Differential expression using Bowtie2

Question

[8d8fc19e]

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.

[ATpoint]

Which will be obtained from NCBI...what does that mean, and which data do you have?

[8d8fc19e]

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]

[ATpoint]

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.

[8d8fc19e]

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?

[ATpoint]

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.