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RNA-seq data of PatchSeq dataset from Pvalb-Cre positive interneurons in the mouse hippocamus CA1 region

ABSTRACT: RNA-seq data of PatchSeq dataset from Pvalb-Cre positive interneurons in the mouse hippocamus CA1 region

PROVIDER: PRJNA542103 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9033940.fastq.gz	Fastqsanger.gz
	SRR9033931.fastq.gz	Fastqsanger.gz
	SRR9033941.fastq.gz	Fastqsanger.gz
	SRR9033932.fastq.gz	Fastqsanger.gz
	SRR9033942.fastq.gz	Fastqsanger.gz

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RNA-seq data of PatchSeq dataset from Pvalb-Cre positive interneurons in the mouse hippocamus CA1 region

Project description:This study takes on the problem of bridging transcriptional data to neuronal phenotype and function by using publicly available datasets characterizing distinct neuronal populations based on gene expression, electrophysiology and morphology. In addition, a non-published PatchSeq dataset of Pvalb-cre positive cells in CA1 was used, which is the dataset submitted here. Taken together, these datasets were used to identify cross-cell type correlations between these data modalities. Detected correlations were classified as “class-driven” if they could be explained by differences between excitatory and inhibitory cell classes, or “non-class driven” if they could be explained by gradient like phenotypic differences within cell classes. Some genes whose relationships to electrophysiological or morphological properties were found to to be specific to either excitatory or inhibitory cell types. The Patch Seq data specifically allowed simultaneous single-cell characterization of gene expression and electrophysiology, showing that the gene-property correlations observed across cell types were further predictive of within-cell type heterogeneity.

2019-06-11 | GSE130950 | GEO

PatchSeq analysis of Pthlh expressing cells of the mouse dorsolateral striatum

Project description:In order to investigate how electrophysiological properties vary within the Pthlh population in the dorsolateral striatum we performed PatchSeq analysis of neurons labeled in 5HT3a(EGFP) and Pvalb(cre)::RCE/tdTomato mouse lines, which included Th, Npy/Mia, Cck, and Cck/Vip expressing cells.

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Patchseq Data of T1D Donor Islets vs ND Matched Controls

Project description:Will be updated closer to manuscript finalization. Patchseq allows for combined electrical and transcriptomic data to be obtained at single cell resolution. Here we performed patchseq on islet cells from human donors

2024-06-25 | GSE270484 | GEO

Transcriptional profiling of interneurons in the cerebral cortex of Htr3a-Cre (NO176) mice

Project description:TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain. Using this technique we obtained RNA-Seq data from actively translating transcripts present in interneurons in the cerebral cortex of adult Htr3a-Cre (NO176) mice x Rosa26-LSL-EGFP/Rpl10a mice

2019-12-16 | GSE141874 | GEO

Single‐cell transcriptomic analysis of mouse CA1 inhibitory neurons

Project description:We studied the transcriptomes of mouse CA1 inhibitory cells. Novel clustering methods identified all 23 previously described CA1 inhibitory types, while also suggesting 6 new inhibitory classes. Latent‐factor analysis revealed a common continuum of expression of many genes within and between classes, which we hypothesized correlates with a continuum from faster‐spiking cells that proximally target pyramidal cells, to slower active cells targeting pyramidal distal dendrites or interneurons.

2018-05-11 | GSE99888 | GEO

Transcriptional profiling of interneurons in the cerebral cortex of Htr3a-Cre (NO176) mice

Project description:Transcriptional profiling of interneurons in the cerebral cortex of Htr3a-Cre (NO176) mice

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A novel hippocampal long-range VIP-GABAergic projection to subiculum contributes to fear memory formation through region-specific connectivity

Project description:We sequenced seven long-range projection vasoactive intestinal peptide (VIP)-expressing interneurons from the mouse CA1 oriens/alveus area using patch-seq technique to determine their molecular identity.

2018-01-30 | GSE109755 | GEO

Landscape of ribosome-engaged alternative transcript isoforms across neuronal cell classes

Project description:The goal of this project was to assess how alternative splicing programs are arrayed across neuronal cells types. We systematically mapped ribosome-associated transcript isoforms in genetically-defined neuron types of the mouse forebrain. The endogenous ribosomal protein Rpl22 was conditionally HA-tagged in glutamatergic neurons (using CamK2-cre for most neocortical pyramidal cells and Scnn1a-cre for spiny stellate and star pyramid layer 4 cells), and GABAergic interneurons [with somatostatin-cre (SST), parvalbumin-cre (PV) and vasointestinal peptide-cre (VIP)]. Within the hippocampus, we further targeted Cornu ammonis 1 (CA1) neurons (CamK2-cre), CA3 neurons (Grik4-cre), and SST-positive interneurons (SST-cre). Four replicates were deep sequenced (~100 million reads) using an Illumina platform. We find that neuronal transcript isoform profiles reliably distinguish even closely-related classes of pyramidal cells and inhibitory interneurons in the mouse hippocampus and neocortex, positing transcript diversification by alternative splicing as a central mechanism for the functional specification of neuronal cell types and circuits.

2019-07-01 | GSE133291 | GEO

The piRNAs bounding to Piwil2 in the CA1 region of the transient Global Cerebral Ischemia rats hippocampus

Project description:Purpose：To identify piRNAs bound to Piwil2 in Sham,transient Global Cerebral Ischemia(tGCI) and transient Global Cerebral Ischemia(tGCI) with Hypoxic Postconditioning (HPC). Methods: Samples from CA1 subregion were lysed in 500 μl lysis buffer and centrifuged. After centrifugation, supernatant was incubated with monoclonal mouse antibody against Piwil2 (Santa Cruz, California, CA, USA), preincubated with Protein A/G Agarose. The beads were washed twice with lysis buffer. After quality check by Western blot, the RNA was extracted from the magnetic beads using Trizol reagent (Invitrogen). Then, the immunoprecipitated RNA was analyzed with piRNAs sequencing. Results: After tGCI, a total of 423 piRNAs interacted with Piwil2 in CA1 was upregulated after 26 h of reperfusion. Of the 423 piRNAs, 317 were significantly upregulated by more than 1.5-fold. Of the 317 piRNAs, 258 showed ≥2-fold change. Comparison between tGCI and HPC groups revealed that 401 piRNAs interacted with Piwil2 in CA1 were significantly downregulated after HPC, whereas only 7 piRNAs were found to be altered in all 3 groups studied (≥1.5-fold change). Conclusions: In our study, we identified a cohort of piRNAs in CA1 of rats. We demonstrated directly contrast changes of piRNAs interacted with Piwil2 in CA1 after tGCI, as compared to those in HPC rats. The results of the prediction showed that DNMT3A may be a potential common target of the 7 differentially expressed piRNAs interacted with Piwil2. Therefore, we focused on the expression of DNMT3A in CA1 after tGCI with or without HPC.

2023-01-18 | GSE163299 | GEO

Single cell RNA sequencing of lateral and medial olivocochlear efferent neurons using PatchSeq

Project description:Olivocochlear (OC) efferent neurons are the final component of the descending auditory system. The lateral olivocochlear (LOC) neurons innervate type I spiral ganglion neurons (SGN). Their role in hearing is unknown, but they may have roles in protection from noise trauma or changing the threshold of SGN activation. The medial olivocochlear (MOC) efferent neurons innervate outer hair cells (OHC), inhibiting OHC function and thus dampening cochlear vibrations. LOC and MOC function is poorly understood at the single cell level, but recent use of transgenic mice (ChAT-IRES-Cre; tdTomato) expressing fluorescent reporters in cholinergic neurons, including LOC and MOC neurons, has allowed patch-clamp recordings from the neurons in mouse brainstem slices to begin to characterize their intrinsic electrical properties and synaptic activity. Recent single nucleus sequencing experiments from LOC and MOC neurons has given insight into the genetic programs that generate their function, including changes to expression profiles following noise trauma. Here we utilize the PatchSeq technique to combine patch-clamp electrophysiological recordings with deep single-cell transcriptome analysis from identified LOC and MOC neurons in transgenic ChAT-IRES-Cre; tdTomato mice. In this preliminary dataset, we generated patch-clamp electrophysiology data and single cell transcriptome data from 18 identified LOC and 13 identified MOC neurons.

2025-09-12 | GSE307618 | GEO

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