This document specifies reliability assessment criteria for high-throughput gene-expression data.<\/p>\n
It is applicable to assessing the accuracy, reproducibility, and comparability of gene-expression data that are generated from microarray, next-generation sequencing, and other forms of high-throughput technologies.<\/p>\n
This document identifies the quality-related data for the process of the next-generation sequencing of RNA (RNA-seq). The sequencing platform covered by this document is limited to short-read sequencers. The use of RNA-seq for mutation detection and virus identification is outside of the scope of this document.<\/p>\n
This document is applicable to human health associated species such as human, cell lines, and preclinical animals. Other biological species are outside the scope of this document.<\/p>\n
From a biological point of view, expression profiles of all genetic sequences including genes, transcripts, isoforms, exons, and junctions are within the scope of this document<\/p>\n
| PDF Pages<\/th>\n | PDF Title<\/th>\n<\/tr>\n | ||||||
|---|---|---|---|---|---|---|---|
| 2<\/td>\n | undefined <\/td>\n<\/tr>\n | ||||||
| 5<\/td>\n | Foreword <\/td>\n<\/tr>\n | ||||||
| 6<\/td>\n | Introduction <\/td>\n<\/tr>\n | ||||||
| 8<\/td>\n | 1 Scope 2 Normative references 3 Terms and definitions <\/td>\n<\/tr>\n | ||||||
| 10<\/td>\n | 4 From sample to RNA 4.1 General 4.2 RNA integrity <\/td>\n<\/tr>\n | ||||||
| 11<\/td>\n | 4.3 RNA concentration 4.4 RNA purity 5 Expression profiling 6 Quality control metrics in RNA-seq analysis 6.1 General 6.2 Sequencing read 6.2.1 Total number of reads <\/td>\n<\/tr>\n | ||||||
| 12<\/td>\n | 6.2.2 Read length 6.2.3 Base call quality 6.2.4 GC content 6.2.5 Overrepresented sequence 6.2.6 Adapter residue 6.3 Alignment 6.3.1 Alignment ratio 6.3.2 Gene body coverage uniformity <\/td>\n<\/tr>\n | ||||||
| 13<\/td>\n | 6.3.3 Strand specificity 6.3.4 Insert size 6.3.5 Mismatch 6.3.6 Contamination from other sources 6.4 Expression 6.4.1 Expression distribution 6.4.2 Expressed genes <\/td>\n<\/tr>\n | ||||||
| 14<\/td>\n | 6.4.3 Saturation 6.4.4 Reproducibility 6.5 Differentially expressed genes 6.6 Biological interpretation of differentially expressed genes <\/td>\n<\/tr>\n | ||||||
| 15<\/td>\n | 6.7 Sample certificate of origin 6.8 Quality control of batch effects 7 Spike-in controls 8 Proficiency testing 8.1 General <\/td>\n<\/tr>\n | ||||||
| 16<\/td>\n | 8.2 RNA sources 8.3 Experimental design 9 Process management <\/td>\n<\/tr>\n | ||||||
| 17<\/td>\n | Bibliography <\/td>\n<\/tr>\n<\/table>\n","protected":false},"excerpt":{"rendered":" Genomics informatics. Reliability assessment criteria for high-throughput gene-expression data<\/b><\/p>\n |