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Series GSE46516 Query DataSets for GSE46516
Status Public on Nov 19, 2014
Title The permanent reduction of TIA proteins molds expression transcriptome in HeLa cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary This study provides, for the first time, TIA1 and TIAR linked-transcriptomic analysis by using RNA-Seq next-generation sequencing technology. Illumina RNA-Seq was used to survey transcriptome profiles from permanent TIA1- and TIAR-(shRNA-mediated) deficient HeLa cells. Analysis of the transcriptomes with the Cufflinks tool revealed that differentially expressed genes, isoforms produced by alternative splicing and/or promoter usage as well as microRNAs generated a great transcriptomic heterogeneity which might reflect the complexity linked to these cell phenotypes. The data of differential expression were validated by using genome-wide microarrays and QPCR analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes term enrichment analysis revealed over-representation of genes associated with cell differentiation, multicellular organismal development, signal transduction, axon guidance and cell adhesion and under-representation of genes associated with positive regulation of migration, cell adhesion, response to organic substance, prostaglandin metabolic process and blood coagulation. Taken together, these results indicate that differential gene expression, alternative pre-mRNA isoforms, promoter usage and microRNA profiling contribute to define the molecular expression phenotypes implied in the progression of proliferative phenotypes associated to the absence of TIA proteins and prioritize candidates for future study.
 
Overall design Each library was run on one RNASeq Multiplex of 76 bp using sequencing from Illumina Genome Analyzer (GAIIx). Three samples were analyzed in this manner, taken from control, TIA1 and TIAR shRNA-depleted HeLa cells.
 
Contributor(s) Nuñez M, Sánchez-Jiménez C, Izquierdo JM
Citation(s) 25405991
Submission date Apr 30, 2013
Last update date May 15, 2019
Contact name Juan Carlos Oliveros
Organization name CNB, CSIC
Street address Darwin 3
City Cantoblanco
State/province Madrid
ZIP/Postal code 28049
Country Spain
 
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (3)
GSM1131563 HeLa shRNA Control
GSM1131564 HeLa shRNA TIA1
GSM1131565 HeLa shRNA TIAR
Relations
BioProject PRJNA200710
SRA SRP021918

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
GSE46516_RAW.tar 1.6 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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