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Series GSE42735 Query DataSets for GSE42735
Status Public on Apr 20, 2014
Title Genome-wide transcriptome profiling of SK-Mel-28, UACC-62 and HCT-116 cells stably expressing scrambled shRNA and RAB7 shRNA
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Asess the transcritpional changes induced upon RAB7 knock-down in melanoma (SK-Mel-28 and UACC-62) and in colon cancer (HCT-116) cell lines.
Methods: mRNA profiles of tumor cell lines (SK-Mel-28, UACC-62, HCT-116) stably expressing scrambled shRNA or RAB7 shRNA (harvested at day 3 after lentiviral infection) were generated by deep sequencing, using three biological replicates per condition. The sequence reads that passed quality filters were analyzed with TopHat and Cufflinks. Validation of induced / silenced genes was performed by western blot.
Results show a differential impact of RAB7 expression in the transcriptomic profile of melanoma vs non-melanoma cell lines, and support a lineage-specific role of this small GTPase in melanoma.
Overall design Examination of the mRNA profiles RAB7-depleted vs wild type cells, performed in parallel in 3 different tumor cell lines (Melanomas: SK-Mel-28 and UACC-62, Non-melanoma: HCT-116) harvested at day 3 after lentiviral infection.
Contributor(s) Soengas MS, Alonso-Curbelo D
Citation(s) 24981740
Submission date Dec 04, 2012
Last update date May 15, 2019
Contact name Maria S Soengas
Organization name Spanish National Cancer Research Institute
Department Molecular Pathology
Lab Melanoma
Street address Melchor Fernandez Almagro, 3
City Madrid
ZIP/Postal code 28029
Country Spain
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (18)
GSM1048945 SK-Mel-28 shControl rep1
GSM1048946 SK-Mel-28 shControl rep2
GSM1048947 SK-Mel-28 shControl rep3
BioProject PRJNA182963
SRA SRP017435

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE42735_RAW.tar 24.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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