NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM605336 Query DataSets for GSM605336
Status Public on Oct 07, 2010
Title Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC-04.01
Sample type SRA
 
Source name Human embryonic stem cells; H1 cell line; renlab.Input.hESC-04.01
Organism Homo sapiens
Characteristics molecule: genomic DNA
disease: None
biomaterial_provider: James Thompson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: Embryonic Stem Cell
differentiation_stage: None
differentiation_method: None
passage: 54
medium: mTeSER
Sex: Male
batch: H1Ep54-25x
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: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: YL262
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3719
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3456
****************
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: GSM605336_UCSD.H1.Input.YL262.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-04.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library YL262 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.4418
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 2


QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0545
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.0803
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.3687
IROC_PERCENTILE: 26
POISSON_SCORE: 0.2465
POISSON_PERCENTILE: 64

**********************************************************************

ANALYSIS FILE NAME: GSM605336_UCSD.H1.Input.YL262.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-04.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library YL262 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.4451
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 2
BROWSER_TRACK_NAME: H1 Input 62
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library YL262 EA Release 2


QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0545
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.0803
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.3687
IROC_PERCENTILE: 26
POISSON_SCORE: 0.2465
POISSON_PERCENTILE: 64

**********************************************************************

 
Submission date Oct 06, 2010
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 SRX027885
BioSample SAMN00114949
Named Annotation GSM605336_UCSD.H1.Input.YL262.wig.gz

Supplementary file Size Download File type/resource
GSM605336_UCSD.H1.Input.YL262.bed.gz 369.6 Mb (ftp)(http) BED
GSM605336_UCSD.H1.Input.YL262.wig.gz 47.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap