|
| Status |
Public on Jul 18, 2013 |
| Title |
ChIP-Seq analysis H3K27me3 hNP; Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3 |
| Sample type |
SRA |
| |
|
| Source name |
neuronal progenitors derived from H9 (WA09) human stem cells; Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3
|
| 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: H3K27Me3
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: CS200603
chip_antibody_provider: Millipore
chip_antibody_lot: DAM1499359
experiment_type: Histone H3K27me3
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:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8062
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: GSM772801_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3-Lib EpiLabSPL Row 1793.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3, 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.17303
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: 54,111,982
FINDPEAKS_SCORE: 0.0929
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.1453
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9579
IROC_PERCENTILE: 78
POISSON_SCORE: 0.3482
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM772801_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3-Lib EpiLabSPL Row 1793.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3, 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.17486
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 H3K27me3 e3
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,111,982
FINDPEAKS_SCORE: 0.0929
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.1453
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9579
IROC_PERCENTILE: 78
POISSON_SCORE: 0.3482
POISSON_PERCENTILE: 54
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 |
SRX088716 |
| BioSample |
SAMN00691452 |
| Named Annotation |
GSM772801_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.113.wig.gz |
