|
| Status |
Public on Jan 07, 2010 |
| Title |
MRE-Seq analysis of H1 embryonic stem cell line (HS1052) |
| Sample type |
SRA |
| |
|
| Source name |
HS1052-1
|
| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: JOC12-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 (HS1052) using Illumina Genome Analyzer II
library name: HS1052
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: 6 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: GSM428286_UCSF-UBC.mre-seq.Run99923Lane5.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.1
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.1816
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: GSM428286_UCSF-UBC.mre-seq.Run101316Lane1.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.2
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.1818
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: GSM428286_UCSF-UBC.mre-seq.Run101317Lane2.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.3
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.1820
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: GSM428286_UCSF-UBC.mre-seq.Run101318Lane3.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.4
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.1822
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: GSM428286_UCSF-UBC.H1.mre-seq.wig
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level2.combined.1
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.1859
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: GSM428286_UCSF-UBC.H1.MRE-Seq.HS1052.bed
ANALYSIS ALIAS: HS1052-1_313MWAAXX-HS1052-1_30WLJAAXX.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 HS1052 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.4210
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: 82.85
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 3
**********************************************************************
ANALYSIS FILE NAME: GSM428286_UCSF-UBC.H1.MRE-Seq.HS1052.wig
ANALYSIS ALIAS: HS1052-1_313MWAAXX-HS1052-1_30WLJAAXX.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 HS1052 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.4182
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 52
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line MRE-Seq Library HS1052 EA Release 2
QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 82.85
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 3
**********************************************************************
|
| |
|
| Submission date |
Jul 15, 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 |
GSM428286_UCSF-UBC.H1.mre-seq.wig.gz |
| Named Annotation |
GSM428286_UCSF-UBC.H1.MRE-Seq.HS1052.wig.gz |
| SRA |
SRX006272 |
| BioSample |
SAMN03416822 |
