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Series GSE40890 Query DataSets for GSE40890
Status Public on Dec 14, 2012
Title Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays [RNA-Seq]
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary In order to study molecular changes in the stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. This is particularly relevant to mouse tumor xenograft models where tumor, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor (human) and stromal (mouse) expression from mixed tumor-stromal samples in terms of the genes and pathways that are involved in cross-alignment (RNA-Seq) and cross-hybridization (microarrays).
Overall design Human samples consisted of total RNA obtained from MDA-MB-231 human breast carcinoma cell line and isolated from three independent cultures of sub-confluent MDA-MB-231 cell lines in exponential phase of growth. Mouse samples were obtained from NOD scid gamma mice, and normal lung tissue was harvested from three independent age-matched mice.
Contributor(s) Valdes C, Clarke J
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Submission date Sep 14, 2012
Last update date May 15, 2019
Contact name Camilo Valdes
Organization name University of Miami
Department Center for Computational Science
Lab Bioinformatics and Computational Biology
Street address Locator C-213. 1120 NW 14 Street
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
Platforms (3)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL16061 Illumina Genome Analyzer IIx (Homo sapiens; Mus musculus)
Samples (19)
GSM1004247 100% Human Replicate 1A
GSM1004248 100% Human Replicate 1B
GSM1004249 100% Human Replicate 2A
This SubSeries is part of SuperSeries:
GSE40892 Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays
BioProject PRJNA175327
SRA SRP015764

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40890_Homo_sapiens.GRCh37.66.gtf.gz 22.6 Mb (ftp)(http) GTF
GSE40890_Mus_musculus.NCBIM37.66.gtf.gz 13.5 Mb (ftp)(http) GTF
GSE40890_RAW.tar 16.1 Mb (http)(custom) TAR (of TXT)
GSE40890_ccds-human.gtf.gz 3.9 Mb (ftp)(http) GTF
GSE40890_ccds-mouse.gtf.gz 3.3 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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