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Sample GSM772738 Query DataSets for GSM772738
Status Public on Jul 18, 2013
Title ChIP-Seq analysis of H3K9me3 in human hN (ES H9 derived Neurons) cells; Lib EpiLabSPL Row 1690
Sample type SRA
 
Source name neurons derived from H9 (WA09) human stem cells; Lib EpiLabSPL Row 1690
Organism Homo sapiens
Characteristics sample alias: 268
sample common name: H9 Derived Neuron Cultured Cells
donor_health_status: NA
molecule: genomic DNA
disease: none
markers: >90% beta III tubulin(+) and >60% MAP2(+)
culture_conditions: Medium: Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions - AB2+ANS+LIF on Matrigel (i.e., differentiation medium)
passage_if_expanded: NA
cell_type: hN (ES H9 derived Neurons)
donor_ethnicity: NA
donor_sex: Female
biomaterial_type: Primary Cell Culture
donor_id: 113
biomaterial_provider: ArunA Biomedical, Athens, GA
donor_age: embryo
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_antibody: H3K9Me3
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: ab8898
chip_antibody_provider: Abcam
chip_antibody_lot: 484088
experiment_type: Histone H3K9me3
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: CL_0000540
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1690
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7999
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8185
****************
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: GSM772738_BI.H9_Derived_Neuron_Cultured_Cells.H3K9me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3-Lib EpiLabSPL Row 1690.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuron Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3, 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.17299
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: 58,237,826
FINDPEAKS_SCORE: 0.0148
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0825
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8105
IROC_PERCENTILE: 48
POISSON_SCORE: 0.2236
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772738_BI.H9_Derived_Neuron_Cultured_Cells.H3K9me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3-Lib EpiLabSPL Row 1690.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuron Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3, 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.17482
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: HDN H3K9me3 e3
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells Histone H3K9me3 Library Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3 EA Release 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,237,826
FINDPEAKS_SCORE: 0.0148
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0825
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8105
IROC_PERCENTILE: 48
POISSON_SCORE: 0.2236
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

 
Submission date Aug 03, 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)
GSE17312 BI Human Reference Epigenome Mapping Project
Relations
SRA SRX088653
BioSample SAMN00691453
Named Annotation GSM772738_BI.H9_Derived_Neuron_Cultured_Cells.H3K9me3.113.wig.gz

Supplementary file Size Download File type/resource
GSM772738_BI.H9_Derived_Neuron_Cultured_Cells.H3K9me3.113.bed.gz 845.0 Mb (ftp)(http) BED
GSM772738_BI.H9_Derived_Neuron_Cultured_Cells.H3K9me3.113.wig.gz 63.8 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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