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Status |
Public on Mar 22, 2013 |
Title |
ChIP-Seq Input of Fetal Muscle, Trunk; Histone.DS23031 |
Sample type |
SRA |
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Source name |
Fetal Muscle, trunk primary tissue, day 115; Histone.DS23031
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Organism |
Homo sapiens |
Characteristics |
sample alias: fMuscle_trunk.H-24854d115 sample common name: Fetal Muscle, Trunk molecule: genomic DNA 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-24854 donor_age: day 115 donor_health_status: NA donor_sex: Female donor_ethnicity: NA experiment_type: ChIP-Seq Input 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: Input chip_protocol_chromatin_amount: 50ng
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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 |
RANDOM |
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: ChIP-Seq Input Library name: Histone.DS23031 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15687 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15686 **************** 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: GSM1102809_UW.Fetal_Muscle_Trunk.Input.H-24854.Histone.DS23031.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Histone.DS23031-Histone.DS23031-Histone.DS23031.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Fetal Muscle Trunk Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Muscle Trunk, Donor H-24854, 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.16812 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: 25,760,287 FINDPEAKS_SCORE: 0.0062 FINDPEAKS_PERCENTILE: 63 HOTSPOT_SCORE: 0.0329 HOTSPOT_PERCENTILE: 66 IROC_SCORE: 0.873 IROC_PERCENTILE: 43 POISSON_SCORE: 0.051 POISSON_PERCENTILE: 48 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1102809_UW.Fetal_Muscle_Trunk.Input.H-24854.Histone.DS23031.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Histone.DS23031-Histone.DS23031-Histone.DS23031.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24854, 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.16908 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 Input 54 31 BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk ChIP-Seq Input Donor H-24854 Library Histone.DS23031 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 25,760,287 FINDPEAKS_SCORE: 0.0062 FINDPEAKS_PERCENTILE: 63 HOTSPOT_SCORE: 0.0329 HOTSPOT_PERCENTILE: 66 IROC_SCORE: 0.873 IROC_PERCENTILE: 43 POISSON_SCORE: 0.051 POISSON_PERCENTILE: 48 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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Submission date |
Mar 20, 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 |
SRX252746 |
BioSample |
SAMN01984901 |
Named Annotation |
GSM1102809_UW.Fetal_Muscle_Trunk.Input.H-24854.Histone.DS23031.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM1102809_UW.Fetal_Muscle_Trunk.Input.H-24854.Histone.DS23031.bed.gz |
411.4 Mb |
(ftp)(http) |
BED |
GSM1102809_UW.Fetal_Muscle_Trunk.Input.H-24854.Histone.DS23031.wig.gz |
46.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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