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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
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer IIx |
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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 ****************
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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
**********************************************************************
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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 |
|
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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 |