|
| Status |
Public on Apr 13, 2011 |
| Title |
Reference Epigenome: ChIP-Seq Input from iPS 19.11 Cells; renlab.Input.iPS-19.11_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-19.11_01.01
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: iPS-19.11-01
sample common name: iPS DF 19.11 Cell Line
molecule: genomic DNA
disease: None
biomaterial_provider: James Thompson Laboratory
biomaterial_type: Cell Line
line: iPS 19.11
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: Between 30 and 40
medium: mTeSR
Sex: Male
batch: iPSC 19.11
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
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SKiPS19.11-1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6824
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
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: GSM706082_UCSD.iPS_DF_19.11.Input.SKiPS19.11-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.iPS-19.11_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS DF 19.11 Cell Line, Library SKiPS19.11-1 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.8286
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: 19,331,754
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0039
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0702
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.943
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1167
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM706082_UCSD.iPS_DF_19.11.Input.SKiPS19.11-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.iPS-19.11_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS DF 19.11 Cell Line, Library SKiPS19.11-1 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.8305
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: iD19.11 Input 1
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line ChIP-Seq Input Library SKiPS19.11-1 EA Release 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,331,754
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0039
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0702
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.943
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1167
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX056716 |
| BioSample |
SAMN00255375 |
| Named Annotation |
GSM706082_UCSD.iPS_DF_19.11.Input.SKiPS19.11-1.wig.gz |
