|
| Status |
Public on Mar 01, 2019 |
| Title |
HCI10 Mammary Gland Tumor from mouse 100277 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary Gland, Human xenograft, Mus musculus
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
histologic subtype: Mammary gland tumor
intrinsic subtype: Basal
model type: Patient-derived xenograft
pdx model: HCI10
|
| Treatment protocol |
All samples are untreated and all tissues flash frozen during extraction
|
| Growth protocol |
PDX cells were grown in various organs in NSG mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested from tissue/cell samples using the Qiagen Rneasy Mini Kit.
KAPA Stranded mRNA-Seq Kit was used for library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.MGT.100277
|
| Data processing |
Alignment: STAR v2.5.2b was used for alignment with the following settings: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read Counting: Salmon v0.8.2 was used for counting reads with the "quant" algorithm and library type set to "IU" using the transcriptome output of STAR.
TPM Calculations: TPM values were calculated using a custom in-house script from the raw read counts and transcript lengths provided by Salmon. TPM values are raw and have not been log2 transformed or further processed in any way.
Genome_build: A custom reference genome was built by concatenating the following three genome builds: GRCh38 human genome from the Genomic Data Commons (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files), GRCm38 M12 Gencode release of the Mouse genome (http://www.gencodegenes.org/mouse_releases/12.html), and the Xenotropic murine leukemia virus accession JF274252.1 (https://www.ncbi.nlm.nih.gov/nuccore/JF274252.1). Prior to concatenation, human chromosomes were concatenated with "HUMAN_" and mouse chromosomes were concatenated with "MOUSE_".
Supplementary_files_format_and_content: The processed data files contain the output from Salmon and include Salmon calculated TPM, gene lengths, and raw counts for the human and mouse genomes.
|
| |
|
| Submission date |
Aug 22, 2018 |
| Last update date |
Mar 01, 2019 |
| Contact name |
Wright Center for Clinical and Translational Research Bioinformatics Core |
| E-mail(s) |
cctrbioinfo@vcu.edu
|
| Phone |
804-828-1621
|
| Organization name |
Virginia Commonwealth University
|
| Street address |
203 E Cary St
|
| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
| |
|
| Platform ID |
GPL22245 |
| Series (1) |
| GSE118942 |
Separation of breast cancer and organ microenvironment transcriptomes in metastases |
|
| Relations |
| BioSample |
SAMN09900927 |
| SRA |
SRX4597984 |
