|
| Status |
Public on Sep 18, 2013 |
| Title |
Bisulfite-Seq analysis of foreskin fibroblast from skin03 (A20919) |
| Sample type |
SRA |
| |
|
| Source name |
A20919-1
|
| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: JOC175-DNA
donor_id: skin03
Sex: male
body site: Penis
histological type: Fibroblast
is tumor: No
biomaterial_type: primary cell culture
cell type: foreskin fibroblast
|
| 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/)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
design description: Bisulfite-Seq analysis of foreskin fibroblast from skin03 (A20919) using Illumina HiSeq 2000
library name: A20919
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: 200-400 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: 96.64
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
****************
|
| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM1127120_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Bisulfite-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A20919-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Penis Foreskin Fibroblast Primary Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18773
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFF BS 03 19
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Bisulfite-Seq Donor skin03 Library A20919 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 328,604,139
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.77
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Apr 22, 2013 |
| 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 |
GPL11154 |
| Series (1) |
| GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
| Relations |
| Named Annotation |
GSM1127120_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Bisulfite-Seq.skin03.wig.gz |
| SRA |
SRX271299 |
| BioSample |
SAMN03416926 |
