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Sample GSM3351580 Query DataSets for GSM3351580
Status Public on Mar 01, 2019
Title WHIM2 Mammary Gland Tumor from mouse 100000
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: WHIM2
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
WHIM2.MGT.100000
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 SAMN09899654
SRA SRX4598025

Supplementary file Size Download File type/resource
GSM3351580_WHIM2mamtu100000_S82_L007_001.human.quant.sf.txt.gz 2.3 Mb (ftp)(http) TXT
GSM3351580_WHIM2mamtu100000_S82_L007_001.mouse.quant.sf.txt.gz 1.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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