|
Status |
Public on Jul 27, 2011 |
Title |
Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Mesenchymal Stem Cells; renlab.H3K27me3.MSC.02.01 |
Sample type |
SRA |
|
|
Source name |
Human embryonic stem cells received from the James Thomson laboratory. Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K27me3.MSC.02.01
|
Organism |
Homo sapiens |
Characteristics |
sample alias: MSC-02 sample common name: H1 Derived Mesenchymal Stem Cells molecule: genomic DNA disease: None biomaterial_provider: James Thomson Laboratory biomaterial_type: Cell Line line: H1 lineage: Embryonic Stem Cell differentiation_stage: Embryonic stem cell differentiated into mesenchymal stem cells differentiation_method: Publication in progress passage: 6 medium: Publication in progress Sex: Male batch: MSC-2 experiment_type: Histone H3K27me3 extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf extraction_protocol_type_of_sonicator: Biorupter extraction_protocol_sonication_cycles: 80 chip_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf chip_protocol_chromatin_amount: 500 micrograms chip_protocol_bead_type: magnetic anti-rabbit chip_protocol_bead_amount: 33,500,000 chip_protocol_antibody_amount: 5 micrograms chip_antibody: H3K27me3 chip_antibody_provider: Millipore chip_antibody_catalog: 07-449 chip_antibody_lot: DAM1612188
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
sample_term_id: EFO_0000586 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: ChIP-Seq Analysis of H3K27me3 in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform. Library name: SK439 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7917 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914 **************** 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: GSM767345_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K27me3.SK439.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.H3K27me3.MSC.02.01.hg19.level.1.release.5 ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K27me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK439, 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.10447 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: 49,035,441 NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49 FINDPEAKS_SCORE: 0.06 FINDPEAKS_PERCENTILE: 69 HOTSPOT_SCORE: 0.15 HOTSPOT_PERCENTILE: 65 IROC_SCORE: 0.89 IROC_PERCENTILE: 59 POISSON_SCORE: 0.34 POISSON_PERCENTILE: 67 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
ANALYSIS FILE NAME: GSM767345_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K27me3.SK439.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.H3K27me3.MSC.02.01.hg19.level.2.release.5 ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K27me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK439, 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.10520 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: HDMSC H3K27me3 39 BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K27me3 Library SK439 EA Release 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 49,035,441 NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49 FINDPEAKS_SCORE: 0.06 FINDPEAKS_PERCENTILE: 69 HOTSPOT_SCORE: 0.15 HOTSPOT_PERCENTILE: 65 IROC_SCORE: 0.89 IROC_PERCENTILE: 59 POISSON_SCORE: 0.34 POISSON_PERCENTILE: 67 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
|
|
|
Submission date |
Jul 26, 2011 |
Last update date |
May 15, 2019 |
Contact name |
UCSD AND SALK |
Organization name |
University of California, San Diego
|
Street address |
Health Sciences Drive
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92092 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX084988 |
BioSample |
SAMN00678167 |
Named Annotation |
GSM767345_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K27me3.SK439.wig.gz |