Post Reply 
 
Thread Rating:
  • 0 Votes - 0 Average
  • 1
  • 2
  • 3
  • 4
  • 5
Question about Stadler&Fire's mRNA data
27-Jan-2016, 12:56 PM (This post was last modified: 27-Jan-2016 12:58 PM by szhang.)
Post: #1
Question about Stadler&Fire's mRNA data
Hi,

Recently, I want to analyze Stadler&Fire's riboprofiling data derived from the database. First, I decide to normalize the elongation riboseq data based on the mRNA seq profiling. However, I only find one file of mRNA-seq, while there are two ribo-seq profiling datasets. For the mRNA data, the database annotates it as 'with & without cyclo', what does it mean?

I have checked their original paper published in RNA. It seems that the mRNA-seq corresponds to ribo-seq with cyclo?

Oh, just more information about S&F data
Human, HeLa: Stadler&Fire2011.

Many thanks.
Find all posts by this user
Quote this message in a reply
27-Jan-2016, 01:59 PM
Post: #2
RE: Question about Stadler&Fire's mRNA data
Hi szhang,

The Stadler&Fire HeLa mRNA-seq data from (http://www.ncbi.nlm.nih.gov/sra/SRX118141[accn] and http://www.ncbi.nlm.nih.gov/sra/SRX118142[accn]) were combined into a single track in GWIPS-viz.

This data represents randomly fragmented mRNA and so cycloheximide is not involved. We will remove the words "with and without cycloheximide" in the description to avoid confusion. It should read "mRNA-seq unique mappers from HeLa cells (Stadler and Fire 2011)".

Hope this answers your question and thanks for bringing it to our attention.

Audrey
Find all posts by this user
Quote this message in a reply
28-Jan-2016, 02:16 AM
Post: #3
RE: Question about Stadler&Fire's mRNA data
Many thanks.

Another quick question. Did you changed the mRNA data of HeLa Stumpf 2013 recently? I find that the files downloaded this time are of different sizes from those downloaded previous... If not, it may be my mistake...


(27-Jan-2016 01:59 PM)audrey Wrote:  Hi szhang,

The Stadler&Fire HeLa mRNA-seq data from (http://www.ncbi.nlm.nih.gov/sra/SRX118141[accn] and http://www.ncbi.nlm.nih.gov/sra/SRX118142[accn]) were combined into a single track in GWIPS-viz.

This data represents randomly fragmented mRNA and so cycloheximide is not involved. We will remove the words "with and without cycloheximide" in the description to avoid confusion. It should read "mRNA-seq unique mappers from HeLa cells (Stadler and Fire 2011)".

Hope this answers your question and thanks for bringing it to our attention.

Audrey
Find all posts by this user
Quote this message in a reply
01-Feb-2016, 10:02 AM
Post: #4
RE: Question about Stadler&Fire's mRNA data
Hi szhang,

Apologies, we only noticed your second question just now.

We confirm that we have not made any changes to the mRNA data of HeLa Stumpf 2013 in GWIPS-viz.

Kind Regards,
Audrey
Find all posts by this user
Quote this message in a reply
Post Reply 


Forum Jump:


User(s) browsing this thread: 1 Guest(s)

GWIPS-viz | Return to Top | Return to Content | Light (Archive) Mode | RSS Syndication