Siryaporn's lab rotation
Runhang / 2022-03-28
2022 Srping, UCI CMB program rotation
Author: Runhang Shu, PhD student
Affiliation: University of California, Irvine
Contact: darsonshu@gmail.com
Date started: 2022-03-28
Date end (last modified): 2022-03-28
This work is licensed under a Creative Commons Attribution 4.0 International License.
Introduction:
Notebook for rotation in Dr. Albert Siryaporn lab. It’ll log notes, ideas and inspirations from papers I read; Save a copy of bioinformatic and statistical analysis I did for reproducible science!
Table of contents
- Page 1: 2022-03-28 Bacterial mRNA extraction and Illuminal library prep protocols (updating).
- Page 2: 2022-03-29 Histone project literature review
Page 1: Purify Bacterial mRNA
Siryaporn lab protocol
- Using Hot-Phenol protocol for nucleic acids extraction from bacterial cells (Day1)
- DNase digest and RiboZero (remove DNA and rRNA from Day1 prep) (Day2)
- NEBNext kit - ligate adapters, generate cDNA, and add index tags (Day3,4)
- note: there is an upgraded NEBNext kit E7760 in replace of E7420 in the old protocol. The total RNA input has broad range between 5 nanograms to 1 microgram.
- Thermo Fisher has a MICROBExpress bacterial mRNA enrichment kit. It will be like RiboZero rRNA depleting kit.
- Ongoing issue with RiboZero kit: ribozero probes can get incorporated into sequencing pipeline. Use reagents stochiometrically to avoid this.
Reviewed the paper:EMBR-seq
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