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This is the first time that I use NCBI-GEO and I've faced with 3 different categories inside it. They are platform, sample and series.

NCBI-GEO have GEO-Overview section to explain these terms to ones who are new to this website, however; although I read it a couple of times, I could not understand it totally.GEO-Overview page The terms are a bit complex for the ones who are not familiar with the concepts. Therefore, is there anyone who could explain them with simpler words ?

In my situation, I use NCBI-GEO to get RNA-seq data for the C. Elegans organism. I've downloaded the following SRA file : NCBI-geo C. Elegans sample

As far as I understood, a sample contains an individual organism's information.(In my case its a single C.elegans organism)

Series are somehow the collection of multiple samples I guess. I wonder what is the criteria to put different samples into same series?

And lastly, what is the differences between platforms and series ? I thought that each organism have a single platform, in other words, I thought I could find all the things about lets say C.elegans in its platform but I saw that a single organism type may have a lot of different platforms.

So, I'm seeking to learn these concepts and I think this website is the correct place to ask it. If my question is off topic, sorry about that I was not aware of it.

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  • $\begingroup$ You should have a look at the overview of GEO more carefully or go through NCBI handbook on GEO $\endgroup$
    – WYSIWYG
    Commented May 15, 2015 at 6:46
  • $\begingroup$ Why is this being closed for homework? $\endgroup$
    – March Ho
    Commented May 15, 2015 at 18:10
  • $\begingroup$ @MarchHo that link answers this completely. I VTDed because reading the help would have been sufficient for the basics. I am not too sure if VTC was appropriate in this case or not. And it is not closed yet; it requires 3 more votes. $\endgroup$
    – WYSIWYG
    Commented May 15, 2015 at 20:53

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The platform at NCBI-GEO means the particular microarray that was used (because originally most of GEO was just microarrays), OR, more recently, it could mean the type of NGS machine that was used. For example, every microarray manufacturer creates an ADF (array data file) that maps the DNA sequence at every position on the Chip to an accession ID. And this ADF mapping file gets registered at GEO as a GPLxxxxxx. This was presumably to facilitate direct comparisons between different experiments from various labs using identical Chips (e.g. Affymetrix, or Nimblegen).

With the advent of NGS the Platform has to be a name from an approved list of companies and devices: ILLUMINA, HiSeq, etc.

A series is constructed by the data providers and allows them to cluster the results from related samples. So, for example, in the modENCODE consortium, I believe all of the C. elegans RNA-Seq from Bob Waterston's lab/Project are clustered together under one overarching GSExxxxxxx. More details at www.modencode.org and links therein.

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  • $\begingroup$ so, every GPLxxxxx number corresponds to either a single microarray or type of NGS right ? I mean, lets assume I have a microarray. It has a GPLxxxx number and if I searched it on NCBI-GEO, I can find the experiments in which same microarray chip was used? "Same microarray" means produced by same factory and have identical features. $\endgroup$
    – stackunderflow
    Commented May 15, 2015 at 8:11
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    $\begingroup$ @stackunderflow Check the link I mentioned. Everything about GEO is nicely explained there. $\endgroup$
    – WYSIWYG
    Commented May 15, 2015 at 9:49
  • $\begingroup$ @WYSIWYG thanks for your helps, I think I got the main idea behind these terms. Since I'm completely new in this area, some keywords are really hard for me to understand at the first time, therefore I really appreciate your helps. $\endgroup$
    – stackunderflow
    Commented May 15, 2015 at 10:20

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