|
| Status |
Public on Nov 01, 2022 |
| Title |
Patient Derived Xenograft model HCI-024 |
| Sample type |
SRA |
| |
|
| Source name |
Patient-Derived Xenograft
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: Human breast tumor tissue graft on mouse mammary fat pad
tumor subtype: human TNBC tumor
strain: SCID/Bg mouse host
treatment: untreated
|
| Treatment protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
NuGEN Ovation RNA-Seq v2 Kit (protocol p/n 7102, kit p/n 7102-08) along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D) and the Rubicon ThruPlex DNA-Seq (protocol: QAM-108-002, kit p/n R400428) library preparation protocolss
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNAseq of human TNBC tumor tissue graft on mouse mammary fat pad
|
| Data processing |
Raw reads were split into human/epithelial (graft) and murine/stromal (host) reads using Xenome v1.0.1
Human and Mouse reads were aligned to hg38 and mm10 reference genomes respectively using RSEM/STAR v2.5.3a_modified
The above STAR run was run internally by rsem-calculate-expression (RSEM v1.2.31), which then quantified transcripts and genes, producing isoform and gene level results.
Genome_build: hg38/mm10
Supplementary_files_format_and_content: A matrix file was generated using expected counts values from RSEM results. Each row represents a gene and each column represents a xenograft model
|
| |
|
| Submission date |
Sep 01, 2021 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Michael T Lewis |
| Organization name |
Baylor College of Medicine
|
| Department |
Breast Center
|
| Lab |
Lewis Lab
|
| Street address |
1 Baylor Plaza N1210
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE183187 |
Total RNA-seq from Patient-Derived Xenograft models of Breast Cancer developed at Baylor College of Medicine |
|
| Relations |
| BioSample |
SAMN21170256 |
| SRA |
SRX11983482 |
