|
Status |
Public on Mar 31, 2011 |
Title |
ChIP-Seq analysis of WCE in BM-MSC cells; Lib:MC:20100706:14--ChIP:MC:20100628:14:BM-MSC:WCE |
Sample type |
SRA |
|
|
Source name |
bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100706:14--ChIP:MC:20100628:14:BM-MSC:WCE
|
Organism |
Homo sapiens |
Characteristics |
sample alias: 76B sample common name: Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells donor_health_status: healthy molecule: genomic DNA disease: none markers: NA culture_conditions: Medium: DMEM/FBS; Differentiation Method: adherence passage_if_expanded: NA cell_type: BM-MSC donor_ethnicity: NA donor_sex: Unknown biomaterial_type: Primary Cell Culture donor_id: 58 biomaterial_provider: Rikshospitalet University Hospital donor_age: 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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|
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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: EFO_0000586 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: Lib:MC:20100706:14--ChIP:MC:20100628:14:BM-MSC:WCE EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5699 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5953 **************** 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: GSM669958_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:MC:20100706:14--ChIP:MC:20100628:14:BM-MSC:WCE.hg19.level.1.release.3 ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 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.6566 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 3
QUALITY SCORES: NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61 FINDPEAKS_SCORE: 0.0059 FINDPEAKS_PERCENTILE: 23 HOTSPOT_SCORE: 0.0166 HOTSPOT_PERCENTILE: 63 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.064 POISSON_PERCENTILE: 67
**********************************************************************
ANALYSIS FILE NAME: GSM669958_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:MC:20100706:14--ChIP:MC:20100628:14:BM-MSC:WCE.hg19.level.2.release.3 ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 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.6776 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 3 BROWSER_TRACK_NAME: BMDMSC Input 58 BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 58 Library Lib:MC:20100706:14--ChIP:MC:20100628:14:BM-MSC:WCE EA Release 3
QUALITY SCORES: NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61 FINDPEAKS_SCORE: 0.0059 FINDPEAKS_PERCENTILE: 23 HOTSPOT_SCORE: 0.0166 HOTSPOT_PERCENTILE: 63 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.064 POISSON_PERCENTILE: 67
**********************************************************************
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|
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Submission date |
Feb 07, 2011 |
Last update date |
Jan 29, 2015 |
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) |
GSE19465 |
BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject |
|
Relations |
BioSample |
SAMN00205689 |
Named Annotation |
GSM669958_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.wig.gz |