EcoEvoDevo Lab

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The Angelini lab group at Colby College.

Standard operating procedures (SOPs)

General Info for Students in the Lab (including how to get involved and lab safety)

Field biology

Entomology

Photographing butterflies in the lab
Bumble bee anatomy and measurement protocols for
Staining insects for micro-CT scanning
Micro-CT scanning

Molecular biology

Autoclave
DNA extraction using the Maxwell 16 for large, soft samples
DNA extraction using Qiagen DNeasy Kit (e.g. for beetles)
Extraction of high-molecular weight (HMW) DNA
RNA extraction
cDNA synthesis
PCR
Agarose gel electrophoresis
RNA synthesis for RNAi and CRISPR
In vitro digestion of DNA with sgRNA/Cas9
Realtime PCR
Miscellaneous Molecular Biology Methods

Developmental biology

Computational biology

Intro to R
Basic Statistics
Geometric morphometrics - updated borealis vigenette coming soon!
Linux basics - A quick introduction of the bash command line
Local BLAST - How to run BLAST in the command line, using custom local databases.
GenBank submission for batch sequences
Microbiome Analysis Tutorial

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Project workflows

Completed

morphDE: Repository for the differential expression analysis for Jadera haematoloma by morph and other factors (Angelini et al. 2022 ICB)
bombus.landscape: Bombus landscape microbiome analysis (Young et al. 2023 bioRxiv)
Qiime2 Classifier Update: Adding SSU rRNA sequences relevant to bumble bees to the SILVA release 132 NR99 dataset

In progress

BeeSeq - Neonic effects on Bombus impatiens gene expression and microbiome (2021 Update)
Cownose ray feeding ecology: Using microbiome analysis to determine the prey and microbiota of Rhinoptera bonasus