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Sample GSM772939 Query DataSets for GSM772939
Status Public on Dec 28, 2011
Title ChIP-Seq analysis of WCE in human stomach mucosa cells; DNA_Lib 314
Sample type SRA
 
Source name Primary stomach mucosal tissue; DNA_Lib 314
Organism Homo sapiens
Characteristics sample alias: 235
sample common name: Stomach Mucosa
collection_method: Surgery
donor_health_status: NK stomach mucosa, stomach rmvd as part of pancr. CA
molecule: genomic DNA
disease: NK stomach mucosa, stomach rmvd as part of pancr. CA
tissue_type: Stomach Mucosa
donor_ethnicity: Caucasian
donor_sex: Male
biomaterial_type: Primary Tissue
tissue_depot: Stomach
donor_id: 157
biomaterial_provider: MGH
donor_age: 59.0 Years
extraction_protocol_sonication_cycles: 1
chip_protocol_chromatin_amount: standard
extraction_protocol: cell/nuclei lysis
experiment_type: ChIP-Seq Input
chip_protocol: Input
extraction_protocol_type_of_sonicator: Branson
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: Single read - Illumina
 
Library strategy ChIP-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Description sample_term_id: UBERON_0001199
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 314
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8629
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
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: GSM772939_BI.Stomach_Mucosa.Input.157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 314-DNA_Lib 314-DNA_Lib 314-DNA_Lib 314.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Stomach Mucosa, Donor 157, 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.10782
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 5


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,935,095
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0049
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0419
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM772939_BI.Stomach_Mucosa.Input.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 314-DNA_Lib 314-DNA_Lib 314-DNA_Lib 314.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Stomach Mucosa, Donor 157, 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.11046
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 5
BROWSER_TRACK_NAME: SM Input 57 14
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa ChIP-Seq Input Donor 157 Library DNA_Lib 314 EA Release 5


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,935,095
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0049
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0419
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

 
Submission date Aug 03, 2011
Last update date Jan 29, 2015
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
BioSample SAMN00691466
Named Annotation GSM772939_BI.Stomach_Mucosa.Input.157.wig.gz

Supplementary file Size Download File type/resource
GSM772939_BI.Stomach_Mucosa.Input.157.bed.gz 559.0 Mb (ftp)(http) BED
GSM772939_BI.Stomach_Mucosa.Input.157.wig.gz 53.3 Mb (ftp)(http) WIG
Processed data provided as supplementary file
Raw data not provided for this record

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