|
Status |
Public on Jul 27, 2011 |
Title |
MRE-Seq analysis of fetal brain tissue from H22510 (A04895) |
Sample type |
SRA |
|
|
Source name |
A04895-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC84-DNA donor_id: H22510 Sex: male body site: Brain histological type: Brain tissue is tumor: No biomaterial_type: primary tissue tissue_type: fetal brain tissue
|
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 fetal brain tissue from H22510 (A04895) using Illumina Genome Analyzer IIx library name: A04895 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, SsiI MRE_PROTOCOL_SIZE_FRACTION: 168-400 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: GSM707015_UCSF-UBC.Fetal_Brain.MRE-Seq.H22510.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A04895-1.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Fetal Brain MRE-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Fetal Brain, Donor H22510 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.7940 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 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 31,477,014 NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.6 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM707015_UCSF-UBC.Fetal_Brain.MRE-Seq.H22510.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A04895-1.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain MRE-Seq Data ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Fetal Brain, Donor H22510 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.7944 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 4 BROWSER_TRACK_NAME: FB MRE 10 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain MRE-Seq Donor H22510 Library A04895-1 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 31,477,014 NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.6 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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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 |
GSM707015_UCSF-UBC.Fetal_Brain.MRE-Seq.H22510.wig.gz |
SRA |
SRX1158000 |
BioSample |
SAMN03416914 |