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| Status |
Public on May 27, 2016 |
| Title |
Bisulfite-Seq analysis of peripheral cd8 naive from TC007 (A27953) |
| Sample type |
SRA |
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| Source name |
A27953-1
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| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: JOC59-DNA
donor_id: TC007
Sex: female
body site: Blood
histological type: CD8 naive cell
is tumor: No
biomaterial_type: primary cell
cell_type: CD8 naive cell
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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 peripheral cd8 naive from TC007 (A27953) using Illumina HiSeq 2000
library name: A27953
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: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 1 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: 151-633 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 95.71
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
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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 |
SRX838271 |
| BioSample |
SAMN03416765 |
| 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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