What do ATAC-Seq peaks represent?
Typically, peaks from ATAC-seq will represent a mixture of different cis-regulatory elements including enhancers and promoters [12].
How do I retrieve data from RNA-seq?
We compiled a list of resources where you can find RNA-seq data to start your oncology bioinformatics project:
- Elixir’s Expression Atlas.
- NCBI – National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/bioproject)
- TCGA – The Cancer Genome Atlas.
How do I get RNA-seq data from TCGA?
In order to download data from TCGA data portal:
- Connect to https://tcga-data.nci.nih.gov/tcga/
- Select the cancer subtype you are interested in (i.e breast invasive carcinoma)
- Select mRNA.
- Now you can see a table where rows are representing different patients.
Which is the best method to validate RNA Seq?
With that simplicity, comes less risk for introducing bias. In the end, qPCR is a mature technology that has withstood the test of time, and for that reason, remains a popular method of validating RNA-Seq data. You can rest assured that qPCR will ultimately increase your confidence in the RNA-Seq data.
When is RNA Seq data only a small part of the story?
1) When the RNA-Seq data is only a small part of the story. Let’s call this the “primary screen” mindset. If you’re using the RNA-Seq results to generate new hypotheses that will be exhaustively tested at a more focused level, then qPCR validation is not always necessary. This is particularly relevant to protein-level approaches.
How is differential gene expression assessed by RNA Seq?
This chapter is focused on assessing differential gene expression by RNA-seq. However, very similar statistical tools are available for other differential studies using sequencing. Sequencing starts with an RNA sample from a tissue. This may be preprocessed to enrich for certain types of RNA, such as RNA with poly-A tails.
Can a single RNA sample be split across multiple lanes?
A single RNA sample may be split across multiple lanes to increase the amount of sequencing done. This is uncommon in current RNA-seq studies, because each lane can now sequence 100’s of millions of RNA fragments, which is more than sufficient for RNA-seq, but it may be done in studies that need very high read counts.