|
| Status |
Public on Oct 15, 2011 |
| Title |
Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells; renlab.H3K27me3.NPC.01.01 |
| 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 neural progenitor cells.; renlab.H3K27me3.NPC.01.01
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: NPC-04
sample common name: H1 Derived Neuronal Progenitor 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 neural progenitor cells
differentiation_method: Publication in progress
passage: Between 20 and 30
medium: Publication in progress
Sex: Male
batch: NPC-4
experiment_type: Histone H3K27me3
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: H3K27me3
chip_antibody_provider: Millipore
chip_antibody_catalog: 07-449
chip_antibody_lot: DAM1612188
|
| 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 |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK203
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9786
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7903
****************
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 |
Various levels of processed data files will be made available as this project proceeds.
|
| |
|
| Submission date |
Oct 14, 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 |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX101235 |
| BioSample |
SAMN00678168 |
