|
Status |
Public on Jun 24, 2013 |
Title |
ChIP-Seq analysis of H3K27ac in human HUES64 derived CD184+ cells; DNA_Lib 3189 |
Sample type |
SRA |
|
|
Source name |
CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 3189
|
Organism |
Homo sapiens |
Characteristics |
cell_type: CD184+ endoderm cultured cells sample alias: BioSam 1246 sample common name: hESC Derived CD184+ Endoderm Cultured Cells lineage: endoderm medium: RPMI 100ng/mL Activin A 50ng/mL Wnt3a disease: presumed normal passage: 23 line: HUES64 derived CD184+ differentiation_method: in vitro culture batch: BioSAli 1888 biomaterial_type: Cell Line differentiation_stage: differentiated Sex: Male biomaterial_provider: Harvard chip_protocol_bead_type: Protein A-Sepharose 4B chip_antibody: H3K27ac 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: 39133 chip_antibody_provider: Active Motif chip_antibody_lot: 31610003 experiment_type: Histone H3K27ac 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 |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
sample_term_id: CL_0000223 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: DNA_Lib 3189 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15387 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15413 **************** 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: GSM1112830_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27ac.DNA_Lib_3189.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 3189.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 3189, 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.17245 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 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 17,628,829 FINDPEAKS_SCORE: 0.1242 FINDPEAKS_PERCENTILE: 9 HOTSPOT_SCORE: 0.0 HOTSPOT_PERCENTILE: 6 IROC_SCORE: 0.973 IROC_PERCENTILE: 15 POISSON_SCORE: 0.3342 POISSON_PERCENTILE: 19 MAXIMUM_REPLICATE_CORRELATION: 0.33
**********************************************************************
ANALYSIS FILE NAME: GSM1112830_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27ac.DNA_Lib_3189.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 3189.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 3189, 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.17428 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 9 BROWSER_TRACK_NAME: hDCE H3K27ac 89 BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27ac Library DNA_Lib 3189 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 17,628,829 FINDPEAKS_SCORE: 0.1242 FINDPEAKS_PERCENTILE: 9 HOTSPOT_SCORE: 0.0 HOTSPOT_PERCENTILE: 6 IROC_SCORE: 0.973 IROC_PERCENTILE: 15 POISSON_SCORE: 0.3342 POISSON_PERCENTILE: 19 MAXIMUM_REPLICATE_CORRELATION: 0.33
**********************************************************************
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|
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Submission date |
Apr 02, 2013 |
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 |
GPL11154 |
Series (1) |
GSE17312 |
BI Human Reference Epigenome Mapping Project |
|
Relations |
Reanalyzed by |
GSE90454 |
SRA |
SRX259075 |
BioSample |
SAMN01997274 |
Named Annotation |
GSM1112830_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27ac.DNA_Lib_3189.wig.gz |