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Status |
Public on Apr 13, 2011 |
Title |
Reference Epigenome: ChIP-Seq Input from iPS 6.9 Cells; renlab.Input.iPS-6.9_01.01 |
Sample type |
SRA |
|
|
Source name |
Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.Input.iPS-6.9_01.01
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Organism |
Homo sapiens |
Characteristics |
sample alias: iPS-6.9-01 sample common name: iPS DF 6.9 Cell Line molecule: genomic DNA disease: None biomaterial_provider: James Thompson Laboratory biomaterial_type: Cell Line line: iPS 6.9 lineage: Induced pluripotent stem cell line derived from foreskin fibroblasts differentiation_stage: Induced pluripotent stem cell differentiation_method: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009). passage: 33 medium: mTeSR Sex: Male batch: iPSC 6.9 experiment_type: ChIP-Seq Input extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf extraction_protocol_type_of_sonicator: Biorupter extraction_protocol_sonication_cycles: 80 chip_protocol: Input chip_protocol_chromatin_amount: 500 micrograms
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina Genome Analyzer IIx |
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Description |
sample_term_id: NTR_0001172 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: ChIP-Seq Input from iPS 6.9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform. Library name: SKiPS6.9-1 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6895 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6880 **************** 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: GSM706083_UCSD.iPS_DF_6.9.Input.SKiPS6.9-1.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.Input.iPS-6.9_01.01.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS DF 6.9 Cell Line, Library SKiPS6.9-1 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.8282 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: 13,724,896 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14 FINDPEAKS_SCORE: 0.0453 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.1863 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.7954 IROC_PERCENTILE: 100 POISSON_SCORE: 0.3004 POISSON_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM706083_UCSD.iPS_DF_6.9.Input.SKiPS6.9-1.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.Input.iPS-6.9_01.01.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS DF 6.9 Cell Line, Library SKiPS6.9-1 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.8301 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: iD6.9 Input 1 BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line ChIP-Seq Input Library SKiPS6.9-1 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 13,724,896 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14 FINDPEAKS_SCORE: 0.0453 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.1863 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.7954 IROC_PERCENTILE: 100 POISSON_SCORE: 0.3004 POISSON_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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Submission date |
Apr 08, 2011 |
Last update date |
May 15, 2019 |
Contact name |
UCSD AND SALK |
Organization name |
University of California, San Diego
|
Street address |
Health Sciences Drive
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92092 |
Country |
USA |
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|
Platform ID |
GPL10999 |
Series (1) |
GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX056717 |
BioSample |
SAMN00255376 |
Named Annotation |
GSM706083_UCSD.iPS_DF_6.9.Input.SKiPS6.9-1.wig.gz |