|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 10, 2013 |
Title |
Histone H3K27ac ChIP-Seq of Fetal Muscle, Leg; Histone.DS21782 |
Sample type |
SRA |
|
|
Source name |
Fetal Muscle, Leg primary tissue, day 110; Histone.DS21782
|
Organism |
Homo sapiens |
Characteristics |
sample alias: fMuscle_Leg.H-24644d110 sample common name: Fetal Muscle, Leg molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Muscle, Leg tissue_depot: UW collection_method: fetal donor_id: H-24644 donor_age: day 110 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
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
sample_term_id: UBERON_0001383 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Histone H3K27ac ChIP-Seq Library name: Histone.DS21782 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14966 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904 **************** 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: GSM1058767_UW.Fetal_Muscle_Leg.H3K27ac.H-24644.Histone.DS21782.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Histone.DS21782-Histone.DS21782.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Fetal Muscle Leg H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16850 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: 26,118,255 FINDPEAKS_SCORE: 0.4844 FINDPEAKS_PERCENTILE: 73 HOTSPOT_SCORE: 0.5044 HOTSPOT_PERCENTILE: 73 IROC_SCORE: 0.9976 IROC_PERCENTILE: 68 POISSON_SCORE: 0.5578 POISSON_PERCENTILE: 72 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1058767_UW.Fetal_Muscle_Leg.H3K27ac.H-24644.Histone.DS21782.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Histone.DS21782-Histone.DS21782.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16946 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: FML H3K27ac 44 82 BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg Histone H3K27ac Donor H-24644 Library Histone.DS21782 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 26,118,255 FINDPEAKS_SCORE: 0.4844 FINDPEAKS_PERCENTILE: 73 HOTSPOT_SCORE: 0.5044 HOTSPOT_PERCENTILE: 73 IROC_SCORE: 0.9976 IROC_PERCENTILE: 68 POISSON_SCORE: 0.5578 POISSON_PERCENTILE: 72 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
|
|
Submission date |
Dec 31, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
rharris1@bcm.tmc.edu
|
Organization name |
University of Washington
|
Street address |
-
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX213492 |
BioSample |
SAMN01881601 |
Named Annotation |
GSM1058767_UW.Fetal_Muscle_Leg.H3K27ac.H-24644.Histone.DS21782.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM1058767_UW.Fetal_Muscle_Leg.H3K27ac.H-24644.Histone.DS21782.bed.gz |
404.5 Mb |
(ftp)(http) |
BED |
GSM1058767_UW.Fetal_Muscle_Leg.H3K27ac.H-24644.Histone.DS21782.wig.gz |
39.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|