|
Status |
Public on Jun 04, 2012 |
Title |
MeDIP-Seq analysis of foreskin melanocyte from skin02 (A09693) |
Sample type |
SRA |
|
|
Source name |
A09693-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC130-DNA donor_id: skin02 Sex: male body site: Penis histological type: Melanocyte is tumor: No biomaterial_type: primary cell culture cell type: foreskin melanocyte
|
Extracted molecule |
genomic DNA |
Extraction protocol |
library construction protocol: Refer to document 'MeDIP-seq library construction protocol v2' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
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Library strategy |
MeDIP-Seq |
Library source |
genomic |
Library selection |
5-methylcytidine antibody |
Instrument model |
Illumina HiSeq 2000 |
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|
Description |
design description: MeDIP-Seq analysis of foreskin melanocyte from skin02 (A09693) using Illumina HiSeq 2000 library name: A09693 EXPERIMENT_TYPE: DNA Methylation EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.972 ug MeDIP_ANTIBODY: Methylcytidine MeDIP_ANTIBODY_PROVIDER: Eurogentec MeDIP_ANTIBODY_CATALOG: BI-MECY-0100 MeDIP_ANTIBODY_LOT: 80808 **************** 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: GSM941727_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin02.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A09693-1-A08304-1.hg19.level.1.release.7 ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12916 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: MeDIP-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: None ALIGNMENT_POSTPROCESSING: None RELEASE_NUMBER: Human Epigenome Atlas 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 115,654,127 NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3 FINDPEAKS_SCORE: 0.4984 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.5187 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.9861 IROC_PERCENTILE: 100 POISSON_SCORE: 0.5848 POISSON_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
ANALYSIS FILE NAME: GSM941727_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin02.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A09693-1-A08304-1.hg19.level.2.release.7 ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Data ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12919 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: MeDIP-Seq GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 200bp GENOMIC_WINDOW: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None RELEASE_NUMBER: Human Epigenome Atlas 7 BROWSER_TRACK_NAME: PFM MeDIP 02 93 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin02 Library A09693 EA Release 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 115,654,127 NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3 FINDPEAKS_SCORE: 0.4984 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.5187 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.9861 IROC_PERCENTILE: 100 POISSON_SCORE: 0.5848 POISSON_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
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Submission date |
Jun 01, 2012 |
Last update date |
May 15, 2019 |
Contact name |
UCSF-UBC CENTER |
Organization name |
UCSF-UBC
|
Street address |
UCSF-UBC
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94143 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Reanalyzed by |
GSE69894 |
Named Annotation |
GSM941727_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin02.wig.gz |
SRA |
SRX1157899 |
BioSample |
SAMN03416781 |