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Status |
Public on May 27, 2016 |
Title |
Bisulfite-Seq analysis of foreskin melanocyte from skin03 (A20920) |
Sample type |
SRA |
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Source name |
A20920-1
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Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC177-DNA donor_id: skin03 Sex: male body site: Penis histological type: Melanocyte is tumor: No biomaterial_type: primary cell culture cell type: foreskin melanocyte
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Extracted molecule |
genomic DNA |
Extraction protocol |
library construction protocol: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
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Description |
design description: Bisulfite-Seq analysis of foreskin melanocyte from skin03 (A20920) using Illumina HiSeq 2000 library name: A20920 EXPERIMENT_TYPE: DNA Methylation EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris-E210 EXTRACTION_PROTOCOL_SONICATION_CYCLES: 0.92 min DNA_PREPARATION_INITIAL_DNA_QNTY: 1.00 ug DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 300 bp DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 215-370 bp BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion BISULFITE_CONVERSION_PERCENT: 96.38 LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5 LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0 LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0 LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification **************** 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 |
Various levels of processed data files will be made available as this project proceeds.
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Submission date |
Jan 12, 2015 |
Last update date |
May 15, 2019 |
Contact name |
UCSF-UBC CENTER |
Organization name |
UCSF-UBC
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Street address |
UCSF-UBC
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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 |
SRA |
SRX838246 |
BioSample |
SAMN03416696 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data not provided for this record |
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