|
Status |
Public on Jan 21, 2012 |
Title |
Reference Epigenome: ChIP-Seq Input from BMP4 Mesendoderm Cells; renlab.Input.BMP4M.03.01 |
Sample type |
SRA |
|
|
Source name |
Human embryonic stem cells received from the James Thomson laboratory. Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.Input.BMP4M.03.01
|
Organism |
Homo sapiens |
Characteristics |
sample alias: BMP4-07 sample common name: H1 BMP4 Derived Mesendoderm Cultured Cells molecule: genomic DNA disease: None biomaterial_provider: James Thomson Laboratory biomaterial_type: Cell Line line: H1 lineage: Embryonic Stem Cell differentiation_stage: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4 differentiation_method: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days passage: Between 25 and 35 medium: E8 Sex: Male batch: BMP4-7 experiment_type: ChIP-Seq Input extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf extraction_protocol_type_of_sonicator: Biorupter extraction_protocol_sonication_cycles: 80 chip_protocol: Input chip_protocol_chromatin_amount: 500 micrograms
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
sample_term_id: NTR_0000856 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: ChIP-Seq Input from BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform. Library name: AK318 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11182 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11177 **************** 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: GSM864037_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK318.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.Input.BMP4M.03.01.hg19.level.1.release.7 ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK318, 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.12850 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 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 39,676,287 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6 FINDPEAKS_SCORE: 0.0111 FINDPEAKS_PERCENTILE: 67 HOTSPOT_SCORE: 0.1395 HOTSPOT_PERCENTILE: 67 IROC_SCORE: 0.7919 IROC_PERCENTILE: 67 POISSON_SCORE: 0.3699 POISSON_PERCENTILE: 83 MAXIMUM_REPLICATE_CORRELATION: 0.94
**********************************************************************
ANALYSIS FILE NAME: GSM864037_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK318.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.Input.BMP4M.03.01.hg19.level.2.release.7 ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK318, 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.12859 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 7 BROWSER_TRACK_NAME: HBDM Input 18 BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK318 EA Release 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 39,676,287 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6 FINDPEAKS_SCORE: 0.0111 FINDPEAKS_PERCENTILE: 67 HOTSPOT_SCORE: 0.1395 HOTSPOT_PERCENTILE: 67 IROC_SCORE: 0.7919 IROC_PERCENTILE: 67 POISSON_SCORE: 0.3699 POISSON_PERCENTILE: 83 MAXIMUM_REPLICATE_CORRELATION: 0.94
**********************************************************************
|
|
|
Submission date |
Jan 19, 2012 |
Last update date |
May 15, 2019 |
Contact name |
UCSD AND SALK |
Organization name |
University of California, San Diego
|
Street address |
Health Sciences Drive
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92092 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX116608 |
BioSample |
SAMN00774086 |
Named Annotation |
GSM864037_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK318.wig.gz |