Transcriptomics

Dataset Information

493

Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumors and matched controls


ABSTRACT: We prepared small RNA libraries from 29 tumor/normal pairs of human cervical tissue samples. Analysis of the resulting sequences (42 million in total) defined 64 new human microRNA (miRNA) genes. Both arms of the hairpin precursor were observed in twenty-three of the newly identified miRNA candidates. We tested several computational approaches for analysis of class differences between high throughput sequencing datasets, and describe a novel application of log linear model that has provided the most datasets, and describe a novel application of log linear model that has provided the most effective analysis for this data. This method resulted in the identification of 67 miRNAs that were differentially-expressed between the tumor and normal samples at a false discovery rate less than 0.001. A total of 29 tumor/normal pairs of human cervical tissue samples were analyzed. Two samples (G699N_2 and G761T_2) were performed in duplicates. No Fastq files for GSM532871 to GSM532889, GSM532929, and GSM532930. Sequence files are provided as text files for these 22 Sample records in GSE20592_RAW.tar. 38 samples with quality scores are available from SRA as SRP002/SRP002326 (see Supplementary file below).

ORGANISM(S): Homo sapiens  

SUBMITTER: Andrew Fire   Sam G Gu  Robert Tibshirani  Weng-Onn Lui  Daniela Witten  Sam Guoping Gu 

PROVIDER: E-GEOD-20592 | ArrayExpress | 2010-04-28

SECONDARY ACCESSION(S): SRP002326GSE20592PRJNA124827

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls.

Witten Daniela D   Tibshirani Robert R   Gu Sam Guoping SG   Fire Andrew A   Lui Weng-Onn WO  

BMC biology 20100511


BACKGROUND:Ultra-high throughput sequencing technologies provide opportunities both for discovery of novel molecular species and for detailed comparisons of gene expression patterns. Small RNA populations are particularly well suited to this analysis, as many different small RNAs can be completely sequenced in a single instrument run. RESULTS:We prepared small RNA libraries from 29 tumour/normal pairs of human cervical tissue samples. Analysis of the resulting sequences (42 million in total) def  ...[more]

Similar Datasets

2013-06-05 | E-GEOD-47650 | ArrayExpress
2014-05-04 | E-GEOD-47462 | ArrayExpress
2010-09-12 | E-GEOD-22024 | ArrayExpress
2015-07-01 | E-GEOD-66550 | ArrayExpress
2010-02-01 | E-GEOD-18542 | ArrayExpress
2017-05-31 | E-MTAB-5775 | ArrayExpress
2014-06-27 | E-GEOD-57911 | ArrayExpress
2014-12-04 | E-GEOD-62826 | ArrayExpress
2014-04-21 | E-GEOD-38636 | ArrayExpress
2012-11-28 | E-GEOD-35638 | ArrayExpress