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Sample GSM669906 Query DataSets for GSM669906
Status Public on Mar 31, 2011
Title ChIP-Seq analysis of H3K9ac; hippocampus mid cls; Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac
Sample type SRA
 
Source name human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac
Organism Homo sapiens
Characteristics sample alias: 172
sample common name: Brain, Hippocampus Middle
collection_method: post-mortem
donor_health_status: NA
molecule: genomic DNA
disease: none
tissue_type: Hippocampus Middle
passage_if_expanded: NA
donor_ethnicity: NA
donor_sex: Female
biomaterial_type: Primary Tissue
tissue_depot: brain
donor_id: 112
biomaterial_provider: Rush University Medical Center
donor_age: 75
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: 455103
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 Genome Analyzer IIx
 
Description sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5647
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5937
****************
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: GSM669906_BI.Brain_Hippocampus_Middle.H3K9ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Brain Hippocampus Middle, Donor 112 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.6556
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 3


QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1722
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.2257
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9912
IROC_PERCENTILE: 40
POISSON_SCORE: 0.3179
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM669906_BI.Brain_Hippocampus_Middle.H3K9ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 112 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.6766
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 3
BROWSER_TRACK_NAME: BHM H3K9ac 12
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K9ac Donor 112 Library Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac EA Release 3


QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1722
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.2257
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9912
IROC_PERCENTILE: 40
POISSON_SCORE: 0.3179
POISSON_PERCENTILE: 60

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

 
Submission date Feb 07, 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 GPL10999
Series (1)
GSE19465 BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject
Relations
BioSample SAMN00205674
Named Annotation GSM669906_BI.Brain_Hippocampus_Middle.H3K9ac.112.wig.gz
SRA SRX533020

Supplementary file Size Download File type/resource
GSM669906_BI.Brain_Hippocampus_Middle.H3K9ac.112.bed.gz 466.8 Mb (ftp)(http) BED
GSM669906_BI.Brain_Hippocampus_Middle.H3K9ac.112.wig.gz 49.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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