|
| Status |
Public on Jun 22, 2013 |
| Title |
H3K4me1 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19296) |
| Sample type |
SRA |
| |
|
| Source name |
A19296-1
|
| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: JOC170-4-DNA
biomaterial_type: cell line
line: UCSF-4
Sex: female
body site: Embryo ICM
histological type: Embryonic stem cell
is tumor: No
|
| 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/)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
design description: H3K4me1 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19296) using Illumina HiSeq 2000
library name: A19296
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: 81-365 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
****************
|
| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19296-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the UCSF-4* Cell Line, Library A19296 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.17034
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 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,385,031
FINDPEAKS_SCORE: 0.1149
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2389
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8904
IROC_PERCENTILE: 16
POISSON_SCORE: 0.439
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
ANALYSIS FILE NAME: GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19296-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4Star Cell Line H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the UCSF-4Star Cell Line, Library A19296 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.17093
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 9
BROWSER_TRACK_NAME: UCSF4* H3K4me1 96
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K4me1 Library A19296 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,385,031
FINDPEAKS_SCORE: 0.1149
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2389
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8904
IROC_PERCENTILE: 16
POISSON_SCORE: 0.439
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
|
| |
|
| 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 |
GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.wig.gz |
| SRA |
SRX1158117 |
| BioSample |
SAMN03416736 |
