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Series GSE56134 Query DataSets for GSE56134
Status Public on Oct 15, 2014
Title RNA sequencing identifies specific PIWI-interacting small non-coding RNA expression patterns in breast cancer
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Third-party reanalysis
Summary PIWI-interacting RNAs (piRNAs) are a novel class of small ncRNAs initially isolated from germ line cells; although recent studies report that they are expressed also in somatic cells. To elucidate the role of piRNAs in somatic cells, in particular from breast cancer, we performed the first extensive next generation sequencing expression analysis of small RNA transcriptomes of hormone responsive breast cancer cell lines in different culture conditions. In addition, to understand the behavior of piRNAs with respect to miRNAs in breast tumor tissues, small RNA sequence data set available in Gene Expression Omnibus (GSE39162) database was used. Results led to the identification of ~100 and ~150 human piRNAs in the breast cancerous cell lines and tumors respectively, several of which differentially expressed in cell lines under different experimental conditions tested or in response to ERβ and in tumor tissues. Western blotting and Q-PCR analysis also revealed the presence in breast cell lines of PIWIL (PIWI Like) subfamily members proteins encoded in the human genome (PIWIL2/HILI and PIWIL4/HIWI2) and of other components of the piRNA biogenesis pathways, suggesting that this might indeed be functional in somatic cells. These results show that piRNAs are expressed in human somatic cells, in particular in cancer, where their expression is influenced by neoplastic transformation, growth conditions and estrogen receptor beta. More important, we demonstrate for the first time a distinct pattern of piRNAs expression in cancerous vs normal breast tissues, which suggests a potential role of these epigenetic modulators in mammary carcinogenesis and maintenance of the cancer cell phenotype.
Overall design In addition, to understand the behavior of piRNAs with respect to miRNAs in breast tumor tissues, small RNA sequence data set available in Gene Expression Omnibus (GEO; GSM957192 TAX577740T ,GSM957194 TAX577740N, GSM957195 TAX577453T, GSM957197 TAX577453N, GSM957198 TAX577745T, GSM957200 TAX577745N, GSM957201 TAX577579T, GSM957203 TAX577579N) was used.
Contributor(s) Weisz A, Hashim A, Rizzo F
Citation(s) 25313140
Submission date Mar 24, 2014
Last update date May 15, 2019
Contact name Judith Staerk
Organization name UiO (University of Oslo)
Department NCMM (Centre for Molecular Medicine Norway)
Street address NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21
City Oslo
State/province Oslo
ZIP/Postal code 0349
Country Norway
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (22)
GSM1356352 MCF10A
GSM1356353 MCF-7
GSM1356354 ZR-75.1
Reanalysis of GSM957192
Reanalysis of GSM957194
Reanalysis of GSM957195
Reanalysis of GSM957197
Reanalysis of GSM957198
Reanalysis of GSM957200
Reanalysis of GSM957201
Reanalysis of GSM957203
BioProject PRJNA242528
SRA SRP040505

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
GSE56134_RAW.tar 60.0 Kb (http)(custom) TAR (of TXT)
GSE56134_TAX577453N_piRNABank_unique.txt.gz 1.9 Kb (ftp)(http) TXT
GSE56134_TAX577453T_piRNABank_unique.txt.gz 1.8 Kb (ftp)(http) TXT
GSE56134_TAX577579N_piRNABank_unique.txt.gz 2.1 Kb (ftp)(http) TXT
GSE56134_TAX577579T_piRNABank_unique.txt.gz 2.3 Kb (ftp)(http) TXT
GSE56134_TAX577740N_piRNABank_unique.txt.gz 2.7 Kb (ftp)(http) TXT
GSE56134_TAX577740T_piRNABank_unique.txt.gz 2.5 Kb (ftp)(http) TXT
GSE56134_TAX577745N_piRNABank_unique.txt.gz 2.5 Kb (ftp)(http) TXT
GSE56134_TAX577745T_piRNABank_unique.txt.gz 2.7 Kb (ftp)(http) TXT
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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