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Sample GSM1027303 Query DataSets for GSM1027303
Status Public on Nov 01, 2012
Title Histone H3K9me3 ChIP-Seq of Fetal Thymus; Histone.DS22904
Sample type SRA
 
Source name Fetal Thymus primary tissue, day 110; Histone.DS22904
Organism Homo sapiens
Characteristics sample alias: fThymus.H-24644d110
sample common name: Fetal Thymus
molecule: genomic DNA
disease: None
biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass
biomaterial_type: Primary Tissue
tissue_type: Fetal Thymus
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 H3K9me3
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: Millipore A/G agarose beads
chip_protocol_bead_amount: 30ul A/G bead slurry
chip_protocol_antibody_amount: 3ug
chip_antibody: Histone H3K9me3
chip_antibody_provider: Active Motif
chip_antibody_catalog: 39161
chip_antibody_lot: 13509002
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_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22904
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14483
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
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: GSM1027303_UW.Fetal_Thymus.H3K9me3.H-24644.Histone.DS22904.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22904.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Thymus, 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.16808
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: 14,850,964
FINDPEAKS_SCORE: 0.1249
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2483
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.8514
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3481
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027303_UW.Fetal_Thymus.H3K9me3.H-24644.Histone.DS22904.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22904.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Thymus, 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.16904
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: FT H3K9me3 44 04
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Histone H3K9me3 Donor H-24644 Library Histone.DS22904 EA Release 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,850,964
FINDPEAKS_SCORE: 0.1249
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2483
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.8514
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3481
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: NA

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

 
Submission date Oct 29, 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 SRX201790
BioSample SAMN01797281
Named Annotation GSM1027303_UW.Fetal_Thymus.H3K9me3.H-24644.Histone.DS22904.wig.gz

Supplementary file Size Download File type/resource
GSM1027303_UW.Fetal_Thymus.H3K9me3.H-24644.Histone.DS22904.bed.gz 231.4 Mb (ftp)(http) BED
GSM1027303_UW.Fetal_Thymus.H3K9me3.H-24644.Histone.DS22904.wig.gz 34.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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