|
| Status |
Public on Apr 11, 2020 |
| Title |
WXS: tumor A rtTA-HER2d16 mouse on FVB background #527 |
| Sample type |
SRA |
| |
|
| Source name |
Whole tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: breast tumor
strain: FVB/NJ
mouse model: rtTA-HER2d16 mouse
|
| Treatment protocol |
No treatment was given.
|
| Growth protocol |
HER2 expression was induced in mammary tissues of one month old mice, spontaneous breast tumor growth were monitored weekly
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SureSelect XT Mouse All Exon Kit (Agilent)
2x150 30M PE (27.7M each site) don eby Admera Health LLC
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq files were aligned to mouse reference genome mm10 using STAR (PMID: 23104886) version 2.4.2a.
Quantification was done using Salmon version 0.6.0 (PMID: 28263959).
Gene-level data were normalized to the upper quartile for non-zero genes and log2 transformed.
Genes with zero reads in more than 80% of samples were excluded.
Mutational load was estimated using a calculated exome length of 209.6285 megabases and only non-synonymous mutations predicted to have a moderate or high impact
Genome_build: mm10
|
| |
|
| Submission date |
Apr 10, 2020 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Zachary Conrad Hartman |
| E-mail(s) |
zch@duke.edu
|
| Phone |
919-684-9197
|
| Organization name |
Duke University
|
| Department |
Surgery
|
| Lab |
Lyerly Lab
|
| Street address |
Research Drive MSRB rm 414
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE148478 |
Stimulation of oncogene-specific tumor infiltrating T-cells through combined vaccine and alpha-PD1 enable sustained anti-tumor responses against established HER2 breast cancer (BC) [WXS] |
| GSE148482 |
Stimulation of oncogene-specific tumor infiltrating T-cells through combined vaccine and alpha-PD1 enable sustained anti-tumor responses against established HER2 breast cancer (BC) |
|
| Relations |
| BioSample |
SAMN14574599 |
| SRA |
SRX8109244 |
