|
Status |
Public on Dec 05, 2011 |
Title |
ChIP-Seq analysis of WCE in human Mobilized CD34 cells; Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE |
Sample type |
SRA |
|
|
Source name |
flow sorted CD34+ cells, mobilized; Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE
|
Organism |
Homo sapiens |
Characteristics |
sample alias: RO 01517 sample common name: CD34 Primary Cells molecule: genomic DNA disease: None biomaterial_provider: FHCRC HEIMFELD biomaterial_type: Primary Cell cell_type: CD34 Primary Cells markers: CD34+ donor_id: RO 01517 donor_age: year 43 donor_health_status: NA donor_sex: Male donor_ethnicity: Caucasian passage_if_expanded: NA extraction_protocol_sonication_cycles: 1 chip_protocol_chromatin_amount: standard extraction_protocol: SDS lysis experiment_type: ChIP-Seq Input chip_protocol: Input extraction_protocol_type_of_sonicator: Bioruptor
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina Genome Analyzer IIx |
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Description |
sample_term_id: CL_0000837 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7514 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3100 **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
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Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM773048_BI.Mobilized_CD34_Primary_Cells.Input.RO_01517.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01517 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.8252 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 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 33,174,619 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14 FINDPEAKS_SCORE: 0.0032 FINDPEAKS_PERCENTILE: 8 HOTSPOT_SCORE: 0.0077 HOTSPOT_PERCENTILE: 42 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.0318 POISSON_PERCENTILE: 25 MAXIMUM_REPLICATE_CORRELATION: 0.92
**********************************************************************
ANALYSIS FILE NAME: GSM773048_BI.Mobilized_CD34_Primary_Cells.Input.RO_01517.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01517 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.8279 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 4 BROWSER_TRACK_NAME: MCD34 Input 17 BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01517 Library Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized Mobilized CD34:WCE EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 33,174,619 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14 FINDPEAKS_SCORE: 0.0032 FINDPEAKS_PERCENTILE: 8 HOTSPOT_SCORE: 0.0077 HOTSPOT_PERCENTILE: 42 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.0318 POISSON_PERCENTILE: 25 MAXIMUM_REPLICATE_CORRELATION: 0.92
**********************************************************************
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Submission date |
Aug 03, 2011 |
Last update date |
Nov 05, 2019 |
Contact name |
BROAD INSTITUTE |
E-mail(s) |
rharris1@bcm.tmc.edu
|
Organization name |
Broad Institute
|
Street address |
-
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
|
|
Platform ID |
GPL10999 |
Series (1) |
GSE17312 |
BI Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX088963 |
BioSample |
SAMN00113491 |
Named Annotation |
GSM773048_BI.Mobilized_CD34_Primary_Cells.Input.RO_01517.wig.gz |