|
| Status |
Public on Nov 01, 2012 |
| Title |
Histone H3K4me3 ChIP-Seq of Fetal Thymus; Histone.DS21539 |
| Sample type |
SRA |
| |
|
| Source name |
Fetal Thymus primary tissue, day 110; Histone.DS21539
|
| 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 H3K4me3
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: 60ul
chip_protocol_antibody_amount: 12ul
chip_antibody: Histone H3K4me3
chip_antibody_provider: Cell Signaling
chip_antibody_catalog: 9751B
chip_antibody_lot: lot 2
|
| 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 H3K4me3 ChIP-Seq
Library name: Histone.DS21539
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14524
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: GSM1027299_UW.Fetal_Thymus.H3K4me3.H-24644.Histone.DS21539.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21539-Histone.DS21539.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 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.16873
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: 25,565,772
FINDPEAKS_SCORE: 0.3697
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3733
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3727
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1027299_UW.Fetal_Thymus.H3K4me3.H-24644.Histone.DS21539.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21539-Histone.DS21539.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 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.16969
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 H3K4me3 44 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Histone H3K4me3 Donor H-24644 Library Histone.DS21539 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,565,772
FINDPEAKS_SCORE: 0.3697
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3733
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3727
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Oct 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Northwest REMC |
| E-mail(s) |
[email protected]
|
| 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 |
SRX201786 |
| BioSample |
SAMN01797281 |
| Named Annotation |
GSM1027299_UW.Fetal_Thymus.H3K4me3.H-24644.Histone.DS21539.wig.gz |
