Global proteomic analysis of WT and GRN-/- HeLa cells
By savannah onGlobal proteomic analysis of WT and GRN-/- HeLa cells. https://www.nature.com/articles/s41467-022-33500-9
Global lipidomics of WT and GRN-/- cells & mouse models, including plus and minus GRN addback
By savannah onThis dataset contains: - Global lipidomics of WT and GRN-/- HeLa cells, including plus and minus GRN addback. - Global lipidomics of WT and NPC1-/- HeLa cells. - Global lipidomics of WT and GRN-/- HeLa cells, including plus and minus GRN addback. Global lipidomics of WT and GRN mutant mouse brain tissue. https://www.nature.com/articles/s41467-022-33500-9
Gene editing of YIPF4 in hESCs V3
By savannah onThis protocol describes the creation of YIPF4 knockout cell lines in H9 hESC cells using CRISPR-Cas9. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Cryo-ET of S. cerevisiae during starvation (tomograms)
By savannah onCryo-ET of S. cerevisiae during starvation (tomograms). Accession number: https://www.ebi.ac.uk/emdb/EMD-15526 https://www.ebi.ac.uk/emdb/EMD-15545 https://www.ebi.ac.uk/emdb/EMD-15546 https://www.ebi.ac.uk/emdb/EMD-15547 https://www.ebi.ac.uk/emdb/EMD-15549 https://www.ebi.ac.uk/emdb/EMD-15548
Code for extraction of any user-defined information from uniprot
By savannah onCode for extraction of any user-defined information from Uniprot.
Code for analysis of ER-phagy in iNeurons via proteomics
By savannah onCode for analysis of ER-phagy in iNeurons via proteomics. Associated with preprint: https://doi.org/10.1101/2023.06.26.546565
Characterizing spatial and temporal properties of ER-phagy receptors
By savannah onAssociated with preprint: https://doi.org/10.1101/2023.06.26.546565
Autophagy preferentially degrades non-fibrillar polyQ aggregates
By savannah onPreprint: These results suggest that the limited efficiency of autophagy in clearing polyQ aggregates is due to the inability of autophagosomes to interact productively with the non-deformable, fibrillar disease aggregates.
Analysis of ER structures in Cultured Induced Neuron axons
By savannah onAssociated with preprint: https://doi.org/10.1101/2023.06.26.546565
Analysis of ER Flux in Cultured Induced Neurons using Keima ER reporters
By savannah onAssociated with preprint: https://doi.org/10.1101/2023.06.26.546565
Long-read RNA seq analysis using Talon
By savannah onThis is a snakemake pipeline that takes Oxford Nanopore Sequencing (ONT) data (fastq) as input, generates fastq stats using nanostat, performs fastq processing and filtering using pychopper, maps the reads to the genome using minimap2, and uses talon to assemble and quantify transcripts. It is forked from ANNSeq. The link includes the dag of the pipeline.
pCAG-TSF-ATG13 (363-517)
By savannah onMammalian expression of TwinStrep-Flag tagged ATG13 (363-517).
Plasmid: V5-KANSL1 pLVX-EF1α-IRES-Puro
By savannah onHuman KANSL1 cDNA with N-terminal V5 tag cloned into the pLVX-EF1α-IRES-Puro plasmid (EcoRI and SpeI restriction sites) from Clontech, Takara Bio.
pCAG-TSF-ATG13 (450-517)-ULK1 (836-1050)
By savannah onMammalian expression of ATG13 C-terminal and ULK1 MIT domain fusion complex.