|
| Status |
Public on Mar 31, 2014 |
| Title |
BP-55 CTC |
| Sample type |
SRA |
| |
|
| Source name |
blood enriched for circulating tumor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
strain: BP-55
genotype/variation: BRAF(CA/+)/PTEN(flox/flox)
induced with: tamoxifen (focal subcutaneous injection)
tissue: blood enriched for circulating tumor cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood samples were collected from mice with high tumor burden following tamoxifen injection. Blood from each mouse was split and processed through the CTC-chips functionalized with anti-CSPG4/MCAM antibody and control IgGs, respectively. Matched primary (from the tamoxifen injection site) and metastatic (from upper or lower back) tumors were harvested from the same mouse and immediately flash-frozen in liquid nitrogen. RNA extraction and single molecular sequencing was described previously in PMID: 22763454)
Qiagen RNeasy MinElute kit followed by Helicos single molecule sequencing: Pubmed ID 18388294, 20133332
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Helicos HeliScope |
| |
|
| Data processing |
Helicos Digital Gene Expression pipeline. Pubmed ID 19581875
Genome_build: mm9
Supplementary_files_format_and_content: matrix of aligned read counts, rownames are UCSC knownGene transcript IDs or gene symbols and are specified in GEO GPL14759, column names are sample IDs.
|
| |
|
| Submission date |
Nov 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ben S. Wittner |
| E-mail(s) |
wittner.ben@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Center for Cancer Research
|
| Lab |
Lawrence
|
| Street address |
149 13th Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL14759 |
| Series (1) |
| GSE52031 |
Isolation and Molecular Characterization of Circulating Melanoma Cells |
|
| Relations |
| BioSample |
SAMN02390989 |
| SRA |
SRX372826 |
