Quality of PolyA-seq data, comparing with Affymetrix GeneChip.mp4

RNA-seq on Illumina GA system might be problematic, and this PolyA-seq approach seems to be better. As authors mentioned, it is likely to be more sensitive than Affymetrix GeneChip data, while GeneChip still has advantages in cost, automation and data handling though.

You can download SSA files of these two data sets.

GSE30198.ssa (PolyA-seq)
https://www.sugarsync.com/​pf/D664412_133640_6678997

GSE2361.ssa (GeneChip)
https://www.sugarsync.com/​pf/D664412_133640_6678983

Data Source:
http://www.ncbi.nlm.nih.go​v/geo/query/acc.cgi?acc=GS​E30198
Summary: We describe PolyA-Seq, a strand-specific method for high-throughput sequencing of the 3' ends of polyadenylated transcripts. PolyA-Seq is as accurate for digital gene expression as existing RNA sequencing approaches, and superior to microarrays. We used the approach to map polyadenylation (polyA) sites in 24 samples from normal tissues in human, rhesus, dog, mouse, and rat.

http://www.ncbi.nlm.nih.go​v/geo/query/acc.cgi?acc=GS​E2361
Summary: We performed expression profiling of 36 types of normal human tissues and identified 2,503 tissue-specific genes. We then systematically studied the expression of these genes in cancers by re-analyzing a large collection of published DNA microarray datasets. Our study shows that integration of each gene's breadth of expression (BOE) in normal tissues is important for biological interpretation of the expression profiles of cancers in terms of tumor differentiation, cell lineage and metastasis.
Twenty five total RNA specimens were purchased from Clontech (Palo Alto, CA), Ambion (Austin, TX) and Strategene (La Jolla, CA). We tried to cover as many tissue types as possible by using pooled RNA samples. In order to define breadth-of-expression (BOE) accurately at a reasonable cost, we tried to cover as many tissue types as possible by using pooled RNA samples. Each specimen represents a human organ. We used RNA samples pooled from 2 to 84 donors to avoid differences at the individual level.
Keywords = Normal human tissues
Keywords = Tissue-specificity

Category:

Science & Technology

Tags:

• rna-seq
• polya-seq
• ngs
• analysis
• software
• tutorial
• illumina