sim1 cre  (Jackson Laboratory)

Journal: bioRxiv

Article Title: Biased synaptic activation of dentate granule cells by exercise reflects inputs from the lateral entorhinal cortex

doi: 10.64898/2026.02.22.707119

Figure Lengend Snippet: A. To validate the TeLC-GFP viral construct, the LEC in one hemisphere was injected with AAV- flex-TeLC-GFP and the contralateral LEC was injected with a control AAV- flex -GFP virus. Extracellular field recordings in acute brain slices were made in the molecular layer of the dentate gyrus following selective stimulation of either the lateral perforant path (LPP, top row) or medial perforant path (MPP, bottom row). Paired stimuli with a bipolar electrode revealed field EPSPs following LPP or MPP stimulation with the control GFP virus (left column, CtrlGFP); however, the field EPSPs following injection with TeLC-GFP showed complete block following LPP stimulation (right column, TeLC, consistent with silencing of the LPP. B. Schematic representation of AAV-flex-TeLC-GFP injection in Sim1-Cre-:TdT mice, targeting the right hemisphere LEC and MEC layer IIa (upper). Representative dentate gyrus images show c-Fos + labeling in magenta and axons expressing AAV- flex -TeLC-GFP + in green (left). There was not a significant difference in c-Fos + (activated) dentate granule cells between the injected (right image) and non-injected hemispheres (left image). Scale bar = 100 µm. C. Timeline for Fos-TRAP activation following a unilateral AAV5-TeLC-mCherry injection in LEC layer IIa of Fos-TRAP mice. Mice received tamoxifen 24 hours before the experiment, followed by two hours of voluntary wheel running and perfusion three days later. Representative images of c-Fos-activated cells in the dentate gyrus of TeLC-injected (lower) and non-injected (upper) hemispheres. c-Fos + cells (red); DAPI (blue). There was no significant difference in the number of c-Fos + DGCs between the AAV5-TeLC-mCherry-injected and non-injected hemispheres (AAV5-TeLC mCherry-injected: 5858 ± 1026 /mm 3 , Non-injected: 6198 ± 761 /mm 3 , p=0.5, n=7). Scale bar = 20 µm.

Article Snippet: The Sim1-Cre line, which expresses Cre under the control of the Single minded homolog-1 (Sim1) promoter, was generated by the OHSU transgenic core and obtained from MMRRC 034614-UCD (strain name: Tg(Sim1cre)KH21Gsat/Mmucd).

Techniques: Construct, Injection, Control, Virus, Blocking Assay, Labeling, Expressing, Activation Assay

Journal: Neuron

Article Title: Ultra-high-density Neuropixels probes improve detection and identification in neuronal recordings

doi: 10.1016/j.neuron.2025.08.030

Figure Lengend Snippet: (A) Example small-footprint waveform recorded from VISp. (B) Histogram of measured spatial footprints across a total of 175 units recorded in the mouse visual cortex with muscimol application ( n = 3 mice, 6 sessions). Dashed line, threshold of small footprint (20 μm). (C) Schematic of NP Ultra recordings in the cortex with surface application of muscimol. Red lines, axonal segments. (D) Firing rates for an example recording. Units sorted by ascending footprint size. Red line, threshold of small footprint. (E) Scatterplot of firing rates pre- and post-muscimol application. Dashed line, identity. Insets: small-footprint waveforms of two example units. (F) Relationship between the spatial footprint and firing rate modulation index. Black boxes, units from (E). (G) Full waveforms of the two units marked in (E). (H) Left: schematic of optotagging experiment in Sim1-Cre;Ai32+ L5b pyramidal neurons. Right: histology showing labeled L5 pyramidal neurons. (I) Peri-stimulus time histogram (PSTH) of an example Sim1+ unit in response to photostimulation. (J) Two example Sim1+ waveforms with visible propagation (diagonal red band). (K) Schematic of an L5 neuron recorded with the linearized (192 × 2) configuration. (L) Example bAPs recorded with NP Ultra (left) and NP 1.0 (right). Traces show spike-triggered average waveforms ( n = 2,000 spikes) recorded from the column of channels that includes the peak amplitude channel. Colored traces, voltage minima. (M) Template SNR as a function of vertical distance from the peak amplitude channel for NP Ultra (192 × 2 configuration, best column selected, green), NP Ultra (192 × 2 configuration, 4-channel average, teal), and NP 1.0 probes (magenta). (N) Template SNR against amplitude. See also – .

Article Snippet: Mouse: Sim1-Cre , The Jackson Laboratory , JAX Stock #006395; RRID: IMSR_JAX:006395.

Techniques: Labeling

Journal: bioRxiv

Article Title: RatDISCO, a tissue clearing and immunolabelling protocol for large rat brains

doi: 10.1101/2025.08.17.670723

Figure Lengend Snippet: RatDISCO enables immunodetection of neuronal markers, viral tracing, and transgenic expression in mice and human brain organoids. Light-sheet microscopy images of whole-mouse brains immunolabelled for endogenous neuronal markers: MECP2 (A), cFOS (B, visualized with Inferno LUT), tyrosine hydroxylase (C), and FoxP2 (G: whole brain MIP; H-Optical slices at 0.84mm lateral to Bregma). D-F. Immunolabelling against virally-labelled medial (MEC) and lateral entorhinal cortex (LEC) neurons and axons in a Sim1 Cre mouse. (D) Whole-brain view of MEC projections. (E) Higher-magnification view of MEC-hippocampal projections. (F) Whole-brain view and a close-up of virally labelled MEC (GFP, green), LEC (mCherry, red) projections and merged image. (I) Immunolabelling of GFP in the transgenic P038 mouse line, highlighting MEC expression. Insets show GFP (green) co-labelling with parvalbumin (red) and the merged signal in a horizontal view. (J–O) Human iPSC-derived brain organoids (J, M; TO-PRO, magenta) co-cultured with GFP-positive single tumour cells (K, cyan) or tumour spheroids (N, cyan), with merged images shown in (L, O). Scale bars A-D, G-H: 500 µm. E: 250 µm, F, J-O and I-insets: 100 µm.

Article Snippet: Sim1 Cre mice (generated by GenSat and obtained from MMRRC: Tg(Sim1cre) KH21Gsat/Mmucd) were bred to be heterozygous for the Cre transgene by crossing male mice carrying the transgene with female C57BL6/J mice (Charles River, UK).

Techniques: Immunodetection, Transgenic Assay, Expressing, Microscopy, Derivative Assay, Cell Culture