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| Status |
Public on Sep 13, 2012 |
| Title |
MRE-Seq analysis of foreskin keratinocyte from skin03 (A13914) |
| Sample type |
SRA |
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| Source name |
A13914-1
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| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: JOC176-DNA
donor_id: skin03
Sex: male
body site: Penis
histological type: Keratinocyte
is tumor: No
biomaterial_type: primary cell culture
cell type: foreskin keratinocyte
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
library construction protocol: Refer to document '5xMRE-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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| Library strategy |
MRE-Seq |
| Library source |
genomic |
| Library selection |
Restriction Digest |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
design description: MRE-Seq analysis of foreskin keratinocyte from skin03 (A13914) using Illumina HiSeq 2000
library name: A13914
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-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: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 156-400 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
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| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM958169_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13914-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13774
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 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,051,340
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.17
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.54
**********************************************************************
ANALYSIS FILE NAME: GSM958169_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13914-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13777
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 8
BROWSER_TRACK_NAME: PFK MRE 03 14
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin03 Library A13914 EA Release 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,051,340
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.17
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.54
**********************************************************************
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| Submission date |
Jul 09, 2012 |
| 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 |
| |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
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| Relations |
| Reanalyzed by |
GSE69894 |
| Named Annotation |
GSM958169_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin03.wig.gz |
| SRA |
SRX1158005 |
| BioSample |
SAMN03416901 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM958169_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin03.bed.gz |
166.7 Mb |
(ftp)(http) |
BED |
| GSM958169_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin03.wig.gz |
3.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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