Lab book of the gilestro lab
This guide helps you creating a split deeplabcut environment. One half will run on your local office computer (no GPU needed) and will be used to annotate images for the training of the NN The other half will run on the ICL cluster, so that it will take full advantage of the higher performance during … Continue reading Create a conda environment for deeplabcut on the ICL cluster
Needed material. A raspberryPi 3 or 3+ with adequate 2.5A or 3A power supply Adafruit raspberryPi LED Bonnet (adafruit link) 6x of 64×64 LED panels (aliexpress link) Entire 3D printed structure (onshape link) 24x M3x10 socket button hex screws (amazon link) A raspberryPI camera A longer ribbon for the camera (aliexpress link) Software. I will … Continue reading Building a 360 LED screen
Lab life. Chances are that you decided to join the lab because you want to learn more about Drosophila melanogaster, or because you find sleep a fascinating topic. This is great. However, my goal as supervisor should be to go beyond the project you picked and expose you to “the lab life”, to give you … Continue reading Lab life and rules
The flyroom The flyroom is located on the third floor of this building and it is space that we share with other three fly groups. Therefore, it is paramount to keep a nice and collaborative behaviour. This means, above everything, to respect common spaces and common resources. Clean after yourself. Do not leave rubbish around. … Continue reading Working in the fly room
The lab NAS serves a first backup destination for all the data produced in the lab. In particular, we have two types of data: auto-generated data, i.e. data generated by machines such as ethoscopes or DAMs user-generated data, i.e. data generated by lab members. These can be raw data (confocal images, gel scans etc) or processed data … Continue reading Backup data to the lab NAS
Reagents needed and providers: Reagents Tris Hcl pH 7.5 VWR A4263.0500 £21.90 500ml PEG 8000 Sigma P1458-25ML £15.63 25ml MgCl2 Thermofisher AM9530G £29.70 100ml DTT VWR A3668.0050 £30.60 50ml NAD NEB B9007S £16.80 0.2ml dNTP Thermofisher 15363397 £49.50 1ml Phusion NEB M0530S £56.00 100U Taq Ligase NEB M0208S £49.60 2000U T5 exonuclease NEB M0363S £41.60 … Continue reading Gibson Assembly – DIY recipe
From Georg Dietzl in Barry Dickson’s Lab, IMP Vienna 12/2002 SQUISHING BUFFER (SB) 10 mM Tris-HCl pH8 1 mM EDTA 25 mM NaCl 200 g/ml Proteinase K Procedure 200 g/ml Proteinase K are added to the squishing buffer (SB) freshly from 20X stock every day. Place 1-2 (I always take 2) flies in a 0.5 … Continue reading Single Fly Genomic DNA Prep
The lab uses a shared server for saving data. Data on the server are safe and go regular backup. You should map the server drive as network drive on your computer. When prompted, you should enter the login credentials for the network hard drive, which are: username: student password: ic_student Here is how to map … Continue reading Mapping Lab Server
The gel machine has now access to the college network and you can easily access the pictures you take in the lab from your own computer. Here is how to do it: If not logged in yet, login with local user “geldoc” ( password “edas%290” ). If you don’t have one yet, create a subfolder … Continue reading How to use the GELDOC computer in the molecular lab
PBS 10X 40 g NaCl 1 g KCl 13.4 g Na2HPO4-7H2O 1.2 g H2O Adjust the pH at 7.4 with HCl. Complete to 500 mL with distilled water. Lysis Buffer 580 µL Nonidet P40 0.58 g CHAPS 0.150 g HEPES 0.508 g NaCl 9.93 g Saccharose 0.022 g Na2EDTA Adjust the pH to 8.0. Complete … Continue reading Western Blot Recipes
PREPARE THE FILES Files should be in AVI or OGV format. Filename should not contain empty spaces or weird characters. The best praxis is to give files a named based on the timestamp or some other number and include a .txt file with a legend of the experiment and any other comments. CREATE A MASK … Continue reading Track flies for odor preference (movie analysis)
Make the RNA/primer/dNTP mix by combining the following components in a sterile RNase-free microfuge tube: Total RNA 1–10 μl (1 ng–1 μg) Primer dT23VN 2 μl dNTP Mix 4 μl nuclease-free H20 variable Total Volume 16 μl Heat for 5 minutes at 70°C. Spin briefly and promptly chill on ice. Add the following components to … Continue reading mRNA RT with ProtoScript® M-MuLV Taq RT-PCR Kit (NEB)
10X TAE Electrophoresis 48.4 g of Tris base [tris(hydroxymethyl)aminomethane] 11.4 mL of glacial acetic acid (17.4 M) 3.7 g of EDTA, disodium salt deionized water Dissolve the Tris, glacial acetic acid and EDTA in 800 ml of deionized water. Dilute the buffer to 1 L. You do not need to sterilize the solution. Store the … Continue reading Common Buffers – TAE
The following is a common method for the preparation of 1 liter of LB [source]: Measure out the following: 10 g tryptone 5 g yeast extract 10 g NaCl Suspend the solids in ~800 ml of distilled or deionized water. Add further distilled or deionized water, in a measuring cylinder to ensure accuracy, to make a … Continue reading Bacterial Growth solutions
NEB Recipe: 1X Gel Loading Dye, Blue (6X): 2.5 % Ficoll 400 11 mM EDTA 3.3 mM Tris-HCl 0.017 % SDS 0.015 % Bromophenol Blue pH 8.0 @ 25°C Simpler alternative Makes 100 ml. Store at room temperature (indefinitely). 0.25 g bromophenol blue (m.w. 669.96) 0.25 g xylene cyanol (m.w. 538.60) 50.00 g sucrose (m.w. … Continue reading DNA Loading Buffer
For reference.
Batch makes about 40 plates. Making the LB Agar Add 250 mL of dH2O to a graduated cylinder. Weigh out 20g of premix LB Agar powder (VWR DF0445-17) or: 5.0 g tryptone 2.5 g yeast extract 5.0 g NaCl 7.5 g agar Mix powder well to bring into solution Add dH2O to total volume of … Continue reading LB Agar Plates
Topo TA cloning is done following loose suggestions of the manufacturer. We currently adopt the kit K204040 from Invitrogen, which is not based on topoisomerase ligation but regular T4 ligation. Comes with “One Shot® aTOP10 Chemically Competent E. coli”. Briefly. Quantify PCR product. The kit suggests to use 10ng of DNA. We usually skip this … Continue reading TOPO TA Cloning
Solutions: Solution A: [Tris HCI 0.1 M (pH 9.0), EDTA 0.1 M, SDS 1%] (keep at RT) Phenol-Cloroform: [If done fresh: mix Phenol and Cloroform 1:1, shake, spin for 10 min at 4.000 rpm] (keep at 4°C) KAc 8 M (keep at RT) Isopropanol (keep at -20°C) EtOH 70% (keep at -20°C) TE (keep at 4°C) … Continue reading Good quality genomic DNA extraction
Kit is NEB E5000-S ($95) Protocol as indicated by NEB. Use attached XLS file for help in creating the mix
Current Kit is N3232S [ 200μl, 200 gel lanes (500 μg/ml) ] To prepare a working dilution, dilute 30 μl in 120 μl TE1X, add 25 μl of Loading Buffer 6X. Use 6 μl of working dilution per well