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Escherichia coli 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 or MICROBExpress Bacterial mRNA Enrichment Kit (formerly Ambion, now 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_000913_CDS.FAS: Coding sequences from E. coli K12 genomic sequences (ACCN: NC_000913) 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 (gene name is not unique in E. coli genome, e.g., insA has multiple copies scattered along the genome). Pseudogenes have been removed.

1. BioProject PRJNA257498, with 4 BLAST databases derived from the original 4 .sra files downloaded from NCBI. They are single reads each with ~50 bases, with RNA treated by MICROBExpress Bacterial mRNA Enrichment Kit (formerly Ambion, now Invitrogen) which is similar to Ribo-Minus rRNA Removal Kit for bacteria (Invitrogen) that has two probes targeting the 5' and 3' ends of 16S and 23S rRNAs.

2. BioProject PRJNA209705, with 24 BLAST databases derived from the original 12 sra files downloaded from NCBI. They are paired-end reads each with 36 bases, with Ribo-Zero 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).

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