|
| Status |
Public on Jun 06, 2016 |
| Title |
PDX_TX_DFBM354_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HER2+ breast cancer brain metastases
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: breast cancer brain metastases
tissue: patient-derived xenograft
tumor type: HER2+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) and the RNeasy Mini Kit (Qiagen).
cDNA libraries were constructed using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher). Samples were barcoded using the Ion Xpress™ Barcode Adapter kits (Thermo Fisher)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
AmpliSeq™ Transcriptome sequencing of patient-derived HER2+ breast cancer brain metastatic xenograft
|
| Data processing |
Data were analyzed by Torrent Suite and ampliSeqRNA analysis plugin (Thermo Fisher) to generate read counts
Bed file for target region is hg19_AmpliSeq_Transcriptome_21K_v1.bed, which was downloaded from https://ioncommunity.thermofisher.com
human genome hg19 fasta, index_version tmap-f3, was downloaded from https://ioncommunity.thermofisher.com
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited matrix table excel files, each includes raw counts of sequencing reads of 5 Samples for each repeat
|
| |
|
| Submission date |
Apr 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean Zhao |
| E-mail(s) |
Jean_zhao@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Cancer Biology
|
| Lab |
Jean Zhao
|
| Street address |
450 Brookline Ave, SM936
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE80722 |
Transcriptome analysis of patient-derived xenograft models of HER2+ breast cancer brain metastases |
|
| Relations |
| BioSample |
SAMN04909401 |
| SRA |
SRX1733567 |
