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Sample GSM5552635 Query DataSets for GSM5552635
Status Public on Nov 01, 2022
Title Patient Derived Xenograft model BCM-0104
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 HiSeq 2500
 
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 GPL22245
Series (1)
GSE183187 Total RNA-seq from Patient-Derived Xenograft models of Breast Cancer developed at Baylor College of Medicine
Relations
BioSample SAMN21170275
SRA SRX11983404

Supplementary file Size Download File type/resource
GSM5552635_BCM-0104_human.genes.results.txt.gz 612.4 Kb (ftp)(http) TXT
GSM5552635_BCM-0104_human.isoforms.results.txt.gz 963.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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