Transcriptomics on TouchingFish.top

The Ways of Eel (PERVADE)

Thu, 24 Jun 2021 00:00:00 +0000

Calling this a popular science article is a stretch. There is no rigorous experimental design here, no systematic literature review. Calling it a book review would be too sentimental — I did not read with my heart on my sleeve, and most of it slipped away after I turned the last page.

I spent my undergraduate years working on Japanese eels with my advisor. The project fizzled out when the department stopped providing lab space, but two-plus years of messing about with eels was enough to leave me with a feeling about this creature that I can't quite put into words.

Through Change, Life Endures

Fri, 21 May 2021 00:00:00 +0000

I received a livestream notification about the "Yunnan Butterfly Explosion" the moment I got to work. I'd been intrigued ever since seeing it on trending topics earlier — back in college, I followed two professors into the mountains to observe butterflies. One was a species identification expert, the other an entomologist. Both were inspiring mentors I deeply respect.

The more I think about butterflies, the more fascinating they become. Caterpillar and butterfly — same genome, yet two radically different lives. The genes are not replaced; the same genetic information is simply "interpreted" differently during metamorphosis. It is as if the same transcript gets spliced under a different scheme, emerging with entirely new form and function. This brings to mind an ancient saying —

Alternative Splicing Analysis - Algorithm and Workflow

Sun, 21 Feb 2021 00:00:00 +0000

1. Biological Background

1.1 What is Alternative Splicing

In eukaryotes, a single gene can produce multiple mRNA isoforms through alternative splicing (AS) -- the process by which different combinations of exons are joined during pre-mRNA splicing. This greatly expands proteomic diversity without increasing gene count.

A gene with N exons can theoretically produce up to 2^(N-1) splice variants. In practice, most genes produce 2-10 isoforms, but some (e.g., Drosophila Dscam) can produce tens of thousands.

Differentially Expressed Gene (DEG) Analysis Across Multiple Tissues of Japanese Eel in Seawater and Freshwater Environments

Thu, 15 Aug 2019 00:00:00 +0000

Abstract

This study conducted differentially expressed gene (DEG) analysis on three key tissues (brain, gonad, pectoral fins) of Japanese eel (Anguilla japonica) under seawater (SEA) and freshwater (TAP) conditions, to elucidate the transcriptomic response mechanisms during salinity adaptation.

Key findings:

Global analysis (controlling for tissue effects) identified 422 DEGs (303 upregulated, 119 downregulated)
The brain was the most salinity-sensitive tissue, with 500 DEGs identified
Eight core response genes were significantly differentially expressed across all three tissues (intersection), all upregulated in the seawater environment

Main conclusions: