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 <-- !
Tips for a 1st Time CRISPR User (by a 1st Time CRISPR User) / http://blog.addgene.org/tips-for-a-1st-time-crispr-user
CRISPR-Cas9 ("Mr. Sandman" Parody) | A Capella Science --> www.youtube.com/watch?v=k99bMtg4zRk&feature=youtu.be
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/
https://crispr.ml/
https://gggenome.dbcls.jp/hg19/2/ <-- !
Oligo pools and arrays /
CustomArray / http://www.customarrayinc.com/oligos_main.htm
Twist Bioscience / https://twistbioscience.com/products/pools
Synthego / http://www.synthego.com/products/custom-arrayed-synthetic-sgrna-plates/
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.
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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
Codon frequency table / https://www.genscript.com/tools/codon-frequency-table
Codon Optimization Tool / https://www.idtdna.com/CodonOpt
Search for cell lines with specific HLA alleles / https://www.cellosaurus.org/search
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Other Links /
ShinyDepmap / https://labsyspharm.shinyapps.io/depmap/ <-- !
Depmap portal / https://depmap.org/portal/ <-- !
cBioPortal for cancer genomics / https://www.cbioportal.org/ <-- !
COSMIC Catalogue Of Somatic Mutations In Cancer / https://cancer.sanger.ac.uk/cosmic
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 Set Enrichment Analysis (GSEA) / http://software.broadinstitute.org/gsea/index.jsp
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/ <-- !
Restriction free cloning/mega primer / http://www.rf-cloning.org/ <-- !
Find antibodies / https://www.benchsci.com/
Analyzing CRISPR mutations with Sanger sequencing 1 / https://ice.synthego.com/#/
Analyzing CRISPR mutations with Sanger sequencing 2 / https://tide.deskgen.com/
Analyzing CRISPR screens / http://crispr-analyzer.dkfz.de/#
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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/
For the generation of random sequences / http://www.bioinformatics.org/sms2/random_dna.html
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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/
FlowJo plugins! http://exchange.flowjo.com/
Bioicons, free science illustrations / https://bioicons.com/ <-- !
Smart, free science illustrations / https://smart.servier.com/ <-- !
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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://wlab.ethz.ch/cspa/#abstract
https://www.proteinatlas.org/humanproteome/secretome
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
http://metascape.org <-- !
Cancer genes / https://cancergenome.nih.gov/
Cancer genes 2 / https://dcc.icgc.org/
Cancer genes 3 / https://cancer.sanger.ac.uk/census
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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
About Codon optimization https://blog.addgene.org/plasmids-101-codon-usage-bias
About lentiviruses http://www.uvm.edu/safety/sites/default/files/lentiviral_vectors_fact_sheet.pdf
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
Here are some links for finding antibodies for different TCR genes!!:
Human TRAV:
http://www.imgt.org/IMGTrepertoire/Regulation/antibodies/human/TRA/TRAV/Hu_TRAVMab.html
Human TRBV:
http://www.imgt.org/IMGTrepertoire/Regulation/antibodies/human/TRB/TRBV/Hu_TRBVMab.html
Mouse TRAV:
http://www.imgt.org/IMGTrepertoire/index.php?section=Regulation&repertoire=antibodies&species=mouse&group=TRAV
Mouse TRBV:
http://www.imgt.org/IMGTrepertoire/index.php?section=Regulation&repertoire=antibodies&species=mouse&group=TRBV
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Good videos:
Highly recommended biology video series --> https://www.ibiology.org/biology-online/ <-- !
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
Analyzing CRISPR screens with CRISPRAnalyzerR --> www.youtube.com/watch?v=zIC8OZBX_5U
Jennifer Listgarten: CRISPR Bioinformatics - Machine learning predictive models for guide design --> www.youtube.com/watch?v=FHzS1fodxlk
CRISPR/CAS9 Screening in Human Pluripotent Stem Cells --> https://www2.twistbioscience.com/CRISPR_Webinar?utm_source=OligoNurture&utm_medium=email&utm_campaign=NUT3-Crispr-Webinar
Facs Doublet Discrimination --> www.youtube.com/watch?v=MjMvwSUucKI
Immunology course --> https://www.youtube.com/playlist?annotation_id=annotation_1453316675&feature=iv&list=PL5703ABB5D07584D7&src_vid=Jshw2sHrk8Y
Immunology basics --> https://www.youtube.com/watch?v=fHRiaAMWFC4
Top 10 CRISPR Podcasts Every Scientist (& Non-Scientist) Will Love --> https://www.synthego.com/blog/10-podcasts-every-crispr-scientist-will-love?
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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
Nine Habits of a Highly Productive Researcher - https://www.stemcell.com/efficient-research/productive-habits/
About Homeostasis - http://adhdboss.com/breaking-homeostasis-review/
"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
The Wermeling lab 