|
Status |
Public on May 17, 2010 |
Title |
MRE-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS1673) |
Sample type |
SRA |
|
|
Source name |
HS1673-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC38-DNA donor_id: RM035 Sex: female body site: Breast histological type: Variant human mammary epithelial cell culture is tumor: No biomaterial_type: primary cell culture cell type: breast variant human mammary epithelial cell
|
Extracted molecule |
genomic DNA |
Extraction protocol |
library construction protocol: Refer to document 'Triple-MRE-seq library construction protocol v5' 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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|
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Library strategy |
MRE-Seq |
Library source |
genomic |
Library selection |
Restriction Digest |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
design description: MRE-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS1673) using Illumina Genome Analyzer IIx library name: HS1673 EXPERIMENT_TYPE: DNA Methylation MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI MRE_PROTOCOL_SIZE_FRACTION: 211-430 bp **************** 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: GSM543007_UCSF-UBC.Breast-vHMEC-Individual-2.MRE-Seq.wig ANALYSIS ALIAS: UCSF-UBC.Breast-vHMEC-Individual-2.MRE-Seq ANALYSIS TITLE: Raw Signal Density Graphs of Breast, vHMEC, Individual 2 MRE-Seq Data ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in Breast, vHMEC, 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.2822 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: MRE-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: GSM543007_UCSF-UBC.Breast_vHMEC.MRE-Seq.RM035.bed ANALYSIS ALIAS: HS1673-1_42TCVAAXX-HS1673-1_430WUAAXX.hg19.level.1 ANALYSIS TITLE: Mapping of Breast vHMEC MRE-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Breast vHMEC, 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.4197 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: MRE-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_MRE-SEQ_EXPERIMENTS_SCORED: 28 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.71 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 57
**********************************************************************
ANALYSIS FILE NAME: GSM543007_UCSF-UBC.Breast_vHMEC.MRE-Seq.RM035.wig ANALYSIS ALIAS: HS1673-1_42TCVAAXX-HS1673-1_430WUAAXX.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC MRE-Seq Data ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Breast vHMEC, 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.4169 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: MRE-Seq GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 0bp GENOMIC_WINDOW: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None RELEASE_NUMBER: Human Epigenome Atlas 2 BROWSER_TRACK_NAME: Bv MRE 35 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC MRE-Seq Donor RM035 EA Release 2
QUALITY SCORES: NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.71 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 57
**********************************************************************
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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 |
GSM543007_UCSF-UBC.Breast_vHMEC.MRE-Seq.RM035.wig.gz |
Named Annotation |
GSM543007_UCSF-UBC.Breast-vHMEC-Individual-2.MRE-Seq.wig.gz |
SRA |
SRX1158011 |
BioSample |
SAMN03416687 |