|
| Status |
Public on May 31, 2013 |
| Title |
BT-549 |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT-549
cancer subtype: breast cancer
|
| Treatment protocol |
No treatment performed
|
| Growth protocol |
Cell lines were cultured in RPMI + 10% FBS until 60-70% confluent. Total RNA was then harvested using the Rneasy Mini Kit (Qiagen)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA Seq-8 Sample Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Samples were mapped to the human genome and RefSeq transcriptome using ELAND.
A custom C# script was used to extract all mate pairs with one read mapping to the candidate rearranged gene (identified by breakpoint analysis) and the other read mapping to a separate genomic locus.
A separate C# script screened mate pairs for single reads mapping to potential exon-exon fusion junctions of nominated gene fusions.
Genome_build: hg18
Supplementary_files_format_and_content: Our pipeline outputs a single file (GeneFusions.txt) after all samples are run through our pipeline. This file is a tab delimited text file with the first column representing the gene fusion name, the second column includes the sample from which the gene fusion was identified, the third column includes the chromosome of the 5' partner gene, the fourth column includes the chromosome of the 3' partner gene, the fifth column includes the exon position of the gene fusion junction, and the sixth column includes the number of mate pairs supporting the specific gene fusion.
|
| |
|
| Submission date |
Mar 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Craig Patrick Giacomini |
| E-mail(s) |
cpg17@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Pathology
|
| Lab |
Jonathan Pollack (M.D./Ph.D.) Laboratory
|
| Street address |
269 Campus Drive (CCSR 3245A)
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5176 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE45133 |
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types (RNA-seq) |
| GSE45137 |
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types |
|
| Relations |
| SRA |
SRX248169 |
| BioSample |
SAMN01974542 |
