|
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
**********************************************************************
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|
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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 |