Related to CRISPR and CRISPR based screens:

General info /

Our YouTube channel link  <-- ! <-- !

Tips for a 1st Time CRISPR User (by a 1st Time CRISPR User) /

CRISPR-Cas9 ("Mr. Sandman" Parody) | A Capella Science -->
gRNA design /!/ <-- !
Oligo pools and arrays /

CustomArray /

Twist Bioscience /

Synthego /
Early Screen papers /

Full genomic reference libraries of gRNAs can be found for example in the following excellent publications. They are intended to be sorted in reversed chronological order and contains both regular KO libraries, as well as repression and activation libraries. (Please cite publications if you use the library):

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic targets in Acute Myeloid Leukemia. Tzelepis et al. Cell Reports 2016. link

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Horlbeck et al. eLife 2016. link

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Doench et al. Nature Biotechnology 2016. link

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Chari et al. Nature Methods 2015. link

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Hart et al. Cell 2015. link

Identification and characterization of essential genes in the human genome. Wang et al. Science 2015. link

A CRISPR-Based Screen Identifies Genes Essential for West-Nile-Virus-Induced Cell Death. Ma et al. Cell Reports 2015. link

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Konermann et al. Nature 2015. link

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Gilbert et al. Cell 2014. link

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Koike-Yusa et al. Nature Biotechnology 2014. link

Improved vectors and genome-wide libraries for CRISPR screening. Sanjana et al. Nature Methods 2014. link

RNA-Guided Human Genome Engineering via Cas9. Mali et al. Science 2013. link

Several of the libraries can be accessed through addgene (link) by clicking the links to the libraries at the end of the page.


Useful working with TCR /

IMGT/V-quest /  (make sure to choose TCR)

Igblast / (make sure to choose TCR)

Ensambl looking at Human TCR sequences /;g=ENSG00000211789;r=14:21887857-21888502;t=ENST00000390437

Blast2seq /

Blastn /

Codon frequency table /

Codon Optimization Tool /

Search for cell lines with specific HLA alleles /


Other Links / 

Depmap portal / <-- !

cBioPortal for cancer genomics / <-- !

COSMIC Catalogue Of Somatic Mutations In Cancer /

Ensembl Genome Browser /

European Bioinformatics Institute /

ImmGen /

Gencode /

Human Protein Atlas /

R2: Genomics Analysis and Visualization Platform /

Integrative Genomics Viewer /

Gene Set Enrichment Analysis (GSEA) /

Gene expression atlas /

The International Knockout Mouse Consortium /

Accense, for analysis of FSC files /   <-- !

Restriction free cloning/mega primer / <-- !

Find antibodies /

Analyzing CRISPR mutations with Sanger sequencing 1 / 

Analyzing CRISPR mutations with Sanger sequencing 2 /

Analyzing CRISPR screens /


Oligonucleotide Properties Calculator /

BioMath Calculators /

Reverse DNA sequence /

Harvard primer bank /

For the generation of random sequences /


Promo, “Identification of putative transcription factor binding sites” /

Transcription factor targets /

GPminer, “Investigation of gene promoters” /

dChip Software: Analysis and visualization of gene expression and SNP microarrays /

Making phylogenetic trees /

SeaView, “Multiple sequence alignment” /

BEAST, “Analysis of molecular sequences” /

FigTree, “Graphical viewer of phylogenetic trees” /

Pipmaker, “Percent identity plot” /

Using ImageJ to Quantify Images /

Making heatmaps 1 /

Making heatmaps 2 /


ApE, “A plasmid Editor” /

SnapGene /

ImageJ /

PyMol, “Molecular visualization tool” /, free alternative to Photoshop /

Inkscape, free alternative to Illustrator /

Cell profiler /

FlowJo plugins!

Bioicons, free science illustrations / <-- !

Smart, free science illustrations / <-- !


Assay Guidance Manual, High Throughput Screening (HTS) / (see and

UniProt ID mappings /

Decipher ( lists of genes and suggested shRNAs /

Protein interactions / <-- !

Cancer genes / 

Cancer genes 2 /

Cancer genes 3 /


Good texts on webpages/blogs like researchgate:

About Codon optimization

About lentiviruses 

Bacterial Transfer Associated with Blowing Out Candles on a Birthday Cake -->

Chicken soup inhibits neutrophil chemotaxis in vitro. -->

Here are some links for finding antibodies for different TCR genes!!:

Human TRAV:

Human TRBV:

Mouse TRAV:

Mouse TRBV:


Good videos:

Highly recommended biology video series --> <-- !

What is CRISPR -->

Jennifer Doudna: CRISPR Systems: From adaptive immunity to genome editing -->

Emmanuelle Charpentier: Gene editing and genome engineering with CRISPR-Cas9

Genome Editing Using CRISPR-Cas Systems: Development and Prospects-Feng Zhang -->

From microbial immunity to genome editing -->

CRISPR Cas Technology and its Applications -->

Analyzing CRISPR screens with CRISPRAnalyzerR -->

Jennifer Listgarten: CRISPR Bioinformatics - Machine learning predictive models for guide design -->

CRISPR/CAS9 Screening in Human Pluripotent Stem Cells -->

Facs Doublet Discrimination -->

Immunology course -->

Immunology basics -->

Top 10 CRISPR Podcasts Every Scientist (& Non-Scientist) Will Love -->

Other /

The Belmont Report 1979 /

WMA Declaration of Helsinki - Ethical Principles for Medical Research Involving Human Subjects /

Clinical Trials /

Progress in Autoimmune Diseases Research, Report to Congress, National Institutes of Health, The Autoimmune Diseases Coordinating Committee, March 2005 /

Gapminder World link

Kahoot - Making Learning Awesome link link

Global Burden of disease link

Steven Johnson on where good ideas come from: link 1, link 2, link 3

Scott Page on Leveraging Diversity link 1, link 2

Organized note-taking: link 1, link 2, link 3

Nine Habits of a Highly Productive Researcher -

About Homeostasis -

"Grantsmanship is the art of acquiring peer-reviewed research funding" link

Work environment and lab safety at KI:

%d bloggers like this: