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Status |
Public on Oct 02, 2014 |
Title |
MeDIP-Seq analysis of breast myoepithelial cell from RM071 (HS2369) |
Sample type |
SRA |
|
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Source name |
HS2369-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC48-DNA donor_id: RM071 Sex: female body site: Breast histological type: Myoepithelial cell is tumor: No biomaterial_type: primary cell cell_type: breast myoepithelial cell
|
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 breast myoepithelial cell from RM071 (HS2369) using Illumina Genome Analyzer IIx library name: HS2369 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: 25 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: 2 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: 80604 **************** 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: GSM1517153_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM071.bed ANALYSIS ALIAS: GSM1517153_hg19.level.1 ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells MeDIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Breast Myoepithelial Cells, Donor RM071 were mapped to the human genome using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT 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: 10 TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 10 positions it is removed from consideration. TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None ALIGNMENT_POSTPROCESSING: None RELEASE_NUMBER: Human Epigenome Atlas 2 NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24 FINDPEAKS_SCORE: 0.3948 FINDPEAKS_PERCENTILE: 75 HOTSPOT_SCORE: 0.4128 HOTSPOT_PERCENTILE: 79 IROC_SCORE: 0.963 IROC_PERCENTILE: 66 POISSON_SCORE: 0.7116 POISSON_PERCENTILE: 83
ANALYSIS FILE NAME: GSM1517153_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM071.wig ANALYSIS ALIAS: GSM1517153_.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells MeDIP-Seq Data ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM071 were processed into density graphs of raw signal representing the aligned read density. ANALYSIS TYPE: ABUNDANCE_MEASUREMENT 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 2 BROWSER_TRACK_NAME: BMC MeDIP 71 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells MeDIP-Seq Donor RM071 EA Release 2 NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24 FINDPEAKS_SCORE: 0.3948 FINDPEAKS_PERCENTILE: 75 HOTSPOT_SCORE: 0.4128 HOTSPOT_PERCENTILE: 79 IROC_SCORE: 0.963 IROC_PERCENTILE: 66 POISSON_SCORE: 0.7116 POISSON_PERCENTILE: 83
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Submission date |
Sep 30, 2014 |
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 |
|
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Platform ID |
GPL10999 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
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Relations |
Reanalyzed by |
GSE69894 |
Named Annotation |
GSM1517153_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM071.bed.gz |
Named Annotation |
GSM1517153_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM071.wig.gz |
SRA |
SRX1157914 |
BioSample |
SAMN03416830 |