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Status |
Public on Jun 22, 2013 |
Title |
Histone H3K27ac ChIP-Seq of Fetal Muscle, Trunk; Histone.DS23303 |
Sample type |
SRA |
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Source name |
Fetal Muscle, Trunk primary tissue, day 115; Histone.DS23303
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Organism |
Homo sapiens |
Characteristics |
sample alias: fMuscle_Trunk.H-24851d115 sample common name: Fetal Muscle, Trunk disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Muscle, Trunk tissue_depot: UW collection_method: fetal donor_id: H-24851 donor_age: day 115 donor_health_status: NA donor_sex: Female donor_ethnicity: NA experiment_type: Histone H3K27ac extraction_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental extraction_protocol_type_of_sonicator: Diagenode Bioruptor extraction_protocol_sonication_cycles: 20-40 cycles of 0.5 minute on and 0.5 minute off chip_protocol: http://www.roadmapepigenomics.org/protocolstype/experimental chip_protocol_chromatin_amount: 60ug chip_protocol_bead_type: Invitrogen Dynabeads chip_protocol_bead_amount: 48ul chip_protocol_antibody_amount: 3ug chip_antibody: Histone H3K27ac chip_antibody_provider: Active Motif chip_antibody_catalog: 39133 chip_antibody_lot: 21311004
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Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
sample_term_id: UBERON_0001774 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Histone H3K27ac ChIP-Seq Library name: Histone.DS23303 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16286 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.16267 **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
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Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM1160189_UW.Fetal_Muscle_Trunk.H3K27ac.H-24851.Histone.DS23303.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Histone.DS23303-Histone.DS23303.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Fetal Muscle Trunk H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Muscle Trunk, Donor H-24851, 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.16806 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 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 17,494,942 FINDPEAKS_SCORE: 0.3078 FINDPEAKS_PERCENTILE: 40 HOTSPOT_SCORE: 0.3516 HOTSPOT_PERCENTILE: 39 IROC_SCORE: 0.9952 IROC_PERCENTILE: 53 POISSON_SCORE: 0.3899 POISSON_PERCENTILE: 27 MAXIMUM_REPLICATE_CORRELATION: NA
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ANALYSIS FILE NAME: GSM1160189_UW.Fetal_Muscle_Trunk.H3K27ac.H-24851.Histone.DS23303.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Histone.DS23303-Histone.DS23303.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24851, 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.16902 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 9 BROWSER_TRACK_NAME: FMT H3K27ac 51 03 BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk Histone H3K27ac Donor H-24851 Library Histone.DS23303 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 17,494,942 FINDPEAKS_SCORE: 0.3078 FINDPEAKS_PERCENTILE: 40 HOTSPOT_SCORE: 0.3516 HOTSPOT_PERCENTILE: 39 IROC_SCORE: 0.9952 IROC_PERCENTILE: 53 POISSON_SCORE: 0.3899 POISSON_PERCENTILE: 27 MAXIMUM_REPLICATE_CORRELATION: NA
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Submission date |
Jun 11, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
rharris1@bcm.tmc.edu
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Organization name |
University of Washington
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Street address |
-
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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Relations |
SRA |
SRX300947 |
BioSample |
SAMN02196321 |
Named Annotation |
GSM1160189_UW.Fetal_Muscle_Trunk.H3K27ac.H-24851.Histone.DS23303.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM1160189_UW.Fetal_Muscle_Trunk.H3K27ac.H-24851.Histone.DS23303.bed.gz |
275.9 Mb |
(ftp)(http) |
BED |
GSM1160189_UW.Fetal_Muscle_Trunk.H3K27ac.H-24851.Histone.DS23303.wig.gz |
35.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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