Question: Where can i find some bacterial RNA-Seq data?
2
gravatar for matija.sosic
5.9 years ago by
matija.sosic80
Croatia/Zagreb/Faculty of Electronical Engineering and Computing
matija.sosic80 wrote:

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.

bacterial rna-seq • 5.5k views
ADD COMMENTlink modified 5.9 years ago by geek_y10k • written 5.9 years ago by matija.sosic80
3
gravatar for matted
5.9 years ago by
matted7.2k
Boston, United States
matted7.2k wrote:

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 COMMENTlink modified 8 weeks ago by RamRS25k • written 5.9 years ago by matted7.2k

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 REPLYlink written 5.9 years ago by matija.sosic80
1

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 REPLYlink modified 8 weeks ago by RamRS25k • written 5.8 years ago by matted7.2k
1
gravatar for PoGibas
5.9 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

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 COMMENTlink modified 8 weeks ago by RamRS25k • written 5.9 years ago by PoGibas4.8k

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 REPLYlink modified 8 weeks ago by RamRS25k • written 5.9 years ago by Istvan Albert ♦♦ 82k
1
gravatar for geek_y
5.9 years ago by
geek_y10k
Barcelona
geek_y10k wrote:

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

ADD COMMENTlink modified 8 weeks ago by RamRS25k • written 5.9 years ago by geek_y10k
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