This page contains common protocols used in the lab. 🔬microscope and cell culture booking 🧫

⚖️  Analyze oligo:

🧬     reverse complementreversecomplementTm 🔥 :           length 📏 : g/mol       µM

⚖️  Molarity Calculator

Mass picograms nanograms micrograms milligrams grams kilograms

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Concentration femtomolar picomolar nanomolar micromolar millimolar molar

x

Volume nanoliter microliter milliliter liter

x

M. Wt* g/mol

* always use the batch-specific molecular weight of the product found on the vial label.

⚖️  Dilution Calculator

Concentration 1 femtomolar picomolar nanomolar micromolar millimolar molar

x

Volume 1 nanoliter microliter milliliter liter

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Concentration 2 femtomolar picomolar nanomolar micromolar millimolar molar

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Volume 2 nanoliter microliter milliliter liter

⚖️  NanoDrop Calculator

Sample concentration:	ng/µL µg/µL pg/µL mg/µL
Molecular weight:	g/mol
Volume:	µL
To:	µM mM nM pM

Your sample is molar concentration: N/A

Volume: N/A µL
Total molecules: N/A pmol
Total mass: N/A µg

Post-phosphoramidite conjugation to oligonucleotides on non-solid support

🧬  NHS ester labeling of amino moeities
🧬  Copper(I)-catalyzed Azide-Alkyne Cycloaddition (CuAAC) of azides to alkyne moeities
🧬  Strain-Promoted Alkyne-Azide Cycloadditions (SPAAC) of ADIBO to azide moeities

Protein labeling

🧬Antibody conjugation

Oligonucleotide purification

🧪 Silica spin column
🧪 PAGE purification
🧪 Ethanol precipitation
🧪 Enzymatic oligo ligation and cleanup

Synthesis

🧬 Fluorescently labeled RNA
🧬 siRNA synthesis by in vitro transcription

Silanization

🪟🔬 Amino functionalized coverslips

Extraction

🧫 Total RNA extraction in Paramecium

Paramecium

Nuclear and membrane co-staining of Paramecium

In situ library preparation

🧫  Targeted: Padlock probes on cDNA
🧫  Targeted: Padlock probes on mRNA
🧫  Untargeted: cDNA circularization.
🧫  smFISH
🧫  In situ proximity ligation assay (PLA)
🧫 DSS (disuccinimidyl suberate) crosslinking in situ

In situ sequencing

🔬 Sequencing-by-synthesis (SBS) using reversible dye-terminator
🔬 Sequencing-by-ligation (SBL) using DNA ligase and 5'phosphate ligation.

Live imaging

Lonza home brewed nucleofector transfection buffer
Transfection for live imaging
Bacteria transfection

Computational pipelines

🤖  Making presentations using Quarto, Markdown and RevealJS
🤖  RNA-seq alignment using bowtie
🤖  Read alignment and visualization using JBrowse2
🤖  Read annotation and feature counting using featureCounts
🤖  RNA-seq alignment using STAR
🤖  In situ transcriptome accessibility ex situ reads pipeline
🤖  In situ transcriptome accessibility in situ reads pipeline

Common lab buffers

🍶 0.5 M carbonate/bicarbonate (pH 8.75)
🍶 10x 1M Sodium acetate (pH 6.0)
🍶 10% Triton X-100
🍶 Formamide strip buffer
🍶 Dryl's buffer
🌾 Paramecium wheat grass medium
🍶 Washbuffer for in situ hybridization
🍶 DEPC-PBST

Buffer stock room

The following buffers are available from the Buffer Stock Room:

• 10x PBS
• 1x PBS
• 20x SSC
• 10x TBE
  
• 5x TBE
• 1x TBS
• 1x TB
• Tripotassium phosphate (labeled in Swedish: Kalium fosfat)
• Sterile water
• 0.9% NaCl
• 5M NaCl
• 0.5M EDTA
• 1M Sodium Citrate
• 20% (w/v) glucose
• 1M CaCl2
• 1M MgSO4
• 1M Tris pH 9.0
• 1M Tris pH 7.9
• 1M Tris pH 7.5
• 3M Sodium Acetate
• LB
• 4 x LB
• LB with 0.3M NaCl
• LSLB
• 2x YT
• 20x M9

Also available are agar plates:

• LA
• LA + 50 Ap, Ampicillin, 50 μg/mL
• LA + 100 Ap, Ampicillin, 100 μg/mL
• LA + 15 Tc, Tetracycline, 15 μg/mL
• LA + 100 sm, Streptomycin, 100 μg/mL
• LA + 50 Km, Kanamycin, 50 μg/mL
• LA + 12.5 Cm, Chloramphenicol, 12.5 μg/mL
• LA + 50 Sp, Spectinomycin, 50 μg/mL