Differential expression using Bowtie2
Hi,
I have a gene and I want to investigate its expression in different organs.
I'm not sure how best to do this though. I am thinking of using Bowtie2 to either:
- Align the transcript of the gene to the transcriptome for a cell in that organ (the RNA-seq data for a cell in an organ will be obtained from NCBI' SRA).
- Align the cell transcriptome to the genome of the organism.
Please could someone advise on what to do?
I then want to repeat the process using transcriptomes of cells from different organs and use DESeq2 to look at differential expression of the gene in each organ.
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Which will be obtained from NCBI...what does that mean, and which data do you have?
NCBI's Sequence Read Archive gives me the transcriptome of an organ (the RNA-seq data) which can be downloaded either as a .fasta or .fastq file, eg. https://www.ncbi.nlm.nih.gov/sra/SRX22553038[accn]
You cannot just randomly pull data from NCBI and then quantitatively compare them. RNA-seq is inherently a relative measure and quantitative comparisons only go for data produced under the exact same experimental setup, same kit, lab, day, everything. Everything else is just batch effects.
Ok, thanks for letting me know. What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq data?
Get a dataset that has everything I need in place, or create it in the lab.
https://www.proteinatlas.org/ has a lot of data available.