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Dataset index

The NCCR Chemical Biology offers the following datasets as open source downloads:

 

2021

Dataset title: Distinct fission signatures predict mitochondrial degradation or biogenesis
DOI: 10.5281/zenodo.3550642
Responsible person: Suliana Manley
Projects involved: 2
Article (2021)

Dataset title: Phosphoproteomic Effects of Acute Depletion of PP2A Regulatory Subunit Cdc55
Link: https://panoramaweb.org/VIy6oo.url
Responsible person: Robbie Loewith
Projects involved: 1
Article (2021)

 

Dataset title: The primary dipole of flipper probes
DOI: 10.5281/zenodo.4584732
Responsible person: Stefan Matile
Projects involved: 3
Article (2021)

 

Dataset title: Oligomers of Cyclic Oligochalcogenides for Enhanced Cellular Uptake
DOI: 10.26037/yareta:vxej5zxx5bhejk5z2aucufscay
Responsible person: Stefan Matile
Projects involved: 4, 5
Article (2021)

 

Dataset title: Fluorescent Membrane Tension Probes for Early Endosomes
DOI: 10.5281/zenodo.4441676
Responsible person: Stefan Matile
Projects involved: 3, 4
Article (2021)

 

Dataset title: SupraFlippers-2
DOI: 10.5281/zenodo.4322986
Responsible person: Stefan Matile
Projects involved: 3, 4
Article (2021)

 

Dataset title: Genetically Encoded Supramolecular Targeting of Fluorescent Membrane Tension Probes within Live Cells: Precisely Localized Controlled Release by External Chemical Stimulation
DOI: 10.5281/zenodo.4322855
Responsible person: Stefan Matile
Projects involved: 3, 4
Article (2021)

 

Dataset title: Oligonucleotide Phosphorothioates Enter Cells by Thiol-Mediated Uptake
DOI: 10.5281/zenodo.5018160
Responsible person: Stefan Matile
Projects involved: 4, 5
Article (in press)

 

Dataset title: Inhibitors of Thiol-Mediated Uptake
DOI: 10.5281/zenodo.4109129
Responsible person: Stefan Matile
Projects involved: 4, 5
Article (2021)

 

Dataset title: Lysosomal retargeting of Myoferlin mitigates membrane stress to enable pancreatic cancer growth
DOI: 10.25345/C5KZ26
Responsible person: Rushika M. Perera
Projects involved: 3
Article (2021)

 

Dataset title: Mitochondrial membrane tension governs fission
DOI: 10.5281/zenodo.4648097
Responsible person: Suliana Manley
Projects involved: 3, 4
Article (2021)

 

Dataset title: A bottom up design approach for the de novo design of functional proteins
GitHub repository: https://github.com/LPDI-EPFL/Bottom-up-de-novo-design
Responsible person: Bruno Correia 
Projects involved: 2
Article (2021)

 

Dataset title: Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly
Data (PDB Data bank): https://www.nature.com/articles/s41467-021-23897-0#data-availability
Responsible person: Pierre Gönczy
Projects involved: 2
Article (2021)

 

Dataset title: Similarities and differences among protein dynamics studied by variable temperature NMR relaxation
DOI: 10.5281/zenodo.4542887
Responsible person: Lyndon Emsley
Projects involved: 2
Article (2021)

Dataset title: Kinesin-1 activity recorded in living cells with a precipitating dye
DOI: 10.5281/zenodo.4461867
Responsible person: Nicolas Winssinger
Projects involved: 1, 2
Article (2021)

 

Dataset title: Minimal Hybridization Chain Reaction (HCR) System using Peptide Nucleic Acids
DOI: 10.5281/zenodo.4740000
Responsible person: Nicolas Winssinger
Projects involved: 2
Article (2021)

 

Dataset title: Identification of a covalent importin-5 inhibitor, goyazensolide from a collective synthesis of furanoheliangolides
DOI: 10.5281/zenodo.4314704
Responsible person: Nicolas Winssinger
Projects involved: 2
Article (2021)

 

Dataset title: Small Peptide Diversification through Photoredox-Catalyzed Oxidative C-Terminal Modification
DOI: 10.5281/zenodo.4384417
Responsible person: Jérôme Waser
Projects involved: 4
Article (2021)

 

Dataset title: Luciferase controlled protein interaction
DOI: 10.5281/zenodo.4554639
Responsible person: Nicolas Winssinger
Projects involved: 1
Article (2021)

 

2020

Dataset title: CURRENT-BIOLOGY-D-20-0012 (Conserved functions of ether lipids and sphingolipids in the early secretory pathway) 
DOI:
10.26037/yareta:bkiubi7cczhgbjkkzx2h6mpzya
Responsible person: Howard Riezman
Projects involved:
1, 3
Article (2020)

 

Dataset title: Genome-wide CRISPRi screen for myriocin sensitivity
Series (GEO):
GSE154045
Responsible person: Howard Riezman
Projects involved:
1, 3
Article (2020)

 

Dataset title: Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides
DOI:
10.5281/zenodo.3925076
Responsible person: Stefan Matile
Projects involved:
4, 5
Article (2020)

 

Dataset title: Mechanosensitive Fluorescent Probes, Changing Color Like Lobsters During Cooking: Cascade Switching Variations
DOI:
10.26037/yareta:r2nggd6havcsxov7etvsjaeq3a
Responsible person: Stefan Matile
Projects involved:
3
Article (2020)

 

Dataset title: Naphthalenediimides with Cyclic Oligochalcogenides in Their Core
DOI:
10.26037/yareta:mskur6ijhjft7cugphvb3wrsum
Responsible person:
Stefan Matile
Projects involved:
4
Article (2020)

 

Dataset title: Fluorescent Membrane Tension Probes for Super-Resolution Microscopy: Combining Mechanosensitive Cascade Switching with Dynamic-Covalent Ketone Chemistry
DOI:
10.26037/yareta:ig23nd7ggvfoxetygmtm7c5x24
Responsible person:
Stefan Matile
Projects involved:
4
Article (2020)

 

Dataset title: HaloFlippers-5
DOI:
10.5281/zenodo.3931232
Responsible person:
Stefan Matile
Projects involved:
3, 4
Article (2020)

 

Dataset title: HaloFlippers-4
DOI:
10.5281/zenodo.3931225
Responsible person:
Stefan Matile
Projects involved:
3, 4
Article (2020)

 

Dataset title: HaloFlippers-3
DOI:
10.5281/zenodo.3931213
Responsible person:
Stefan Matile
Projects involved:
3, 4
Article (2020)

 

Dataset title: HaloFlippers-2
DOI:
10.5281/zenodo.3930957
Responsible person:
Stefan Matile
Projects involved:
3, 4
Article (2020)

 

Dataset title: HaloFlippers: A General Tool for the Fluorescence Imaging of Precisely Localized Membrane Tension Changes in Living Cells-1
DOI:
10.5281/zenodo.3929530
Responsible person:
Stefan Matile
Projects involved:
3, 4
Article (2020)

 

Dataset title: Endosomal membrane tension regulates ESCRT-III-dependent intra-lumenal vesicle formation
DOI:
10.5281/zenodo.3833867
Responsible person:
Aurélien Roux
Projects involved:
3
Article (2020)

 

Dataset title: Dynamic Nuclear Polarisation Enhancement of 200 at 21.15 T Enabled by 65 kHz Magic Angle Spinning
DOI:
10.5281/zenodo.4032323
Responsible person:
Lyndon Emsley
Projects involved:
2
Article (2020)

 

Dataset title:Wnt-controlled sphingolipids modulate Anthrax Toxin Receptor palmitoylation to regulate oriented mitosis in zebrafish
Mass spectrometry lipidomic data:
https://www.nature.com/articles/s41467-020-17196-3#data-availability
Responsible person:
Gisou van der Goot
Projects involved:
4
Article (2020)

 

Dataset title: Pico-meter resolution structure of the coordination sphere in the metal-binding site in a metalloprotein by NMR
DOI:
10.5281/zenodo.4028768
Responsible person:
Lyndon Emsley
Projects involved:
2
Article (2020)

 

Dataset title: Homogeneous multifocal excitation for high-throughput super-resolution imaging – Expanded centriole particles
DOI: 10.5281/zenodo.3613906
Responsible person: Suliana Manley
Projects involved: 2
Article (2020)

 

Dataset title: Small-molecule modulators of the ATPase VCP/p97 affect specific p97 cellular functions
DOI: 10.5281/zenodo.3539008
Responsible person: Monica Gotta
Projects involved: 1
Article (2020)

 

Dataset title: High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus
Data: IDR Open microscopy
Responsible person: Fanny Georgi
Projects involved: ACCESS
Article (2020)

 

Dataset title: Mechanosensitive Membrane Probes: Push-Pull Papillons
DOI: 10.26037/yareta:5b2y3rzii5hufg6hpled2yyrlm
Responsible person: Stefan Matile
Projects involved: 4
Article (2020)

 

Dataset title: Anisotropic ESCRT-III architecture governs helical membrane tube formation
Electron Microscopy Data Bank: EMD-10136, EMD-10137, EMD-10138, EMD-10139
Responsible person: Aurélien Roux
Projects involved: 3
Article (2020)

 

Dataset title: An ESCRT-III polymerization sequence drives membrane deformation and fission
DOI: 10.5281/zenodo.3878199
Responsible person: Aurélien Roux
Projects involved: 3

 

Dataset title: Luciferase-Induced Photouncaging: Bioluminolysis
DOI: 10.5281/zenodo.3374180
Responsible person: Nicolas Winssinger
Projects involved: 1
Article (2020)

 

Dataset title: Caprin-1 promotes cellular uptake of nucleic acids with backbone and sequence discrimination
DOI: 10.26037/yareta:grrtg4elinhphfldoeto5rwhpy
Responsible person: Aurélien Roux
Projects involved: 4
Article (2020)

 

Dataset title: Buckling of epithelium growing under spherical confinement Trushko et al.
DOI: 10.17632/3vfxhr2m34.1
Responsible person: Aurélien Roux
Projects involved: 3
Article (2020)

 

Dataset title: Probing for Thiol-Mediated Uptake into Bacteria
DOI: 10.5281/zenodo.3336270
Responsible person: Stefan Matile
Projects involved: 4
Article (2020)

 

Dataset title: Cell-Penetrating Streptavidin: A General Tool for Bifunctional Delivery with Spatiotemporal Control, Mediated by Transport Systems such as Adaptive Benzopolysulfane Networks
DOI: 10.26037/yareta:v7airh7g7rfrlpa3s7m64unefy
Responsible person: Stefan Matile
Projects involved: 4, 5
Article (2020)

 

Dataset title: Next generation sequencing data for phage selection against FXIa
DOI: 10.6084/m9.figshare.11921139.v2
Responsible person: Christian Heinis
Projects involved: 1
Article (2020)

 

Dataset title: Computational design of anti-CRISPR proteins with improved inhibition potency and expanded specificity
Link: https://github.com/LPDI-EPFL
Responsible person: Bruno Correia
Projects involved: 2
Article (2020)

 

Dataset title: Smartphone DNA or RNA-Sensing Using Semisynthetic Luciferase-Based Logic Device
DOI: 10.5281/zenodo.3689190
Responsible person: Nicolas Winssinger
Projects involved: 1
Article (2020)

 

Dataset title: PNA-Based Dynamic Combinatorial libraries (PDCL) and screening of lectins
DOI: 10.5281/zenodo.3712677
Responsible person: Nicolas Winssinger
Projects involved: 1
Article (2020)

 

Dataset title: PRM of Nth1 phospho-peptides in response to AGC-kinase inhibition
Data: PRM data have been deposited at Panorama Public: https://panoramaweb.org/wMKBjd.url and are accessible at ProteomeXchange via identifier PXD015760.
Responsible person: Robbie Loewith
Projects involved: 1
Article (2020)

 

Dataset title: Chemical genetics of AGC-kinases reveals shared targets of Ypk1, Protein Kinase A and Sch9
DOI: 10.6084/m9.figshare.11474685
Responsible person: Robbie Loewith
Projects involved: 1
Article (2020)

 

Dataset title: Yeast AGC-kinases phospho-proteomics
Data: DDA data have been deposited to the ProteomeXchange Consortium via the PRIDEpartner repository with the data set identifier PXD015668 and 10.6019/PXD015668.
Spectra were additionally deposited to MS-Viewer and are accessible using key 99yh6tladc.
Responsible person: Robbie Loewith
Projects involved: 1
Article (2020)

 

Dataset title: Next generation sequencing data for phage selection against FXIa
DOI: 10.6084/m9.figshare.11921139.v2
Responsible person: Christian Heinis
Projects involved: 1
Article (2020)

 

2019

Dataset title: Fluorescent Flipper Probes: Comprehensive Twist Coverage
DOI: 10.26037/yareta:netxbo6p6rhvtaf2fjasfyvvkq
Responsible person: Stefan Matile
Projects involved: 4
Article (2019)

 

Dataset title: Methyl Scanning for Mechanochemical Chalcogen-Bonding Cascade Switches
DOI: 10.26037/yareta:5yjhzxle4ffzbfgjxebqmlulhq
Responsible person: Stefan Matile
Projects involved: 4
Article (2019)

 

Dataset title: Role of the mRNA-binding protein HuR in the global transcriptomic status of cells stimulated with electrophiles and oxidants
Data: RNA-Sequencing data are available at the Gene Expression Omnibus (GEO; accession number GSE127444); all other data are in supporting info.
Responsible person: Yimon Aye
Projects involved: 4
Article (2019)

 

Dataset title: A Chalcogen-Bonding Cascade Switch for Planarizable Push-Pull Probes
DOI: 10.5281/zenodo.3369793
Responsible person: Stefan Matile
Projects involved: 4
Article (2019)

 

Dataset title: Coupling of DNA Circuit and Templated Reactions for Quadratic Amplification and Release of Functional Molecules
DOI: 10.5281/zenodo.3337874
Responsible person: Nicolas Winssinger
Projects involved: 1
Article (2019)

 

Dataset title: “Doubly Orthogonal” Labeling of Peptides and Proteins
DOI: 10.5281/zenodo.3246280
Responsible person: Beat Fierz
Projects involved: 3, 4
Article (2019)

 

Dataset title: Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging
DOI: 10.5281/zenodo.1475055
Responsible person: Suliana Manley
Projects involved: 2
Article (2019)

 

Dataset title: Cell-Penetrating Dynamic-Covalent Benzopolysulfane Networks – Raw data
DOI: 10.5281/zenodo.3044493
Responsible person: Stefan Matile
Projects involved: 4
Article (2019)

 

2018

 

Dataset title: SPARTAN example data
DOI: 10.5281/zenodo.1288783
Responsible person: Suliana Manley
Projects involved: 2, 3
Article (2018)

 

Dataset title: LUPIN
DOI: 10.5281/zenodo.1312221
Responsible person: Nicolas Winssinger
Projects involved: 1
Article (2018)