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Sample GSM1058788 Query DataSets for GSM1058788
Status Public on Jan 10, 2013
Title ChIP-Seq Input of Fetal Muscle, Leg; Histone.DS21509
Sample type SRA
 
Source name Fetal Muscle, Leg primary tissue, day 110; Histone.DS21509
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: 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
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: Single read - Illumina
 
Library strategy ChIP-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Description sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21509
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14972
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: GSM1058788_UW.Fetal_Muscle_Leg.Input.H-24644.Histone.DS21509.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21509.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.16876
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: 23,511,773
FINDPEAKS_SCORE: 0.0035
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0112
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0426
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058788_UW.Fetal_Muscle_Leg.Input.H-24644.Histone.DS21509.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21509.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.16972
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 Input 44 09
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg ChIP-Seq Input Donor H-24644 Library Histone.DS21509 EA Release 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,511,773
FINDPEAKS_SCORE: 0.0035
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0112
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0426
POISSON_PERCENTILE: 38
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 SRX213513
BioSample SAMN01881601
Named Annotation GSM1058788_UW.Fetal_Muscle_Leg.Input.H-24644.Histone.DS21509.wig.gz

Supplementary file Size Download File type/resource
GSM1058788_UW.Fetal_Muscle_Leg.Input.H-24644.Histone.DS21509.bed.gz 366.0 Mb (ftp)(http) BED
GSM1058788_UW.Fetal_Muscle_Leg.Input.H-24644.Histone.DS21509.wig.gz 44.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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