|
Status |
Public on Mar 01, 2019 |
Title |
HCI09 Mammary Gland Tumor from mouse 100508 |
Sample type |
SRA |
|
|
Source name |
Mammary Gland, Human xenograft, Mus musculus
|
Organisms |
Homo sapiens; Mus musculus |
Characteristics |
histologic subtype: Mammary gland tumor intrinsic subtype: LumB model type: Patient-derived xenograft pdx model: HCI09
|
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.
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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 HCI09.MGT.100508
|
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.
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|
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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 |
SAMN09900941 |
SRA |
SRX4597970 |