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Status |
Public on Sep 18, 2013 |
Title |
Bisulfite-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A17784) |
Sample type |
SRA |
|
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Source name |
A17784-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC163-4-5-DNA donor_id: HuFNSC02 Sex: female body site: Brain histological type: Ganglionic eminence neurosphere culture is tumor: No biomaterial_type: primary cell culture cell type: ganglionic eminence neural stem and progenitor cells
|
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 ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A17784) using Illumina HiSeq 2000 library name: A17784 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: 15 min DNA_PREPARATION_INITIAL_DNA_QNTY: 5 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: 280-440 bp BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion BISULFITE_CONVERSION_PERCENT: 99.93 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: 15 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: GSM1127055_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Bisulfite-Seq.HuFNSC02.A17784.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A17784-1-A13819-1.hg19.level.2.release.9 ANALYSIS TITLE: Methylation Proportion Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Data ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.18770 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: NGED BS 02 84 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 313,154,881 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.72 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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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 |
|
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Platform ID |
GPL11154 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Reanalyzed by |
GSE84998 |
Named Annotation |
GSM1127055_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Bisulfite-Seq.HuFNSC02.A17784.wig.gz |
SRA |
SRX271234 |
BioSample |
SAMN03416843 |