How to Get Back to Insert Mode in VIM When You Accidentally Hit C-x C-s

How to get back to insert mode in VIM when you accidentally hit C-x C-s

Gene Targeting

Cited from Gene targeting

"Gene targeting requires the creation of a specific vector for each gene of interest. However, it can be used for any gene, regardless of transcriptional activity or gene size."

"To target genes in mice, this construct is then inserted into mouse embryonic stem cells in culture. After cells with the correct insertion have been selected, they can be used to contribute to a mouse's tissue via embryo injection. Finally, chimeric mice where the modified cells made up the reproductive organs are selected for via breeding. After this step the entire body of the mouse is based on the previously selected embryonic stem cell."

RNAi siRNA and shRNA

Cited from RNAi (RNA interference) defined

1. Synthetic (siRNA) or single stranded RNA (ssRNA) containing two complementary sequences separated by a non-complementary sequence, which folds back on itself to form a synthetic short hairpin RNA (shRNA).
2. Expressed from a DNA construct which encodes an shRNA molecule. This is the dd (DNA-directed) RNAi approach.

siNT: non-target siRNA

Cited from the paper "A Novel Multiplex Cell Viability Assay for High-Throughput RNAi Screening"


"Nucleus or DNA stain using fluorescent molecules, such as Hoechst 33342, Hoechst 33258, DAPI or other dyes have been long-serving and commonly applied indicators of cellular viability."

R Markdown Cheatsheet

R Markdown Cheatsheet

Visualising random variables

Visualising random variables

Quntile Normalisation in R

Quantile normalisation in R

Pausing an R Script for User Input

Cited from Pausing an R script: a generic pause function

pause = function(){
    if (interactive()) {
        invisible(readline(prompt = "Press <Enter> to continue..."))
    }
    else {
        cat("Press <Enter> to continue...")
        invisible(readLines(file("stdin"), 1))
    }
}

Define Bivalent Promoters Computationally

Cited from Lossof the PolycombMark from Bivalent Promoters Leads to Activation of Cancer-Promoting Genes in Colorectal Tumors

A promoter was defined as bivalent if it contained overlapping H3K4me3 and H3K27me3 peaks at expanded promoter areas (2.4 kb < TSS < 0.6 kb).

Convert Excel File to Text File in Linux

Convert xlsx to csv in linux command line

Split and Merge PDF Files in Ubuntu

The easiest way to split and merge pdf files in Ubuntu

High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment)

Cited from SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways

"Systematic Evolution of Ligands by EXponential enrichment (SELEX) is an experimental procedure that allows extraction, from an initially random pool of oligonucleotides, of the oligomers with a desired binding affinity for a given molecular target."

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Cited from Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

Aptamers: short (20–100 nucleotides), synthetic, single-stranded (ribo)-nucleic molecules.

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Cited from Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing.

Nature Reviews Molecular Cell Biology: Naive to Primed Pluripotency

Stem cell states: naive to primed pluripotency

MyLabStocks

MyLabStocks

TF Target Genes Overlap with Active/Repressive Histone Marks

Cited from Supplementary Figure 4 of "Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis".

The Axoneme of Cilia

Cited from The Axoneme of Cilia

A cilium, like a flagellum, is composed of a central core (the axoneme), which contains two central microtubules that are surrounded by an outer ring of nine pairs of microtubules. 

Perl: Slurp Mode - Reading a File in One Step

slurp mode - reading a file in one step

Manual for Bash "declare"

Typing variables: declare or typeset

Pass Array(s) as a Parameter to a Bash Function

Passing arrays as parameters in bash

FUCCI and Nocodazole in Studying Cell Cycle

FUCCI Cell Cycle Sensor

Cdt1 is a DNA replication factor. It licenses for the formation of pre-replication complex.

Geminin is a DNA replication inhibitor.

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Cited from Aphidicolin

Aphidicolin is an antiviral and antimitotic antibiotic extracted from a fungus, and it is produced as the secondary metabolite. It reversibly inhibits DNA polymerase A,D in eukaryotic cells and therefore inhibits eukaryotic nuclear DNA replication. It arrests cells in early S phase. 

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Cited from G1 versus G2 cell cycle arrest after adriamycin-induced damage in mouse Swiss3T3 cells

Adriamycin is a DNA damaging agent, inducing DNA intercalating. Adriamycin is known to arrest cells in G1 or G2 phase.

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Cited from Nocodazole

Nocodazole interferes with polymerization of microtubules, and cells treated with nocodazole arrests in G2- or M- phase. Prolonged nocodazole leads to apoptosis.