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Sample GSM433176 Query DataSets for GSM433176
Status Public on Aug 05, 2009
Title ChIP-Seq analysis of H3K36me3 in human H1 cells, 30HCBAAXX090610-7-S
Sample type SRA
 
Source name H1 cells; 30HCBAAXX090610-7-S
Organism Homo sapiens
Characteristics molecule: genomic DNA
disease: none
biomaterial_provider: Cellular Dynamics
biomaterial_type: Cell Line
line: H1
lineage: undifferentiated
differentiation_stage: stage_zero
differentiation_method: none
passage: 42
medium: TESR
sex: Unknown
batch: 39877
experiment_type: Histone H3K36me3
extraction_protocol: SDS lysis
extraction_protocol_type_of_sonicator: Bioruptor
extraction_protocol_sonication_cycles: 1
chip_protocol: standard
chip_protocol_chromatin_amount: standard
chip_protocol_bead_type: standard
chip_protocol_bead_amount: standard
chip_protocol_antibody_amount: standard
chip_antibody: H3K36Me3
chip_antibody_provider: Abcam
chip_antibody_catalog: ab9050
chip_antibody_lot: 136353
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 II
 
Description sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: Solexa-12524
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.964
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.965

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
Data processing **********************************************************************

ANALYSIS FILE NAME: GSM433176_BI.H3K36me3.bam
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1504
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM433176_BI.H3K36me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K36me3 in the H1 cell line 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.1505
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM433176_BI.H1.H3K36me3.Solexa-12524.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30HCBAAXX090610-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H1 Cell Line, Library Solexa-12524 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.4677
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_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0671
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1645
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.8243
IROC_PERCENTILE: 13
POISSON_SCORE: 0.2662
POISSON_PERCENTILE: 6

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

ANALYSIS FILE NAME: GSM433176_BI.H1.H3K36me3.Solexa-12524.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30HCBAAXX090610-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-12524 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.4951
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 H3K36me3 24
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K36me3 Library Solexa-12524 EA Release 2


QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0671
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1645
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.8243
IROC_PERCENTILE: 13
POISSON_SCORE: 0.2662
POISSON_PERCENTILE: 6

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

 
Submission date Jul 24, 2009
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 GPL9115
Series (1)
GSE17312 BI Human Reference Epigenome Mapping Project
Relations
SRA SRX007388
BioSample SAMN00002934
Named Annotation GSM433176_BI.H3K36me3.wig.gz
Named Annotation GSM433176_BI.H1.H3K36me3.Solexa-12524.wig.gz

Supplementary file Size Download File type/resource
GSM433176_BI.H1.H3K36me3.Solexa-12524.bed.gz 156.4 Mb (ftp)(http) BED
GSM433176_BI.H1.H3K36me3.Solexa-12524.wig.gz 31.0 Mb (ftp)(http) WIG
GSM433176_BI.H3K36me3.bam 864.1 Mb (ftp)(http) BAM
GSM433176_BI.H3K36me3.wig.gz 31.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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