|
| Status |
Public on Jun 01, 2014 |
| Title |
GM12878-p300-1F4_E10-Rep1-SL31838 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878-p300
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
chip antibody: mose monoclonal p300
chip antibody info: custom generated; 1F4_E10
|
| Biomaterial provider |
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Growth protocol |
GM12878 and Jurkat cells were grown under the standard ENCODE protocols (http://genome.ucsc.edu/encode/protocols/cell/human/Jurkat_protocol.pdf and http://genome.ucsc.edu/encode/protocols/cell/human/GM12878_protocol.pdf)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed using 1% formaldehyde (NRSF samples) or 1% formaldehyde at 37C (p300 samples).
Libraries were generated following Illumina's DNA Sample Prep Kit protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
base calling: Casava1.8
read alignment: Bowtie 0.12.7
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)
|
| |
|
| Submission date |
Dec 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Georgi Kolev Marinov |
| Organization name |
STANFORD UNIVERSITY
|
| Department |
Genetics
|
| Street address |
279 Campus Drive West, Beckman Center, B-257A/259
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5101 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE53366 |
Automated high-throughput chromatin immunoprecipitation |
|
| Relations |
| BioSample |
SAMN02444949 |
| SRA |
SRX392808 |
