-DNA_Lib 983.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Hippocampus Middle, Donor 150, 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.12278
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,668,869
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.3154
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.3478
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9996
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3794
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM916040_BI.Brain_Hippocampus_Middle.H3K4me3.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 983-DNA_Lib 983.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 150, 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.12325
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 6
BROWSER_TRACK_NAME: BHM H3K4me3 50 83
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K4me3 Donor 150 Library DNA_Lib 983 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,668,869
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.3154
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.3478
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9996
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3794
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 983

tag: sample alias

tag: sample common name

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD present

tag: molecule

value: genomic DNA

value: Hippocampus Middle

value: 73.0 Years

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Branson


title: polyA RNA sequencing of H1 cells; polyA-RNA-seq_h1_r2a

status: Public on Apr 18 2012

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 cells
Library name: polyA-RNA-seq_h1_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12097
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12095
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

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

ANALYSIS FILE NAME: GSM915329_UCSD.H1.mRNA-Seq.polyA-RNA-seq_h1_r2a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1_r2a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the H1 Cell Line, Library polyA-RNA-seq_h1_r2a 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.13724
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 327,201,303
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 74.93
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM915329_UCSD.H1.mRNA-Seq.polyA-RNA-seq_h1_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1_r2a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the H1 Cell Line, Library polyA-RNA-seq_h1_r2a 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.13734
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: H1 mRNA 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r2a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 327,201,303
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 74.93
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

molecule: total RNA

organism: Homo sapiens

source_name: H1 Cell Line, biological replicate 2 (r2); polyA-RNA-seq_h1_r2a

extract_protocol: Library construction protocol: Four µg of total RNA was extracted from frozen cell pellets using the RNeasy Mini Kit (Qiagen, Valencia, CA). PolyA RNA was isolated from total RNA using Dynabeads oligo(dt)25 (Invitrogen). PolyA selected RNA was eluted in 2x Superscript III buffer supplemented with 10mM DTT and was fragmented by incubation at 94°C for 4 minutes. First-strand cDNA was synthesized with the following reaction composition: 0.5 µL random hexamer, 0.5 µL RNase Out, 1 µL DTT (100 mM), 0.5 µL dNTP (25 mM), 0.5 µL SuperScript III (20 µL final). The reaction was incubated at 25°C for 10 min then 50°C for 50 min.  Single-stranded cDNA was isolated by purification with RNAClean XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing second-strand was synthesized with the following reaction: 1.5 µL NEBuffer 2 (NEB), 1 µL dNTP mix (10 mM dATP, dCTP, dGTP, and dUTP), 0.2 µL RNase H, 1 µL DNA Polymerase I (E. coli) (New England Biolabs) (15 µL final). The reaction was incubated at 16°C for 2.5 hours. The dUTP-containing cDNA was isolated by purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing cDNA was then end repaired and a 3' A base was added. TruSeq adapters (Illumina, San Diego, CA) were ligated to the dUTP-containing cDNA at 16°C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated cDNA was isolated by two rounds of purification with AMPure XP beads. The dUTP-containing strands were digested at 37°C for 30 min with uracil DNA glycosylase (Enzymatics). Adapter-ligated, single-stranded DNA molecules were enriched by 10 cycles of PCR with the following reaction composition: 5 µL TruSeq PCR Primer Cocktail (Illumina), 25 µL TruSeq PCR Master Mix (Illumina) (50 µL final). The thermocycling parameters were: 98°C 30 sec, then 10-15 cycles of 98°C 10 sec, 60°C 30 sec and 72°C 30 sec, ending with one 72°C 5 min step. The reaction products were purified using AMPure XP beads.

value: H1 Cell Line

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

tag: passage

tag: medium

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

tag: Sex

value: Male

tag: batch

value: Replicate 2

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: ChIP-Seq analysis of H3K27ac in human hippocampus middle cells; DNA_Lib 984

status: Public on Apr 17 2012

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 984
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9609
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM916035_BI.Brain_Hippocampus_Middle.H3K27ac.150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 984-DNA_Lib 984.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on Brain Hippocampus Middle, Donor 150, 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.12308
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,545,793
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4643
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4902
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.996
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5564
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM916035_BI.Brain_Hippocampus_Middle.H3K27ac.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 984-DNA_Lib 984.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 150, 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.12355
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 6
BROWSER_TRACK_NAME: BHM H3K27ac 50 84
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K27ac Donor 150 Library DNA_Lib 984 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,545,793
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4643
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4902
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.996
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5564
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

molecule: genomic DNA

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 984

extract_protocol: Library construction protocol: Single read - Illumina

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD present

value: genomic DNA

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 73.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human CD25- IL17+ Th17 stim cells; DNA_Lib 739

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 739
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9602
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9446
****************
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: GSM916028_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K36me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 739-DNA_Lib 739-DNA_Lib 739.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 62, 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.12321
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,536,709
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0677
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.1946
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.8288
IROC_PERCENTILE: 31
POISSON_SCORE: 0.2865
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916028_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K36me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 739-DNA_Lib 739-DNA_Lib 739.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 62, 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.12368
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 6
BROWSER_TRACK_NAME: CCIPsT H3K36me3 62 39
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 739 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,536,709
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0677
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.1946
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.8288
IROC_PERCENTILE: 31
POISSON_SCORE: 0.2865
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 739

value: BioSam 134

value: presumed normal

tag: markers

value: CD4+ T cell

value: CD25- IL17+ Th17 stim

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Abcam

value: Histone H3K36me3


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: ChIP-Seq input analysis of cortex neural stem and progenitor cells from HuFNSC01 (A03287) using Illumina HiSeq 2000
library name: A03287
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: 74-339 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: GSM817244_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.Input.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03287-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.12528
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,039,749
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.001
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0007
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0061
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.77

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

ANALYSIS FILE NAME: GSM817244_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.Input.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03287-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.12551
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 6
BROWSER_TRACK_NAME: NCD Input 01 87
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived ChIP-Seq Input Donor HuFNSC01 Library A03287 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,039,749
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.001
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0007
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0061
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.77

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

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/)

tag: submitted sample id

value: female

tag: body site

value: Brain

tag: histological type

value: Cortex neurosphere culture

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: cortex neural stem and progenitor cells


title: polyA RNA sequencing of H1 BMP4 Derived Mesendoderm Cells; polyA-RNA-seq_h1-mesendoderm_r1a

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 BMP4 Derived Mesendoderm Cells
Library name: polyA-RNA-seq_h1-mesendoderm_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12100
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12098
****************
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: GSM915324_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-mesendoderm_r1a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-mesendoderm_r1a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library polyA-RNA-seq_h1-mesendoderm_r1a 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.13722
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 302,561,309
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 83.47
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM915324_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-mesendoderm_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-mesendoderm_r1a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from H1 BMP4 Derived Mesendoderm Cultured Cells, Library polyA-RNA-seq_h1-mesendoderm_r1a 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.13732
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDM mRNA 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r1a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 302,561,309
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 83.47
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: H1 BMP4 Derived Mesendoderm Cultured Cell Line, biological replicate 1 (r1); polyA-RNA-seq_h1-mesendoderm_r1a

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Male

value: Replicate 1

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


description:
design description: H3K36me3 ChIP-Seq analysis of foreskin fibroblast from skin02 (A08399) using Illumina HiSeq 2000
library name: A08399
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: 74-294 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: GSM817241_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K36me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08399-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-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.12534
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,296,751
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1279
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1703
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9541
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4149
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817241_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K36me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08399-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-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.12557
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 6
BROWSER_TRACK_NAME: PFF H3K36me3 02 99
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin02 Library A08399 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,296,751
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1279
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1703
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9541
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4149
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: male

value: Penis

value: Fibroblast

value: No

value: primary cell culture

value: foreskin fibroblast


description:
design description: ChIP-Seq input analysis of fetal brain tissue from HuFNSC02 (A03499) using Illumina HiSeq 2000
library name: A03499
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: 57-365 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: GSM817243_UCSF-UBC.Fetal_Brain.Input.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03499-1-A03499-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Brain ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Brain, Donor HuFNSC02 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.12538
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,551,310
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0045
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1109
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.5067
IROC_PERCENTILE: 13
POISSON_SCORE: 0.165
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

ANALYSIS FILE NAME: GSM817243_UCSF-UBC.Fetal_Brain.Input.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03499-1-A03499-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Brain, Donor HuFNSC02 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.12561
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 6
BROWSER_TRACK_NAME: FB Input 02 99
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain ChIP-Seq Input Donor HuFNSC02 Library A03499 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,551,310
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0045
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1109
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.5067
IROC_PERCENTILE: 13
POISSON_SCORE: 0.165
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

value: female

value: Brain

value: Brain tissue

value: primary tissue

value: fetal brain tissue


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin fibroblast from skin02 (A08398) using Illumina HiSeq 2000
library name: A08398
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: 94-294 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: GSM817240_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08398-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-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.12526
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 78,276,129
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0429
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1094
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8882
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3769
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817240_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08398-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-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.12549
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 6
BROWSER_TRACK_NAME: PFF H3K27me3 02 98
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin02 Library A08398 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 78,276,129
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0429
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1094
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8882
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3769
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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


description:
design description: H3K4me1 ChIP-Seq analysis of foreskin fibroblast from skin01 (A08389) using Illumina HiSeq 2000
library name: A08389
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: 15 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: 94-284 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: GSM817234_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me1.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08389-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Penis Foreskin Fibroblast 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.12537
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 84,071,162
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2697
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.3064
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9684
IROC_PERCENTILE: 64
POISSON_SCORE: 0.5199
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817234_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me1.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08389-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Penis Foreskin Fibroblast 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.12560
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 6
BROWSER_TRACK_NAME: PFF H3K4me1 01 89
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin01 Library A08389 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 84,071,162
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2697
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.3064
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9684
IROC_PERCENTILE: 64
POISSON_SCORE: 0.5199
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K4me3 ChIP-Seq analysis of foreskin fibroblast from skin01 (A08390) using Illumina HiSeq 2000
library name: A08390
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: 15 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: 74-274 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: GSM817235_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08390-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Penis Foreskin Fibroblast 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.12540
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,059,783
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.5651
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5688
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9978
IROC_PERCENTILE: 36
POISSON_SCORE: 0.6044
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817235_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08390-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast 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.12563
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 6
BROWSER_TRACK_NAME: PFF H3K4me3 01 90
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin01 Library A08390 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,059,783
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.5651
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5688
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9978
IROC_PERCENTILE: 36
POISSON_SCORE: 0.6044
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K36me3 ChIP-Seq analysis of foreskin fibroblast from skin01 (A08393) using Illumina HiSeq 2000
library name: A08393
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: 15 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: 104-364 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: GSM817238_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K36me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08393-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Penis Foreskin Fibroblast 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.12533
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 59,868,535
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.2009
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.2141
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9693
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4789
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817238_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K36me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08393-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast 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.12556
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 6
BROWSER_TRACK_NAME: PFF H3K36me3 01 93
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin01 Library A08393 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 59,868,535
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.2009
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.2141
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9693
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4789
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


title: ChIP-Seq analysis of H2A.Z in human hN r1 cells; DNA_Lib 294

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 294
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9596
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8185
****************
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: GSM916022_BI.H9_Derived_Neuron_Cultured_Cells.H2A.Z.DNA_Lib_294.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 294-DNA_Lib 294.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H9 Derived Neuron Cultured Cells Histone H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2A.Z ChIP-Seq on H9 Derived Neuron Cultured Cells, Donor DNA_Lib 294, 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.12314
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,806,380
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.1249
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2016
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9797
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3033
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916022_BI.H9_Derived_Neuron_Cultured_Cells.H2A.Z.DNA_Lib_294.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 294-DNA_Lib 294.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuron Cultured Cells Histone H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2A.Z ChIP-Seq read mappings from H9 Derived Neuron Cultured Cells, Donor DNA_Lib 294, 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.12361
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 6
BROWSER_TRACK_NAME: HDN H2A.Z 94
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells Histone H2A.Z Library DNA_Lib 294 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,806,380
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.1249
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2016
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9797
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3033
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neurons derived from H9 (WA09) human stem cells; DNA_Lib 294

value: H9 Derived Neuron Cultured Cells

value: genomic DNA

value: >90% beta III tubulin(+) and >60% MAP2(+)

value: Medium:Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions - AB2+ANS+LIF on Matrigel (i.e., differentiation medium)

value: hN (ES H9 derived Neurons)

value: Female

value: Primary Cell Culture

value: ArunA Biomedical, Athens, GA

value: embryo

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Upstate

value: Histone H2A.Z

value: Branson


description:
design description: H3K9me3 ChIP-Seq analysis of foreskin fibroblast from skin01 (A08391) using Illumina HiSeq 2000
library name: A08391
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: 15 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: 84-294 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: GSM817236_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K9me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08391-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Penis Foreskin Fibroblast 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.12521
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,028,950
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0992
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.1942
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.8922
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4669
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM817236_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K9me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08391-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast 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.12544
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 6
BROWSER_TRACK_NAME: PFF H3K9me3 01 91
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin01 Library A08391 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,028,950
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0992
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.1942
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.8922
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4669
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: male

value: Penis

value: Fibroblast

value: No

value: primary cell culture

value: foreskin fibroblast


description:
design description: H3K4me1 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC01 (A03275) using Illumina HiSeq 2000
library name: A03275
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: 5 ug
SIZE_FRACTION: 109-319 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 3.75 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-0011
****************
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: GSM817232_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me1.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03275-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.12519
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 91,492,727
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3647
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.3892
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9908
IROC_PERCENTILE: 86
POISSON_SCORE: 0.5319
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM817232_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me1.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03275-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.12542
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 6
BROWSER_TRACK_NAME: NGED H3K4me1 01 75
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 Donor HuFNSC01 Library A03275 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 91,492,727
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3647
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.3892
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9908
IROC_PERCENTILE: 86
POISSON_SCORE: 0.5319
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

value: female

value: Brain

value: Ganglionic eminence neurosphere culture


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin fibroblast from skin01 (A08392) using Illumina HiSeq 2000
library name: A08392
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: 15 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: 94-289 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: GSM817237_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08392-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Penis Foreskin Fibroblast 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.12524
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,986,998
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.1521
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.1915
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9542
IROC_PERCENTILE: 70
POISSON_SCORE: 0.4677
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817237_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08392-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast 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.12547
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 6
BROWSER_TRACK_NAME: PFF H3K27me3 01 92
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin01 Library A08392 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,986,998
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.1521
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.1915
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9542
IROC_PERCENTILE: 70
POISSON_SCORE: 0.4677
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.97

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


description:
design description: H3K9me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC01 (A03277) using Illumina HiSeq 2000
library name: A03277
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: 5 ug
SIZE_FRACTION: 104-324 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: GSM817233_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K9me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03277-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.12518
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,056,144
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.17
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.1972
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9332
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4326
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.81

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

ANALYSIS FILE NAME: GSM817233_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K9me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03277-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.12541
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 6
BROWSER_TRACK_NAME: NGED H3K9me3 01 77
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 Donor HuFNSC01 Library A03277 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,056,144
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.17
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.1972
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9332
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4326
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.81

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


title: hyl1-2-dcl1-20_rosetteleaf_5week

status: Public on Apr 25 2012

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

data_processing: The raw colorspace reads containing inserts derived from 20-25nt RNAs were identified by searching for 3' matches (allowing up to two mismatches) to the sequencing adapter sequence (in colorspace); the inferred adapter sequences were then trimmed, leaving 20-25nt colorspace reads.  These data were then translated into DNA space while simultaneously discarding any reads with ambiguous (e.g., one or more "." characters) data.  The data in the Sample data tables are simple counts of each of these 20-25nt total RNAs.

organism: Arabidopsis thaliana

source_name: rosette leaves, hyl1-2/dcl1-20

growth_protocol: 12hr light / 12hr dark, 21C.

extract_protocol: Life Tech Total RNA-seq kit, total RNA modification, per manufacturer's instructions.

tag: ecotype

tag: genotype

tag: tissue

value: rosette leaves


title: ChIP-Seq analysis of H3K9me3 in human cingulate gyrus cells; DNA_Lib 616

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 616
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9597
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9759
****************
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: GSM916023_BI.Brain_Cingulate_Gyrus.H3K9me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 616-DNA_Lib 616-DNA_Lib 616.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Cingulate Gyrus, Donor 149, 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.12317
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,002,195
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0222
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0869
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.6883
IROC_PERCENTILE: 23
POISSON_SCORE: 0.2096
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM916023_BI.Brain_Cingulate_Gyrus.H3K9me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 616-DNA_Lib 616-DNA_Lib 616.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 149, 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.12364
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 6
BROWSER_TRACK_NAME: BCG H3K9me3 49 16
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K9me3 Donor 149 Library DNA_Lib 616 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,002,195
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0222
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0869
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.6883
IROC_PERCENTILE: 23
POISSON_SCORE: 0.2096
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 616

tag: sample alias

tag: sample common name

value: Brain, Cingulate Gyrus

value: Post-Mortem

value: no AD evident at demise

tag: molecule

value: genomic DNA

value: Cingulate Gyrus

value: Male

value: Primary Tissue

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Abcam

value: Histone H3K9me3


description:
design description: H3K9me3 ChIP-Seq analysis of cortex neural stem and progenitor cells from HuFNSC01 (A03271) using Illumina HiSeq 2000
library name: A03271
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: 5 ug
SIZE_FRACTION: 74-314 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: GSM817231_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.H3K9me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03271-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.12525
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,305,271
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0965
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1463
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.8831
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3486
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

ANALYSIS FILE NAME: GSM817231_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.H3K9me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03271-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.12548
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 6
BROWSER_TRACK_NAME: NCD H3K9me3 01 71
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K9me3 Donor HuFNSC01 Library A03271 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,305,271
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0965
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1463
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.8831
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3486
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

value: female

value: Cortex neurosphere culture

value: No

value: primary cell culture

value: cortex neural stem and progenitor cells


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin keratinocyte from skin01 (A05937) using Illumina HiSeq 2000
library name: A05937
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: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 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: 5 ug
SIZE_FRACTION: 88-338 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9733S
CHIP_ANTIBODY_LOT: GR16377-1
****************
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: GSM817229_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin01.A05937.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02886-1-A05937-1.hg19.level.1.release.6
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 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.12530
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,957,162
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.089
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.6779
IROC_PERCENTILE: 20
POISSON_SCORE: 0.2195
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.76

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

ANALYSIS FILE NAME: GSM817229_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin01.A05937.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02886-1-A05937-1.hg19.level.2.release.6
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 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.12553
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 6
BROWSER_TRACK_NAME: PFK H3K27me3 01 37
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin01 Library A02886 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,957,162
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.089
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.6779
IROC_PERCENTILE: 20
POISSON_SCORE: 0.2195
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.76

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

value: male

value: Penis

value: Keratinocyte

value: foreskin keratinocyte