|
Status |
Public on Mar 22, 2013 |
Title |
ChIP-Seq Input of CD4 Primary Cells; Histone.DS21541 |
Sample type |
SRA |
|
|
Source name |
flow sorted CD4+ Cells,year 21; Histone.DS21541
|
Organism |
Homo sapiens |
Characteristics |
sample alias: CD4.RO_01721 sample common name: CD4 Primary Cells molecule: genomic DNA disease: None biomaterial_provider: FHCRC HEIMFELD biomaterial_type: Primary Cell cell_type: CD4 Primary Cells markers: CD4+ donor_id: RO 01679 donor_age: year 21 donor_health_status: NA donor_sex: Male donor_ethnicity: Caucasian passage_if_expanded: 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: CL_0000492 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: ChIP-Seq Input Library name: Histone.DS21541 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15773 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345 **************** 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: GSM1102805_UW.CD4_Primary_Cells.Input.RO_01679.Histone.DS21541.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Histone.DS21541-Histone.DS21541.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of CD4 Primary Cells Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4 Primary Cells, Donor RO 01679, 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.16807 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: 40,969,799 FINDPEAKS_SCORE: 0.0044 FINDPEAKS_PERCENTILE: 22 HOTSPOT_SCORE: 0.0028 HOTSPOT_PERCENTILE: 8 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.025 POISSON_PERCENTILE: 17 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1102805_UW.CD4_Primary_Cells.Input.RO_01679.Histone.DS21541.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Histone.DS21541-Histone.DS21541.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4 Primary Cells, Donor RO 01679, 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.16903 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: CD4 Input 79 41 BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells ChIP-Seq Input Donor RO 01679 Library Histone.DS21541 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 40,969,799 FINDPEAKS_SCORE: 0.0044 FINDPEAKS_PERCENTILE: 22 HOTSPOT_SCORE: 0.0028 HOTSPOT_PERCENTILE: 8 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.025 POISSON_PERCENTILE: 17 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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|
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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
|
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 |
SRX252742 |
BioSample |
SAMN00204016 |
Named Annotation |
GSM1102805_UW.CD4_Primary_Cells.Input.RO_01679.Histone.DS21541.wig.gz |