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Status |
Public on Dec 28, 2011 |
Title |
ChIP-Seq analysis of H3K9ac in human chondrogenic dif cells; Lib EpiLabSPL Row 1390 |
Sample type |
SRA |
|
|
Source name |
chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1390
|
Organism |
Homo sapiens |
Characteristics |
sample alias: 80 sample common name: Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells donor_health_status: healthy molecule: genomic DNA disease: none markers: NA culture_conditions: Medium: NA; Differentiation Method: alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011) passage_if_expanded: NA cell_type: chondrogenic dif cells donor_ethnicity: NA donor_sex: Unknown biomaterial_type: Primary Cell Culture donor_id: 58 biomaterial_provider: Rikshospitalet University Hospital donor_age: NA chip_protocol_bead_type: Protein A-Sepharose 4B chip_antibody: H3K9Ac chip_protocol_chromatin_amount: 10 million cells extraction_protocol: SDS lysis chip_protocol_antibody_amount: 2-15 ug chip_protocol_bead_amount: 70 ul bed volume chip_protocol: Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles: 1 chip_antibody_catalog: ab4441 chip_antibody_provider: Abcam chip_antibody_lot: 455103 experiment_type: Histone H3K9ac extraction_protocol_type_of_sonicator: Bioruptor
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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 |
ChIP |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
sample_term_id: CL_0000138 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: Lib EpiLabSPL Row 1390 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8047 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951 **************** 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: GSM772786_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.58.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib EpiLabSPL Row 1390.hg19.level.1.release.5 ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Chondrocytes from 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.10840 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 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 30,793,260 NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19 FINDPEAKS_SCORE: 0.2608 FINDPEAKS_PERCENTILE: 79 HOTSPOT_SCORE: 0.3076 HOTSPOT_PERCENTILE: 79 IROC_SCORE: 0.9966 IROC_PERCENTILE: 63 POISSON_SCORE: 0.3663 POISSON_PERCENTILE: 79 MAXIMUM_REPLICATE_CORRELATION: 0.99
**********************************************************************
ANALYSIS FILE NAME: GSM772786_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.58.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib EpiLabSPL Row 1390.hg19.level.2.release.5 ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Chondrocytes 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.11104 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 5 BROWSER_TRACK_NAME: CfBMDMSC H3K9ac 58 90 BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 58 Library Lib EpiLabSPL Row 1390 EA Release 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 30,793,260 NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19 FINDPEAKS_SCORE: 0.2608 FINDPEAKS_PERCENTILE: 79 HOTSPOT_SCORE: 0.3076 HOTSPOT_PERCENTILE: 79 IROC_SCORE: 0.9966 IROC_PERCENTILE: 63 POISSON_SCORE: 0.3663 POISSON_PERCENTILE: 79 MAXIMUM_REPLICATE_CORRELATION: 0.99
**********************************************************************
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Submission date |
Aug 03, 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) |
GSE17312 |
BI Human Reference Epigenome Mapping Project |
|
Relations |
BioSample |
SAMN00205687 |
Named Annotation |
GSM772786_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.58.wig.gz |