NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM706854 Query DataSets for GSM706854
Status Public on Dec 05, 2011
Title ChIP-Seq analysis of H3K9ac in human fetal lung cells; DNA_Lib 393
Sample type SRA
 
Source name Primary fetal lung tissue; DNA_Lib 393
Organism Homo sapiens
Characteristics sample alias: BioSAli 187
sample common name: Fetal Lung
collection_method: Post-Mortem
donor_health_status: presumed normal
molecule: genomic DNA
disease: presumed normal
tissue_type: Fetal Lung
donor_ethnicity: NA
donor_sex: Female
biomaterial_type: Primary Tissue
tissue_depot: Lung
donor_id: UW H22772
biomaterial_provider: University of Washington
donor_age: 82 Days
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_antibody: H3K9ac
chip_protocol_chromatin_amount: 10 million cells
extraction_protocol: SDS lysis
chip_protocol_antibody_amount: 2-15 ug
chip_protocol_bead_amount: 70 ul bed volume
chip_protocol: Bernstein_BROAD_ENCODE_protocol
extraction_protocol_sonication_cycles: 1
chip_antibody_catalog: ab4441
chip_antibody_provider: Abcam
chip_antibody_lot: 550799
experiment_type: Histone H3K9ac
extraction_protocol_type_of_sonicator: Bioruptor
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: Single read - Illumina
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 393
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7135
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7162
****************
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: GSM706854_BI.Fetal_Lung.H3K9ac.UW_H22772.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 393.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Fetal Lung, Donor UW H22772 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.8240
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: 17,321,198
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1404
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2297
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9834
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2941
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM706854_BI.Fetal_Lung.H3K9ac.UW_H22772.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 393.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Fetal Lung, Donor UW H22772 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.8267
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: FL H3K9ac 72 93
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K9ac Donor UW H22772 Library DNA_Lib 393 EA Release 4


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,321,198
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1404
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2297
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9834
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2941
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

 
Submission date Apr 12, 2011
Last update date May 15, 2019
Contact name BROAD INSTITUTE
E-mail(s) rharris1@bcm.tmc.edu
Organization name Broad Institute
Street address -
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (1)
GSE17312 BI Human Reference Epigenome Mapping Project
Relations
SRA SRX056806
BioSample SAMN00259533
Named Annotation GSM706854_BI.Fetal_Lung.H3K9ac.UW_H22772.wig.gz

Supplementary file Size Download File type/resource
GSM706854_BI.Fetal_Lung.H3K9ac.UW_H22772.bed.gz 268.4 Mb (ftp)(http) BED
GSM706854_BI.Fetal_Lung.H3K9ac.UW_H22772.wig.gz 37.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data not provided for this record
Raw data are available in SRA

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