NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM543017 Query DataSets for GSM543017
Status Public on May 17, 2010
Title MeDIP-Seq analysis of breast myoepithelial cell from RM035 (HS1394)
Sample type SRA
 
Source name HS1394-1
Organism Homo sapiens
Characteristics submitted sample id: JOC23-DNA
donor_id: RM035
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/)
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina Genome Analyzer IIx
 
Description design description: MeDIP-Seq analysis of breast myoepithelial cell from RM035 (HS1394) using Illumina Genome Analyzer IIx
library name: HS1394
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: N/A ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A 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
****************
Data processing **********************************************************************

ANALYSIS FILE NAME: GSM543017_UCSF-UBC.Breast-Myoepithelial-Cells-Individual-2.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast-Myoepithelial-Cells-Individual-2.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, Myoepithelial Cells, Individual 2 MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment in Breast, Myoepithelial Cells, Individual 2 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.2818
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

**********************************************************************

ANALYSIS FILE NAME: GSM543017_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM035.bed
ANALYSIS ALIAS: HS1394-1_42TE4AAXX-HS1394-1_42TEUAAXX.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 RM035 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.4245
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 2


QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.4689
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4554
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9828
IROC_PERCENTILE: 87
POISSON_SCORE: 0.7228
POISSON_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM543017_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM035.wig
ANALYSIS ALIAS: HS1394-1_42TE4AAXX-HS1394-1_42TEUAAXX.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 RM035 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.4221
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 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells MeDIP-Seq Donor RM035 EA Release 2


QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.4689
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4554
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9828
IROC_PERCENTILE: 87
POISSON_SCORE: 0.7228
POISSON_PERCENTILE: 100

**********************************************************************

 
Submission date May 12, 2010
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
Named Annotation GSM543017_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM035.wig.gz
Named Annotation GSM543017_UCSF-UBC.Breast-Myoepithelial-Cells-Individual-2.MeDIP-Seq.wig.gz
SRA SRX1157904
BioSample SAMN03416842

Supplementary file Size Download File type/resource
GSM543017_UCSF-UBC.Breast-Myoepithelial-Cells-Individual-2.MeDIP-Seq.wig.gz 54.2 Mb (ftp)(http) WIG
GSM543017_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM035.bed.gz 715.1 Mb (ftp)(http) BED
GSM543017_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM035.wig.gz 54.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap