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Status |
Public on Jul 06, 2011 |
Title |
Reference Epigenome: ChIP-Seq Input from BMP4 Trophoblast Cells; renlab.Input.BMP4T.02.01 |
Sample type |
SRA |
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Source name |
Human embryonic stem cells received from the James Thomson laboratory. Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.Input.BMP4T.02.01
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Organism |
Homo sapiens |
Characteristics |
sample alias: BMP4-06 sample common name: H1 BMP4 Derived Trophoblast 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 trophoblast by treatment with BMP4 differentiation_method: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days passage: 28 medium: mTeSR1 Sex: Male batch: BMP4-6 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
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Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
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Description |
sample_term_id: UBERON_0000088 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: ChIP-Seq Input from BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform. Library name: SK458 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7867 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7847 **************** 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: GSM753449_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Input.SK458.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.Input.BMP4T.02.01.hg19.level.1.release.5 ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 BMP4 Derived Trophoblast Cultured Cells, Library SK458, 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.10476 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 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 38,541,238 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61 FINDPEAKS_SCORE: 0.0 FINDPEAKS_PERCENTILE: 10 HOTSPOT_SCORE: 0.01 HOTSPOT_PERCENTILE: 48 IROC_SCORE: 0.0 IROC_PERCENTILE: 33 POISSON_SCORE: 0.05 POISSON_PERCENTILE: 46 MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
ANALYSIS FILE NAME: GSM753449_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Input.SK458.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.Input.BMP4T.02.01.hg19.level.2.release.5 ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library SK458, 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.10549 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 5 BROWSER_TRACK_NAME: HBDT Input 58 BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Library SK458 EA Release 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 38,541,238 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61 FINDPEAKS_SCORE: 0.0 FINDPEAKS_PERCENTILE: 10 HOTSPOT_SCORE: 0.01 HOTSPOT_PERCENTILE: 48 IROC_SCORE: 0.0 IROC_PERCENTILE: 33 POISSON_SCORE: 0.05 POISSON_PERCENTILE: 46 MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
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Submission date |
Jul 01, 2011 |
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 |
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Platform ID |
GPL11154 |
Series (1) |
GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
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Relations |
SRA |
SRX081165 |
BioSample |
SAMN00631723 |
Named Annotation |
GSM753449_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Input.SK458.wig.gz |