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Status |
Public on Apr 19, 2017 |
Title |
Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in BMP4 Mesendoderm Cells; renlab.H3K9me3.BMP4M.01.01 |
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 mesendoderm by treatment with BMP4.; renlab.H3K9me3.BMP4M.01.01
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Organism |
Homo sapiens |
Characteristics |
sample alias: BMP4-03 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 20 and 30 medium: E8 Sex: Male batch: BMP4-3 experiment_type: Histone H3K9me3 extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf extraction_protocol_type_of_sonicator: Biorupter extraction_protocol_sonication_cycles: 80 chip_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf chip_protocol_chromatin_amount: 500 micrograms chip_protocol_bead_type: magnetic anti-rabbit chip_protocol_bead_amount: 33,500,000 chip_protocol_antibody_amount: 5 micrograms chip_antibody: H3K9me3 chip_antibody_provider: Abcam chip_antibody_catalog: ab8898 chip_antibody_lot: 699671
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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 |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
sample_term_id: NTR_0000856 assay_term_id: OBI_0000716 nucleic_acid_term_id: Design description: ChIP-Seq Analysis of H3K9me3 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform. Library name: AK136 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7830 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805 **************** 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 |
Various levels of processed data files will be made available as this project proceeds.
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Submission date |
Jul 01, 2011 |
Last update date |
Apr 19, 2017 |
Contact name |
UCSD AND SALK |
Organization name |
University of California, San Diego
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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 |
BioSample |
SAMN00631730 |