Runcell posts tagged “biotech”
Dam/Dcm Methylation Tutorial: Which Restriction Sites Are Blocked in pUC19, pBR322, pACYC184 and Lambda
A site-by-site table of which restriction sites Dam and Dcm methylation block in four standard DNAs, for the 114 enzymes in Runcell's restriction site finder, using REBASE sensitivity data. Covers the enzymes that are on the 'blocked' list but still cut your vector, how often a cloning junction creates a new blocked site, and a script to check your own plasmid.Read More →
BCA vs Bradford: How Far Off Each Assay Reads 13 Proteins Against a BSA Standard
A protein-by-protein bias table for BCA, Micro BCA, Modified Lowry, Bradford and Bradford Plus, built from the vendor's own response ratios, plus an A280 column computed from UniProt. Shows where the assays disagree by up to 3.4×, what switching to a BGG standard fixes for antibodies, and why the Bradford numbers are a best case.Read More →
Primer Dimer Check Tutorial: Testing ΔG Rules on the CDC qPCR Primers
We ran the CDC SARS-CoV-2 N1, N2, N3 and RNase P primers and probes through two dimer models and Primer3. A consecutive-pair checker at common ΔG limits misses the N3 set that CDC withdrew. Ranked by Primer3's 3′-end stability, the N3 pair comes first and two of three reported N2 interactions land in the top four. With the numbers, the code, and how to read a dimer flag.Read More →
A280 Protein Concentration Tutorial: ε280 for 11 Proteins, and Why A280 ≠ mg/mL
Computed ε280, molecular weight and Abs 0.1% for 11 common lab proteins from UniProt mature chains. Shows how far the '1 A280 = 1 mg/mL' shortcut is off (0.17× to 2.65×), what pasting the precursor sequence costs, and why nucleic-acid contamination skews proteins with a low Abs 0.1% the most.Read More →
DNA Molecular Weight in Python: A Runnable ng/µL → nM Workflow
Why ng/µL → nM calculators disagree by 7%, measured on real NCBI sequences with Biopython. Covers free acid vs sodium salt, the 650/660/330 rules of thumb, 5' phosphates, and a full pUC19 digest-to-ligation workflow.Read More →
DESeq2 in Python: Step-by-Step PyDESeq2 Tutorial
Run DESeq2 differential expression analysis entirely in Python with PyDESeq2. Covers count matrices, normalization, statistical testing, LFC shrinkage, and visualization.Read More →
Differential Expression Analysis: Guide with R & Python Code
Complete guide to differential expression analysis for RNA-seq. Includes ready-to-run code for DESeq2, edgeR, limma-voom, and Scanpy with bulk and single-cell workflows.Read More →