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Sample GSM1112823 Query DataSets for GSM1112823
Status Public on Jul 18, 2013
Title ChIP-Seq analysis of H3K9me3 in human CD56+ mesoderm cells; DNA_Lib 3197
Sample type SRA
 
Source name HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 3197
Organism Homo sapiens
Characteristics sample alias: BioSam 1249
sample common name: hESC Derived CD56+ Mesoderm Cultured Cells
lineage: mesoderm
medium: CD56 mesoderm - Day 0-1: DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5: DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)
disease: presumed normal
passage: 23
line: CD56+ mesoderm
differentiation_method: adherence
batch: BioSAli 1892
biomaterial_type: Cell Line
differentiation_stage: intermediate
Sex: Male
biomaterial_provider: Harvard
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: 877391
experiment_type: Histone H3K9me3
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_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3197
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15380
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15410
****************
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: GSM1112823_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_3197.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3197.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 3197, 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.17315
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: 13,638,106
FINDPEAKS_SCORE: 0.0413
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.6868
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3546
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112823_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_3197.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3197.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 3197, 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.17498
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: hDCM H3K9me3 97
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 3197 EA Release 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,638,106
FINDPEAKS_SCORE: 0.0413
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.6868
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3546
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

 
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
SRA SRX259068
BioSample SAMN01997271
Named Annotation GSM1112823_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_3197.wig.gz

Supplementary file Size Download File type/resource
GSM1112823_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_3197.bed.gz 213.4 Mb (ftp)(http) BED
GSM1112823_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_3197.wig.gz 30.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data not provided for this record
Processed data provided as supplementary file
Raw data are available in SRA

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