many papers I read mentioned "RNA-seq data". While searching for the meaning of this word, I could not find any layman's definition.

As far as I understand, RNA-seq data is the complete RNA information in a cell (or all of the cells) of a species that is extracted at a certain time.

Am I correct with this definition? If yes, does this mean that by extracting all the RNA information ones knows all the RNA sequences in that species (like AUGGUCAUCAG....)? Or does it mean I have the RNA, but not the sequence?

  • $\begingroup$ @terdon could you explain it if it is possible ? $\endgroup$ – stackunderflow Mar 7 '15 at 21:14

RNA-seq data usually provides a snapshot in time of the transcriptome of that which is being sequenced. Single-cell sequencing is possible, but less common than RNA-seq on a sample (containing many cells).

You are correct that RNA-seq provides one with knowledge of RNA sequences, like AUGGUCAUCAG and so on. However, one will not necessarily have information about all possible RNA sequences from a particular species. Performing RNA-seq on the same cell type of a species at two different time points, or two different cell types at the same time point, may result in different profiles for the RNA sequences you get back. It depends on which parts of the genome are being expressed by the cells in a sample at the time of RNA extraction.

The data one gets back from RNA sequencing depends on the technology and company used. Typically, RNA-seq involves using a reverse transcription step so that the sequence data you get back is actually reported as the cDNA version of your original mRNA transcripts. Usually one gets a (very large) file of sequencing 'reads'. One can either then 'assemble' these directly to form a snapshot of the transcriptome or one can map them to a known reference genome. One of the main benefits of RNA-seq is that we learn not just what the sequences of the RNA molecules are, but also their relative abundances within the sample. Knowledge of this can be particularly useful in testing or developing a large range of biological hypotheses.

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    $\begingroup$ +1, being able to know relative RNA abundances is an important feature $\endgroup$ – Macond Mar 9 '15 at 14:35

RNA sequencing occurs when you perform an RNA extraction and then sequence them, which usually involves fragmenting them.

You do in fact know all of the sequences for all of the RNA molecules that are being sequenced. I can't see an interpretation that does not result in you having the sequences of the molecules, what with it being called "sequencing" and all.

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  • $\begingroup$ we start to know sequence of the RNA after sequencing right ? $\endgroup$ – stackunderflow Mar 8 '15 at 8:16
  • $\begingroup$ Yes, you will only know the sequence of the RNA after sequencing. Prior to sequencing, you will only know they are fragments of RNA. $\endgroup$ – March Ho Mar 8 '15 at 8:16

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