|
Status |
Public on Jan 07, 2010 |
Title |
MRE-Seq analysis of H1 embryonic stem cell line (HS1153) |
Sample type |
SRA |
|
|
Source name |
HS1153-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC14-DNA biomaterial_type: cell line line: H1 Sex: male body site: Embryo ICM histological type: Embryonic stem cell is tumor: No
|
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 II |
|
|
Description |
design description: MRE-Seq analysis of H1 embryonic stem cell line (HS1153) using Illumina Genome Analyzer IIx library name: HS1153 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: 150-400 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: GSM450236_UCSF-UBC.mre-seq.Run101596Lane3.bam ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.5 ANALYSIS TITLE: Mapping of H1 MRE-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1824 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: MRE-Seq 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
**********************************************************************
ANALYSIS FILE NAME: GSM450236_UCSF-UBC.mre-seq.Run104065Lane1.bam ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.6 ANALYSIS TITLE: Mapping of H1 MRE-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1826 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: MRE-Seq 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
**********************************************************************
ANALYSIS FILE NAME: GSM450236_UCSF-UBC.mre-seq.Run104066Lane2.bam ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.7 ANALYSIS TITLE: Mapping of H1 MRE-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1828 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: MRE-Seq 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
**********************************************************************
ANALYSIS FILE NAME: GSM450236_UCSF-UBC.mre-seq.Run104205Lane1.bam ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.8 ANALYSIS TITLE: Mapping of H1 MRE-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1830 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: MRE-Seq 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
**********************************************************************
ANALYSIS FILE NAME: GSM450236_UCSF-UBC.H1.mre-seq.wig ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level2.combined.3 ANALYSIS TITLE: Raw Signal Density Graphs of H1 MRE-Seq Data ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in the H1 cell line 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.1861 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: GSM450236_UCSF-UBC.H1.MRE-Seq.HS1153.bed ANALYSIS ALIAS: HS1153-1_42F2TAAXX-HS1153-1_313MYAAXX-HS1153-1_42EMFAAXX.hg19.level.1 ANALYSIS TITLE: Mapping of H1 Cell Line MRE-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on the H1 Cell Line, Library HS1153 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.4214 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: 89.07 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 7
**********************************************************************
ANALYSIS FILE NAME: GSM450236_UCSF-UBC.H1.MRE-Seq.HS1153.wig ANALYSIS ALIAS: HS1153-1_42F2TAAXX-HS1153-1_313MYAAXX-HS1153-1_42EMFAAXX.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line MRE-Seq Data ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from the H1 Cell Line, Library HS1153 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.4186 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: H1 MRE 53 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line MRE-Seq Library HS1153 EA Release 2
QUALITY SCORES: NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 89.07 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 7
**********************************************************************
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|
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Submission date |
Sep 04, 2009 |
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 |
GPL9115 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Named Annotation |
GSM450236_UCSF-UBC.H1.mre-seq.wig.gz |
Named Annotation |
GSM450236_UCSF-UBC.H1.MRE-Seq.HS1153.wig.gz |
SRA |
SRX010885 |
BioSample |
SAMN03416742 |