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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 ****************
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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
**********************************************************************
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|
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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 |
|
|
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 |