|
Status |
Public on Jul 27, 2011 |
Title |
MeDIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A02758) |
Sample type |
SRA |
|
|
Source name |
A02758-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC101-DNA donor_id: HuFGM02 Sex: male body site: Brain histological type: Germinal matrix tissue is tumor: No biomaterial_type: primary tissue tissue_type: brain (germinal matrix) tissue
|
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 Genome Analyzer IIx |
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|
Description |
design description: MeDIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A02758) using Illumina Genome Analyzer IIx library name: A02758 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: 1 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 ****************
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Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM707023_UCSF-UBC.Brain_Germinal_Matrix.MeDIP-Seq.HuFGM02.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A02758-1.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Brain Germinal Matrix MeDIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Brain Germinal Matrix, Donor HuFGM02 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.7930 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 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 79,145,077 NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5 FINDPEAKS_SCORE: 0.0174 FINDPEAKS_PERCENTILE: 20 HOTSPOT_SCORE: 0.1612 HOTSPOT_PERCENTILE: 20 IROC_SCORE: 0.7825 IROC_PERCENTILE: 20 POISSON_SCORE: 0.3329 POISSON_PERCENTILE: 20 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM707023_UCSF-UBC.Brain_Germinal_Matrix.MeDIP-Seq.HuFGM02.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A02758-1.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix MeDIP-Seq Data ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 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.7935 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 4 BROWSER_TRACK_NAME: BGM MeDIP 02 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix MeDIP-Seq Donor HuFGM02 Library A02758-1 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 79,145,077 NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5 FINDPEAKS_SCORE: 0.0174 FINDPEAKS_PERCENTILE: 20 HOTSPOT_SCORE: 0.1612 HOTSPOT_PERCENTILE: 20 IROC_SCORE: 0.7825 IROC_PERCENTILE: 20 POISSON_SCORE: 0.3329 POISSON_PERCENTILE: 20 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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|
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Submission date |
Apr 12, 2011 |
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 |
GPL10999 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Reanalyzed by |
GSE69894 |
Named Annotation |
GSM707023_UCSF-UBC.Brain_Germinal_Matrix.MeDIP-Seq.HuFGM02.wig.gz |
SRA |
SRX1157896 |
BioSample |
SAMN03416919 |