Where can i find some bacterial RNA-Seq data?
3
2
Entering edit mode
9.9 years ago
matija.sosic ▴ 110

Where can i find some bacterial RNA-Seq data, e.g. of Escherichia Coli?

I would like to analayse single bacteria's transcriptome to see which genes get expressed.

RNA-Seq bacterial • 7.5k views
ADD COMMENT
3
Entering edit mode
9.9 years ago
matted 7.8k

I like DNAnexus's search engine for the SRA, where you can make a nice query and drill down to get what you want. You can see any experiment with "Escherichia" in the name that's categorized as whole-transcriptome analysis here.

ADD COMMENT
0
Entering edit mode

Thanks, this looks great! Do you maybe know how to find out how long are the reads? I tried first result with 36bp, that seems really short to me. Also, when I use fastq-dump to get .fastq file almost half of each read is 'N'.

ADD REPLY
1
Entering edit mode

If you look at the run on the SRA website (e.g. this one), it will tell you the number of reads ("spots") and the total number of bases, and you can calculate the read length. I don't know a way of checking for N's without downloading the files, though.

ADD REPLY
1
Entering edit mode
9.9 years ago
PoGibas 5.1k

Similar question was asked on Seqanswers - total RNA/transcriptome of E.coli or S.cerevisiae.

See sudhirvarma's answer: "The NCBI Short Read Archive has several E. coli and datasets".

ADD COMMENT
0
Entering edit mode

I going to just paste the link here for reference:

http://www.ncbi.nlm.nih.gov/sra/?term=%22Escherichia+coli%22[orgn%3A__txid562]

ADD REPLY
1
Entering edit mode
9.9 years ago

A very good data set is here with different conditions and biological replicates

ADD COMMENT

Login before adding your answer.

Traffic: 1507 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6