Entering edit mode
10 months ago
firefox91
•
0
Hello,
I am looking for a few human trophoblast transcriptome files to see if the RNA I am studying is expressed in embryos. So I searched in SRA database but the results gather several transcriptomes in one file and do not indicate how many transcriptomes there is in the file. Are there other ways to find what I am searching for ? Other databases or an other way to search in SRA ? An other question : Does a "reference" transcriptom exist for embryos ? Thank you
I would suggest to directly search articles that have generated (sc)RNA-seq data. I think you would find some high quality studies that produced and shared such data.
Concerning the "reference" transcriptome, I think it is complex to answer such a question. There are some great papers that applied scRNA-seq to understand the transcriptional waves controlling the first days of development (i.e. Petropoulos et al. 2016, Yan et al. 2013, etc). I personally use the data generated from these teams to compare with my data at the same embryonic stages, or to identify the genes that are likely to be expressed at some stages, and which genes are specific from the different embroynic lineages.
So maybe you could improve your question but I think there are great datasets generated to date that you could rely on and could be considered as "reference" datasets.
Thank you so much ! I find the articles but not the data of the papers, do you have a link please ?
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
I do not understand what this means. One cannot see your screen, so please describe the problem better. SRA is usually the place to go.
No, the genome (and as such the encoded genes) are the same, regardless of developmental stage. Standard hg38 with its annotations, for example from GENCODE is fine.
This result from SRA for example. I can download the file with the SRA toolkit but how to know how many transcriptomes this file co
ntains ?
Just one, that is how the convention is. One sample (SRX...) can have one or many SRR entries. If many you can merge them prior to quantification.