|
| Status |
Public on Mar 31, 2011 |
| Title |
H3K4me3 ChIP-Seq analysis of paracentral neural stem and progenitor cells from HuFNSC-T (A02880) |
| Sample type |
SRA |
| |
|
| Source name |
A02880-1
|
| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: PF123B-DNA
donor_id: HuFNSC-T
body site: Brain
histological type: Paracentral cortex neurosphere culture
is tumor: No
biomaterial_type: primary cell culture
cell type: paracentral neural stem and progenitor cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
design description: H3K4me3 ChIP-Seq analysis of paracentral neural stem and progenitor cells from HuFNSC-T (A02880) using Illumina Genome Analyzer IIx
library name: A02880
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab 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: 53-342 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 2
****************
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: GSM669624_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC-T.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02880-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Fetal Brain, Donor HuFNSC-T 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.6309
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 3
QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.3981
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.4014
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4014
POISSON_PERCENTILE: 44
**********************************************************************
ANALYSIS FILE NAME: GSM669624_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC-T.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02880-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC-T 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.6651
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 3
BROWSER_TRACK_NAME: FB H3K4me3 T
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K4me3 Donor HuFNSC-T Library A02880-1 EA Release 3
QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.3981
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.4014
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4014
POISSON_PERCENTILE: 44
**********************************************************************
|
| |
|
| Submission date |
Feb 07, 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 |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
| Relations |
| Named Annotation |
GSM669624_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC-T.wig.gz |
| SRA |
SRX1140274 |
| BioSample |
SAMN03416773 |
