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| Status |
Public on Dec 28, 2011 |
| Title |
ChIP-Seq analysis of H3K9me3 in human Duodenum smooth muscle cells; DNA_Lib 460 |
| Sample type |
SRA |
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| Source name |
Primary duodenum smooth muscle tissue; DNA_Lib 460
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: 238
sample common name: Duodenum Smooth Muscle
collection_method: Surgery
donor_health_status: NL smooth muscle, duodenum rmvd as part of pancr.,VA
molecule: genomic DNA
disease: NL smooth muscle, duodenum rmvd as part of pancr.,VA
tissue_type: Smooth Muscle
donor_ethnicity: Caucasian
donor_sex: Male
biomaterial_type: Primary Tissue
tissue_depot: Duodenum
donor_id: 160
biomaterial_provider: MGH
donor_age: 59.0 Years
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_antibody: H3K9me3
chip_protocol_chromatin_amount: 0.5 to 3 million cells
extraction_protocol: cell/nuclei lysis
chip_protocol_antibody_amount: ~1 ug
chip_protocol_bead_amount: 10 ul bed volume
chip_protocol: Bernstein_BROAD_ENCODE_protocol
extraction_protocol_sonication_cycles: 1
chip_antibody_catalog: ab8898
chip_antibody_provider: Abcam
chip_antibody_lot: 484088
experiment_type: Histone H3K9me3
extraction_protocol_type_of_sonicator: Branson
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
sample_term_id: UBERON_0012488
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 460
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8599
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9450
****************
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: GSM772909_BI.Duodenum_Smooth_Muscle.H3K9me3.160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 460-DNA_Lib 460-DNA_Lib 460-DNA_Lib 460.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Duodenum Smooth Muscle, Donor 160, 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.10800
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: 32,280,370
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0206
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.0602
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.872
IROC_PERCENTILE: 61
POISSON_SCORE: 0.1591
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM772909_BI.Duodenum_Smooth_Muscle.H3K9me3.160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 460-DNA_Lib 460-DNA_Lib 460-DNA_Lib 460.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor 160, 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.11064
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: DSM H3K9me3 60 60
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K9me3 Donor 160 Library DNA_Lib 460 EA Release 5
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,280,370
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0206
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.0602
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.872
IROC_PERCENTILE: 61
POISSON_SCORE: 0.1591
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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| Submission date |
Aug 03, 2011 |
| Last update date |
Jan 29, 2015 |
| Contact name |
BROAD INSTITUTE |
| E-mail(s) |
rharris1@bcm.tmc.edu
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| Organization name |
Broad Institute
|
| Street address |
-
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE17312 |
BI Human Reference Epigenome Mapping Project |
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| Relations |
| BioSample |
SAMN00691463 |
| Named Annotation |
GSM772909_BI.Duodenum_Smooth_Muscle.H3K9me3.160.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM772909_BI.Duodenum_Smooth_Muscle.H3K9me3.160.bed.gz |
501.0 Mb |
(ftp)(http) |
BED |
| GSM772909_BI.Duodenum_Smooth_Muscle.H3K9me3.160.wig.gz |
51.0 Mb |
(ftp)(http) |
WIG |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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