NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM772810 Query DataSets for GSM772810
Status Public on Jul 18, 2013
Title ChIP-Seq analysis H3K9me3: hNP; Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3
Sample type SRA
 
Source name neuronal progenitors derived from H9 (WA09) human stem cells; Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3
Organism Homo sapiens
Characteristics sample alias: 269
sample common name: H9 Derived Neuronal Progenitor Cultured Cells
donor_health_status: NA
molecule: genomic DNA
disease: none
markers: >90% nestin(+) and <5% Oct-4(+)
culture_conditions: Medium: Cultured in defined proliferation medium containing AB2+ANS plus FGF2 and LIF on Matrigel-coated surfaces.
passage_if_expanded: NA
cell_type: hNP (ES H9 derived Nuronal Progenitors)
donor_ethnicity: NA
donor_sex: Unknown
biomaterial_type: Primary Cell Culture
donor_id: 113
biomaterial_provider: ArunA Biomedical, Athens, GA
donor_age: NA
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_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8071
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8184
****************
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: GSM772810_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1792-Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib EpiLabSPL Row 1792, 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.17217
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: 49,908,005
FINDPEAKS_SCORE: 0.0326
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.1043
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8484
IROC_PERCENTILE: 60
POISSON_SCORE: 0.2907
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772810_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1792-Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib EpiLabSPL Row 1792, 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.17400
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: HDNP H3K9me3 92
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library Lib EpiLabSPL Row 1792 EA Release 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,908,005
FINDPEAKS_SCORE: 0.0326
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.1043
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8484
IROC_PERCENTILE: 60
POISSON_SCORE: 0.2907
POISSON_PERCENTILE: 48
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 SRX088726
BioSample SAMN00691452
Named Annotation GSM772810_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.113.wig.gz

Supplementary file Size Download File type/resource
GSM772810_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.113.bed.gz 726.9 Mb (ftp)(http) BED
GSM772810_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.113.wig.gz 59.2 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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap