Useful links for lab

Good overview of basic histology techniques:  http://home.cse.edu/~ikessler/histo/lab/labtech4.html

Single cell analysis in R: http://satijalab.org/seurat/

Easy to use and fast web based platform for differential analysis of RNAseq: http://ge-lab.org:3838/idep/

Stem cell in testis http://www.stembook.org/node/457.html

Staining substrates for IHC: https://www.thermofisher.com/es/es/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/ihc-immunodetection.html

miRNA ISH protocol: https://www.exiqon.com/ls/Documents/Scientific/miRCURY-LNA-microRNA-Detection-Probes-instruction-manual.pdf

Tools for miRNA analysis: https://tools4mirs.org/

Excellent summary of deconvolution using Fiji

https://pages.stolaf.edu/opn-lab/files/2016/12/Giannini_Giannini_Deconvolution_Manual_20161215.pdf

Linux on older intelmacs

How to install Ubuntu 16.04 on Intel Macs; even older. Start with burning ubuntu server 14.04 to CD (it fits on CDs 700MB), press option key, press on CD logo and install ubuntu on entire disk (it will format and erase all your data). Use GRUB as loader. it works even on 12 year old mabbooks with coreduo. Then sudo reboot, after you remove CD. Do sudo apt-get update, sudo apt-get upgrade to get all packages on 14.04 up to date. Sudo reboot again. Now log into your server and while connected to network with ethernet (not static IP at this point), type sudo do-release-upgrade. Leave computer on overnight, it may take few hours. Next follow the outstanding write up on this page: https://medium.com/@racter/how-to-install-ubuntu-16-04-on-a-retina-macbook-11-2-74e7779c0e47

You may not need to do all described in the linked page. Enjoy. 

Instructions on setting static IP on ubuntu 16.04 server: https://help.ubuntu.com/lts/serverguide/network-configuration.html

 

50 common linux commands

http://www.thegeekstuff.com/2010/11/50-linux-commands/

good RNAseq bioinformatics intro

http://mmg434.readthedocs.io/en/latest/daytwomod.html#basic-unix-coms