Prokaryotic RNA sequencing

Prokaryotic RNA sequencing uses next generation sequencing (NGS) to reveal the presence and quantity of RNA at a given moment, by analyzing the changing cellular transcriptome. Our company‘s prokaryotic RNA sequencing, specifically aims at prokaryotes with reference genomes, providing you with transcriptome profiling, gene structure analysis, etc. It has been widely applied to basic science research, drug research and development, and more.

Platform: Illumina NovaSeq 6000

Service Details

Service Specifications

Platform: NovaSeq 6000 platform, PE150

Library type: 350bp insert cDNA library (depends on peak distribution)

Sequencing strategy: Paired-End 150 bp

Recommend data amount: 2 Gb raw data/sample

Bioinformatics

(1) Sequencing data quality control: Nucleotide distribution, Base quality distribution, rRNA ratio assessment;

(2) Sequence alignment analysis: Alignment result statistics, Saturation of sequencing, Coverage of sequencing;

(3) Reference genome annotation (NR, Swiss-Prot, Pfam, COG, GO, KEGG);

(4) Expression analysis: Expression distribution (With two or more samples), Analysis of expression between samples (Venn analysis, Correlation analysis, PCA analysis);

(5) Differential expression analysis (With two or more samples);

(6) Gene set analysis: Venn analysis, Cluster analysis, Function annotation analysis (COG, GO, KEGG), Function enrichment analysis (GO, KEGG), Function enrichment chordal graph, Ipath analysis;

(7) sRNA analysis: sRNA prediction, sRNA annotation (Blast, sRNAMap, sRNATarBase, SIPHT, Rfam), sRNA secondary structure prediction, sRNA target gene prediction;

(8) Transcript structure analysis: Operon analysis, Transcription start and end sites prediction, UTR annotation and analysis, Promoter sequence prediction, SNP/InDel analysis (SNP/InDel annotation, SNP/InDel regional distribution, SNP statistics).