|
| Status |
Public on Jun 09, 2015 |
| Title |
MCF7_ChIPSeq_Input |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
chip-antibody: Input
cell type: Luminal cells
cell line: MCF7
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. ChIPseq libraries were prepared by following Rubicon Thruplex-FD kit. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by PAGE gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format: refer to UCSC file format FAQ (http://www.genome.ucsc.edu/FAQ/FAQformat.html#format6.1)
|
| |
|
| Submission date |
May 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE38548 |
Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer |
| GSE69112 |
Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 3] |
|
| Relations |
| BioSample |
SAMN03703696 |
| SRA |
SRX1035341 |
