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  • H9 ES AAVS1-NGN2 FAM134B-/-; PiggyBac-Keima-RAMP4

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    ES cells modified to lack FAM134B and express Keima-RAMP4 ER-phagy reporter using CRISPR/Cas9. NEUROG2 construct added to AAVS1 locus. Transfected with SERP1 and mKeima. Derived from human embryonic stem cells at blastocyst stage.

  • pCAG- WIPI2dK128E- cs-TEV -STREP

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    Plasmid: Mammalian expression of human WIPI2d K128E with C-terminal Strep.

  • pCAG-TSF-ATG13 (363-517)

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    Plasmid: Mammalian expression of TwinStrep-Flag tagged ATG13 (363-517).

  • pBMN HA-ATG13(W50D)

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    Plasmid for expression of human ATG13(W50D).

  • Sample Collection and Measurement of Serum Neurofilament Light (NfL)

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    This protocol details the steps for the preparation of serum from human blood samples and the measurement of NfL concentration using the NF-Light Advantage kit on the HD-X Analyzer (Quanterix, Billerica, MA).

  • Expression and purification GST-tagged ATG13:ATG101 constructs

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    Expression and purification of GST-tagged ATG13/ATG101 constructs.

  • Photometry Analysis Code

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    This set of functions extracts GCaMP Fiber Photometry data obtained with a TDT system, performs isosbestic and exponential correction, and computes the number and amplitude of transients over time. The code was originally used for the following experiment: MFB-lesioned 6-OHDA D1-cre or A2A-cre mice were injected with a cre-dependent GCaMP6f in dorsolateral striatum and implanted with 400um optical fibers. Mice were placed in an open field arena and recorded for 30 minutes before levodopa injection, and 120 minutes after levodopa injection. The experiment includes video from 2 cameras and a TTL pulse from an Arduino indicating the time when levodopa was injected.

  • Image processing and 3D reconstruction

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    Protocol describing image processing and 3D reconstruction.

  • Generation of CRISPR constructs

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    This protocol details the procedure of generation of CRISPR constructs.

  • pU6-pegRNA-LRRK2-G2019S-3b

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    It can be used to introduce LRRK2-G2019S mutation using prime editing.

  • AAV injection in the nodose ganglia of mouse

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    The gut-brain axis links the visceral organs to the medulla oblongata via the vagus nerve. Accessing to the afferent vagal pathway is important to dissect the role of cell populations in the bidirectional communication between brain and body. The jugular-nodose ganglion (JNG) complex contains the cell bodies of many heterogenous neural subpopulations responsible for sensing the physiological and pathological conditions of the thoracic and abdominal organs. However, the study of these ganglia is challenging in small animals due to size and location. Hence, in this protocol we describe a practical surgical approach to the vagal trunk, and the JNG complex in mice.

  • Incentivized Vigor Task

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    Code for an fMRI task in which human participants use a joystick to make speeded reaches to cued targets. This task examines incentive effects on movement, part of the Socal Kinesia and Incentivization for Parkinson's Disease (SKIP) dataset.

  • His-ATG3-R265A

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    Plasmid for ATG3 mutant R265A overexpression in E.Coli.

  • pCAG-MBP-Foldon-ATG9 (830-839)

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    Plasmid: To make ATG9 C-terminal tail trimer for expression in mammalian cells.

  • Pseudogenes limit the identification of novel common transcripts generated by their parent genes

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    Genomic sequences with high sequence similarity cause short sequencing reads to align to multiple locations, thus complicating genomic analyses. The authors investigated the impact of pseudogenes on transcriptomic analyses.

  • Bulk NGS/allele quantification – Highly efficient generation of isogenic pluripotent stem cell models using prime editing

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    This file contains sequencing results for amplicons covering specific regions of interest related to prime editing of hPSCs

  • cDNA clones for expression of MitoTag (OMP25) in mammalian cells

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    Plasmids for expression of OMP25 (MitoTag) in human and mouse cells.

  • Detection of Tau ubiquitylation

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    This protocol is associated with the following preprint, published on February 19th 2022: The AAA+ chaperone VCP disaggregates Tau fibrils and generates aggregate seeds Itika Saha, Patricia Yuste-Checa, Miguel Da Silva Padilha, Qiang Guo, Roman Körner, Hauke Holthusen, Victoria A. Trinkaus, Irina Dudanova, Rubén Fernández-Busnadiego, Wolfgang Baumeister, David W. Sanders, Saurabh Gautam, Marc I. Diamond, F. Ulrich Hartl, Mark S. Hipp bioRxiv 2022.02.18.481043; doi: https://doi.org/10.1101/2022.02.18.481043

  • Rapalog-induced chemical dimerization experiments

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    This protocol describes how to conduct Rapalog-induced chemical dimerization experiments.

  • Single-cell dissociation of brain organoids

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    This protocol details single cell dissociation of brain organoids. This protocol is part of a Collection of protocols (dx.doi.org/10.17504/protocols.io.8epv593dng1b/v1) for the paper "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" (https://doi.org/10.21203/rs.3.rs-1521848/v1)

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