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Sample GSM613898 Query DataSets for GSM613898
Status Public on Oct 28, 2010
Title MRE-Seq analysis of peripheral mononuclear cell from TC007 (HS2627)
Sample type SRA
 
Source name HS2627-1
Organism Homo sapiens
Characteristics submitted sample id: JOC56-DNA
donor_id: TC007
Sex: female
body site: Blood
histological type: Peripheral blood mononuclear cell
is tumor: No
biomaterial_type: primary cell
cell_type: Peripheral blood mononuclear 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/)
 
Library strategy MRE-Seq
Library source genomic
Library selection Restriction Digest
Instrument model Illumina Genome Analyzer IIx
 
Description design description: MRE-Seq analysis of peripheral mononuclear cell from TC007 (HS2627) using Illumina Genome Analyzer IIx
library name: HS2627
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: 167-384 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: GSM613898_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MRE-Seq.TC007.bed
ANALYSIS ALIAS: HS2627-1_705WMAAXX-HS2627-1_70601AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC007 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.4206
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: 99.15
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 71

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

ANALYSIS FILE NAME: GSM613898_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MRE-Seq.TC007.wig
ANALYSIS ALIAS: HS2627-1_705WMAAXX-HS2627-1_70601AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC007 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.4178
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: PBM MRE 07
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells MRE-Seq Donor TC007 EA Release 2


QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.15
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 71

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

 
Submission date Oct 28, 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
Reanalyzed by GSE69894
Named Annotation GSM613898_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MRE-Seq.TC007.wig.gz
SRA SRX1158023
BioSample SAMN03416828

Supplementary file Size Download File type/resource
GSM613898_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MRE-Seq.TC007.bed.gz 399.9 Mb (ftp)(http) BED
GSM613898_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MRE-Seq.TC007.wig.gz 8.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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