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Status |
Public on Sep 13, 2012 |
Title |
Bisulfite-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A04698) |
Sample type |
SRA |
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Source name |
A04698-1
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Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC091-DNA donor_id: HuFGM02 Sex: male body site: Brain histological type: Germinal matrix tissue is tumor: No biomaterial_type: primary tissue tissue_type: brain (germinal matrix) tissue
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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 brain (germinal matrix) tissue from HuFGM02 (A04698) using Illumina HiSeq 2000 library name: A04698 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: 25 min DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 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: 231-688 bp BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion BISULFITE_CONVERSION_PERCENT: 99.4 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: 12 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 |
**********************************************************************
ANALYSIS FILE NAME: GSM941747_UCSF-UBC.Brain_Germinal_Matrix.Bisulfite-Seq.HuFGM02.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A04698-1.hg19.level.2.release.8 ANALYSIS TITLE: Methylation Proportion Graphs of Brain Germinal Matrix Bisulfite-Seq Data ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 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.13770 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 8 BROWSER_TRACK_NAME: BGM BS 02 98 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix Bisulfite-Seq Donor HuFGM02 Library A04698 EA Release 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 1,295,657,686 NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.58 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 83 MAXIMUM_REPLICATE_CORRELATION: NA
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Submission date |
Jun 01, 2012 |
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 |
Named Annotation |
GSM941747_UCSF-UBC.Brain_Germinal_Matrix.Bisulfite-Seq.HuFGM02.wig.gz |
SRA |
SRX1122663 |
BioSample |
SAMN03416821 |
Supplementary file |
Size |
Download |
File type/resource |
GSM941747_UCSF-UBC.Brain_Germinal_Matrix.Bisulfite-Seq.HuFGM02.wig.gz |
191.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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