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Status |
Public on Sep 02, 2011 |
Title |
H3K4me1 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A03477) |
Sample type |
SRA |
|
|
Source name |
A03477-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC78-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
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Extracted molecule |
genomic DNA |
Extraction protocol |
library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' 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 |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
design description: H3K4me1 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A03477) using Illumina HiSeq 2000 library name: A03477 EXPERIMENT_TYPE: Histone H3K4me1 EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug SIZE_FRACTION: 93-397 bp CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug CHIP_ANTIBODY: H3K4me1 CHIP_ANTIBODY_PROVIDER: Diagenode CHIP_ANTIBODY_CATALOG: pAb-037-050 CHIP_ANTIBODY_LOT: A399-002341P **************** 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: GSM707008_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me1.HuFNSC02.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A03477-1.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 were mapped to the human genome using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8204 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: ChIP-Seq GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: Pash SOFTWARE_VERSION: 3.0 MAXIMUM_ALIGNMENT_LENGTH: Read length MISMATCHES_ALLOWED: 10% of read length ALIGNMENTS_ALLOWED: 1 TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration. 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. ALIGNMENT_POSTPROCESSING: None READ_EXTENSION: 200bp RELEASE_NUMBER: Human Epigenome Atlas 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 40,901,968 NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12 FINDPEAKS_SCORE: 0.0292 FINDPEAKS_PERCENTILE: 15 HOTSPOT_SCORE: 0.1825 HOTSPOT_PERCENTILE: 15 IROC_SCORE: 0.8887 IROC_PERCENTILE: 8 POISSON_SCORE: 0.3468 POISSON_PERCENTILE: 15 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM707008_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me1.HuFNSC02.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A03477-1.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 were processed into density graphs of raw signal representing the aligned read density. ANALYSIS TYPE: ABUNDANCE_MEASUREMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8224 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: ChIP-Seq GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 200bp 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: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None RELEASE_NUMBER: Human Epigenome Atlas 4 BROWSER_TRACK_NAME: NGED H3K4me1 02 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 Donor HuFNSC02 Library A03477-1 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 40,901,968 NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12 FINDPEAKS_SCORE: 0.0292 FINDPEAKS_PERCENTILE: 15 HOTSPOT_SCORE: 0.1825 HOTSPOT_PERCENTILE: 15 IROC_SCORE: 0.8887 IROC_PERCENTILE: 8 POISSON_SCORE: 0.3468 POISSON_PERCENTILE: 15 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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Submission date |
Apr 12, 2011 |
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 |
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Relations |
Reanalyzed by |
GSE99453 |
Named Annotation |
GSM707008_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me1.HuFNSC02.wig.gz |
SRA |
SRX1157616 |
BioSample |
SAMN03416705 |