XiaLab at University of Ottawa

Skip Navigation Links
Home
Research
Publications
Teaching
Software
Members
Resource
About Xia
Contact

Bacillus subtilis data

This page contains two sets of RNA-Seq data. Please keep in mind that most transcriptomic studies will use an rRNA removal kit to remove the large rRNAs, i.e., 16S and 23S rRNA in bacteria because otherwise sequence reads from these large rRNAs will dominate the RNA-seq data. There are two main types of rRNA Remove Kits in the markets: 1) RiboMinus Kit from Invitrogen which have two probes located within the conserved sequence region at each ends of 16S and 23S rRNAs. Full-length rRNA or partial rRNA that pairs with these probes are removed. However, fragments that do not includes these probe regions will participate in the amplification and sequencing step and appear in the reads. If you wish to know the 5' and 3' ends of the mature 16S and 23S rRNA, then these data will not give you the desired answer because there will be no read mapped to the 5' or 3' ends. The other rRNA removal kit is the Ribo-Zero Kit from Epicentre (an Illumina company). This kit removes rRNA across the entire length and does not specifically targets the 5' and 3' ends. If the removal is not quite complete, you will find a number of reads mapped to the 5' and 3' ends (but not beyond).

NC_000964_CDS.FAS: Coding sequences from B. subilis genomic sequences (ACCN: NC_000964) for you to practise gene expression characterization using the BLAST databases listed below. The FASTA file has sequence IDs being a combination of gene name and map location on the genome.

1. BioProject PRJNA319983, with 12 BLAST databases derived from the original 12 .sra files downloaded from NCBI. They are single reads each with ~75 bases, with Ribo-Zero rRNA Removal Kit for bacteria (Epicentre).

2. BioProject PRJNA336278, with 12 BLAST databases derived from the original 6 sra files downloaded from NCBI. They are paired-end reads each with ~77 bases, with RiboMinus rRNA Removal Kit for bacteria (Invitrogen). The reverse read and the forward reads differ substantially in read quality and are stored separately (Forward reads: SRR#######_1.zip; reverse reads: SRR#######_2.zip).

© 2016. XiaLab. All Rights Reserved.