Dear all.
I have been trying to retrieve the mRNA data set from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213070 (Accession id 213070) But it seems that only the lncRNA and miRNA data have been uploaded. Moreover, if I am going to the "DOWNLOAD RNA-SEQ COUNTS" option on the page, there is a section called NCBI-generated data wherein the raw counts are available. But I just want to understand from where NCBI has generated this data when it's not showing on the page...
When I open the Excel sheet of mRNA (data generated by NCBI), it is showing 11 columns...whereas inside the paper, there is a figure which shows only three controls and three inflamed...then from where are these extra columns coming?
Can someone please check this once and let me know?
I am pasting the column names of the mRNA raw counts generated by NCBI GeneID GSM6571156 GSM6571157 GSM6571158 GSM6571159 GSM6571160 GSM6571161 GSM6571162 GSM6571163 GSM6571164 GSM6571165 GSM6571166
Also, the picture from the paper
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rajdeepboral00 •
This is highly custom and not a general technical question so you have dive into their paper (which has a methods section that, frankly, "sucks") and the GEO entry.
My guess is that the lncRNA contains both mRNA and lncRNA because after all these RNA species are all "not short" in terms of "they don't need a special library prep" like miRNAs. I would download the count matrices and simply see whether they contain mRNA counts. If not, contact the corresponding author.
I just downloaded the lncRNA file and yes you were correct, i found the mRNA counts in that file. Thanks alot for your help.
The authors have performed total RNA-seq, which captured both mRNA and lncRNA, as mentioned by ATpoint . The generated count matrix should have 12 columns, 6(miRNA case and controls) + 6(lncRNA case controls)
To know how NCBI generated the count file, check: https://www.ncbi.nlm.nih.gov/geo/info/rnaseqcounts.html#how
If you are looking for the raw data: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA879078&o=acc_s%3Aa
Raw+normalised counts are provided in GSE213070_lncRNA_expression.txt.gz and GSE213070_miRNA_expression.txt.gz.
Thank you for the clarification
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