Question: Are There Publicly Available Rna-Seq Datasets From Human Adult Pancreas And Stomach?
3
gravatar for camelbbs
6.2 years ago by
camelbbs650
China
camelbbs650 wrote:

Hi all,

I searched GEO and didn't find the RNASeq data from human adult pancreas and stomach tissues (not cell lines). Anyone can help looking for that? Or anyone can share with your own data, can treat you as co-author.

Thanks, Ch

rna-seq • 4.1k views
ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 6.2 years ago by camelbbs650
2

What kind of samples are you looking for? Any rna extract from pancreatic or stomach is fine? Cell lines fine? Tumor cells? Have a look at the sequence read archive and invest some time to read the documentation on their search function

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Irsan6.8k

just rna sequencing from normal adult pancreas and stomach tissues, not from cell lines. I've done with searching SRA but don't find.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by camelbbs650

InSilico DB has just released a beta integration with Ingenuity iReport. You can export public RnaSeq data from GEO/SRA and get a free iReport preview. 

 

ADD REPLYlink written 5.0 years ago by alaincoletta110
2
gravatar for Obi Griffith
6.2 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

Check out the GTEx project. They are working on collecting a wide array of normal tissues and performing genotyping and gene expression analysis (including RNAseq). RNAseq has been performed for 20 pancreas samples so far. There are none for stomach yet, although they are collecting a large number of stomach samples and presumably will process some of them with RNAseq. Apparently the gene and exon level expression data are available open access (with login). If you want actual sequence data you will most likely have to go through dbgap.

ADD COMMENTlink written 6.2 years ago by Obi Griffith17k

Thanks, It seems only PIs can apply for acessing the dbgap, right?

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by camelbbs650

I'm not sure about that. But, you will for sure need someone who knows how to work your IRB. dbgap - the greatest way to make your data available in such a way that almost nobody else ever uses it. :-(

ADD REPLYlink written 6.2 years ago by Obi Griffith17k
1
gravatar for Irsan
6.2 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

Pancreas 1

Pancreas 2

Stomach 1

Stomach 2

ADD COMMENTlink written 6.2 years ago by Irsan6.8k

Thanks very much for your help. I even didn't find it. The only thing is the one of the pancreas are from cultured-cells. So I can't get replicates for pancreas. But still thanks a lot!

ADD REPLYlink written 6.2 years ago by camelbbs650

When you go to the sra home page and search for "human[organism] AND pancreas[tissue]" you find them.

ADD REPLYlink written 6.2 years ago by Irsan6.8k

all the data are stored in dbgap and need acess authorization.

ADD REPLYlink written 6.2 years ago by camelbbs650

then you need to apply for an era-commons and request the dataset. And probably you will have to use the aspera client to download the data. Therefore you need to make sure firewall port 33001 (not only on your own pc but also in your corporate/university firewall) is open for UDP traffic

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Irsan6.8k
0
gravatar for alaincoletta
5.8 years ago by
alaincoletta110
Belgium
alaincoletta110 wrote:

In InSilico DB (https://insilicodb.org), you can download public RNA-Seq data pre-processed and ready to analyse. See https://insilicodb.org/differential-gene-expression-heatmap-from-rnaseq-data-using-cummerbund/ for a step-by-step example.

ADD COMMENTlink written 5.8 years ago by alaincoletta110
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