Links

Related to CRISPR and CRISPR based screens:

General info /

Our YouTube channel link

https://www.addgene.org/crispr/

https://www.addgene.org/crispr/guide/

http://blog.addgene.org/plasmids-simplified

http://wwwuser.cnb.csic.es/~montoliu/CRISPR/  <– !

http://blog.addgene.org/genome-wide-screening-using-crispr/cas9

https://www.addgene.org/crispr/libraries/

http://dharmacon.gelifesciences.com/resources/webinars/crispr-cas9-shrna-sgrna-pooled-lentiviral-screening/

https://portals.broadinstitute.org/gpp/public/resources/protocols <– !

CRISPR-Cas9 (“Mr. Sandman” Parody) | A Capella Science –> www.youtube.com/watch?v=k99bMtg4zRk&feature=youtu.be

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gRNA design /

http://blog.addgene.org/how-to-design-your-grna-for-crispr-genome-editing

https://www.addgene.org/crispr/reference/#grna

http://crisprgold.mdc-berlin.de/

http://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design

http://cistrome.org/crispr/

http://genomecrispr.dkfz.de/#!/

http://research.microsoft.com/en-us/projects/azimuth/

http://www.broadinstitute.org/rnai/public/analysis-tools/sgrna-design

https://crispr.med.harvard.edu/main/

https://chopchop.rc.fas.harvard.edu/

http://crispr.wustl.edu/

http://crispr.mit.edu/

http://bioconductor.org/packages/release/bioc/html/CRISPRseek.html

https://www.dna20.com/eCommerce/cas9/input

http://bioinfogp.cnb.csic.es/tools/breakingcas/index.php

http://www.rgenome.net/about/

http://cistrome.org/crispr-focus/

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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):

  1. A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic targets in Acute Myeloid Leukemia. Tzelepis et al. Cell Reports 2016. link
  2. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Horlbeck et al. eLife 2016. link
  3. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Doench et al. Nature Biotechnology 2016. link
  4. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Chari et al. Nature Methods 2015. link
  5. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Hart et al. Cell 2015. link
  6. Identification and characterization of essential genes in the human genome. Wang et al. Science 2015. link
  7. A CRISPR-Based Screen Identifies Genes Essential for West-Nile-Virus-Induced Cell Death. Ma et al. Cell Reports 2015. link
  8. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Konermann et al. Nature 2015. link
  9. Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Gilbert et al. Cell 2014. link
  10. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Koike-Yusa et al. Nature Biotechnology 2014. link
  11. Improved vectors and genome-wide libraries for CRISPR screening. Sanjana et al. Nature Methods 2014. link
  12. 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.

Please let me know if there is any missed publication in this list. Note that suggested full genomic gRNA libraries, listed here, should be available through the publication. I’m sorry for not finding them earlier.

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Useful working with TCR

IMGT/V-quest / http://www.imgt.org/IMGT_vquest/vquest  (make sure to choose TCR)

Igblast / https://www.ncbi.nlm.nih.gov/igblast/ (make sure to choose TCR)

Ensambl looking at Human TCR sequences / http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000211789;r=14:21887857-21888502;t=ENST00000390437

Blast2seq / https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq

Blastn / https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch

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Other Links / 

Ensembl Genome Browser / www.ensembl.org/index.html

European Bioinformatics Institute / www.ebi.ac.uk/

ImmGen / www.immgen.org/

Gencode / www.gencodegenes.org/

Human Protein Atlas / www.proteinatlas.org

R2: Genomics Analysis and Visualization Platform / http://hgserver1.amc.nl/cgi-bin/r2/main.cgi

Integrative Genomics Viewer /  www.broadinstitute.org/igv

Gene expression atlas / www.ebi.ac.uk/gxa

The International Knockout Mouse Consortium /  www.knockoutmouse.org

Accense, for analysis of FSC files / www.cellaccense.com/   <– !

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Oligonucleotide Properties Calculator /  www.basic.northwestern.edu/biotools/oligocalc.html

BioMath Calculators / www.promega.com/resources/tools/biomath-calculators/

Reverse DNA sequence / 
www.cellbiol.com/scripts/complement/reverse_complement_sequence.html

Harvard primer bank / pga.mgh.harvard.edu/primerbank

http://www.hemocytometer.org/

Barcodes! / https://github.com/EnvGen/LabProtocols/blob/master/BarcodeCombinations.txt

MiSeq Amplicon Sequencing Sample Prep with Dual Barcoding / https://github.com/EnvGen/LabProtocols/blob/master/Amplicon_dual_index_prep.rst

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Promo, “Identification of putative transcription factor binding sites” / alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3

Transcription factor targets / rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchTFGeneForm

GPminer, “Investigation of gene promoters” / gpminer.mbc.nctu.edu.tw/index.php

dChip Software: Analysis and visualization of gene expression and SNP microarrays / www.hsph.harvard.edu/cli/complab/dchip/

Making phylogenetic trees / http://www.the-scientist.com/?articles.view/articleNo/30930/title/Learning-to-Become-a-Tree-Hugger/

SeaView, “Multiple sequence alignment” / http://pbil.univ-lyon1.fr/software/seaview.html

BEAST, “Analysis of molecular sequences” /  http://beast.bio.ed.ac.uk/

FigTree, “Graphical viewer of phylogenetic trees” /  tree.bio.ed.ac.uk/software/figtree

Pipmaker, “Percent identity plot” /  pipmaker.bx.psu.edu/pipmaker

Using ImageJ to Quantify Images /  http://lukemiller.org/index.php/2010/11/analyzing-gels-and-western-blots-with-image-j/

Making heatmaps 1 /  http://flowingdata.com/2010/01/21/how-to-make-a-heatmap-a-quick-and-easy-solution/

Making heatmaps 2 /  http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm

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ApE, “A plasmid Editor” / biologylabs.utah.edu/jorgensen/wayned/ape

SnapGene / http://www.snapgene.com/

ImageJ / rsbweb.nih.gov/ij

PyMol, “Molecular visualization tool” / www.pymol.org

Paint.net, free alternative to Photoshop / www.getpaint.net

Inkscape, free alternative to Illustrator / inkscape.org

Cell profiler / http://cellprofiler.org/

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Assay Guidance Manual, High Throughput Screening (HTS) / www.ncbi.nlm.nih.gov/books/NBK53196/

http://amigo.geneontology.org/amigo/landing

http://www.pantherdb.org/ (see http://pantherdb.org/help/PANTHER_user_manual.pdf and http://www.ncbi.nlm.nih.gov/pubmed/23868073)

http://cgap.nci.nih.gov/Pathways

http://www.ensembl.org/biomart/martview/e0d9f22f75299873b6c9dba1ffe56d96

http://cbl-gorilla.cs.technion.ac.il/

http://www.kinase.com/

http://dgidb.genome.wustl.edu/

http://www.pathwaycommons.org/about/

http://www.transomic.com/Products/RNAi/Pooled-shRNA.aspx

UniProt ID mappings /  http://www.uniprot.org/mapping/

Decipher (https://www.addgene.org/pooled-library/decipher-human-cell-surface-targets/#) lists of genes and suggested shRNAs / http://www.decipherproject.net/support/#gene-lists

Protein interactions / www.intomics.com/inbio/map/#home 

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Good texts on webpages/blogs like researchgate:

https://www.researchgate.net/post/How_can_I_improve_my_lentivirus_titer

https://www.researchgate.net/post/Could_we_use_the_DH5alpha_instead_of_Stbl3_for_lentiviral_plasmid_transformation_and_cloning

https://www.researchgate.net/post/Difference_between_a_2nd_and_3rd_generation_transfer_plasmid_vector

https://www.researchgate.net/post/what_is_the_optimal_amount_of_each_lentiviral_vector_2nd_and_3rd_generation_for_packaging_by_lipofectamine_3000_in_HEK293T

https://www.researchgate.net/post/How_to_calculate_the_Multiplicity_of_infection_MOI

Bacterial Transfer Associated with Blowing Out Candles on a Birthday Cake –> http://www.ccsenet.org/journal/index.php/jfr/article/view/67217

Chicken soup inhibits neutrophil chemotaxis in vitro. –> https://www.ncbi.nlm.nih.gov/pubmed/11035691

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Good videos:

Facs Doublet Discrimination –> www.youtube.com/watch?v=MjMvwSUucKI

What is CRISPR –> www.youtube.com/watch?v=MnYppmstxIs

Jennifer Doudna: CRISPR Systems: From adaptive immunity to genome editing –> www.youtube.com/watch?v=TyZGM-QNXgA

Emmanuelle Charpentier: Gene editing and genome engineering with CRISPR-Cas9   www.youtube.com/watch?v=CQPtd-rtiUo&app=desktop

Genome Editing Using CRISPR-Cas Systems: Development and Prospects-Feng Zhang –>  www.youtube.com/watch?v=rnLHmtb50jUhttps://www.youtube.com/watch?time_continue=123&v=6MH-_GVEgnY

From microbial immunity to genome editing –> www.youtube.com/watch?v=ihmt9MkQY34

CRISPR Cas Technology and its Applications –>www.youtube.com/watch?time_continue=123&v=6MH-_GVEgnY

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Other:

The Belmont Report 1979 / www.hhs.gov/ohrp/humansubjects/guidance/belmont.html

WMA Declaration of Helsinki – Ethical Principles for Medical Research Involving Human Subjects / http://www.wma.net/en/30publications/10policies/b3/

Clinical Trials / clinicaltrials.gov/ct2/home

Progress in Autoimmune Diseases Research, Report to Congress, National Institutes of Health, The Autoimmune Diseases Coordinating Committee, March 2005 /  www.niaid.nih.gov/topics/autoimmune/documents/adccfinal.pdf

Gapminder World link

Kahoot – Making Learning Awesome link

Edpuzzle.com 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

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

Work environment and lab safety at KI:

http://www.ki.se/uu/Introutb/Labsafety/story.html

https://internwebben.ki.se/en/introduction-package-new-staff