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Single-nucleus multiome (RNA+ATAC) sequencing of the axolotl pallium

ABSTRACT: Single-nucleus multiome (RNA+ATAC) sequencing of the axolotl pallium

PROVIDER: PRJEB52517 | ENA |

REPOSITORIES: ENA

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Single-nucleus multiome (RNA+ATAC) sequencing of the axolotl pallium

Project description:In order to understand the genomic and transcriptomic variability of the axolotl pallium, as well as reconstruct their intrinsic gene regulatory networks, we performed single-nucleus multiome sequencing (RNA and open chromatin) of whole axolotl pallium.

2022-07-20 | E-MTAB-11666 | biostudies-arrayexpress

snRNA-seq of microdissected regions from the axolotl pallium

Project description:In order to understand the relationship between cellular diversity and pallium regions, single-nucleus RNA-seq (snRNA-seq) was performed in 3 microdissected regions from the axolotl pallium: medial, dorsal, and lateral.

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Div-seq of axolotl pallium injury time course

Project description:The goal of this experiment is to track cellular regeneration after a dorsal injury to the axolotl pallium. To this end, we employed Div-seq, that is, performed snRNA-seq on cells labelled with EdU, which have thus recently replicated. We performed this in a time course, in order to observed the cell populations that were generated as regeneration progressed.

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Div-seq of axolotl pallium injury time course

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snRNA-seq of microdissected regions from the axolotl pallium

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Multiome RNA+ATAC on human PBMCs (snRNA-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

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Multiome RNA+ATAC on human PBMCs (snATAC-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

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Single-nucleus multiome analysis of the adult anthropoid cerebellar cortex across four primate species

Project description:This study generated a single-nucleus multiomic dataset of the adult cerebellar cortex across four anthropoid primate species: Homo sapiens (n=4), Pan troglodytes (n=3), Macaca mulatta (n=4), and Callithrix jacchus (n=4). Paired single-nucleus RNA sequencing and chromatin accessibility profiling were performed using the 10x Genomics Chromium Multiome platform. After quality control, 69,302 nuclei were retained for RNA analysis and 63,491 nuclei for ATAC analysis, with 60,824 nuclei profiled in both modalities. The dataset provides single-nucleus transcriptomic and chromatin accessibility profiles for comparative analysis of cerebellar cell types across primates.

2026-03-11 | GSE322785 | GEO

Single-nucleus multiome RNA and ATAC sequencing of mouse kidney in kidney-specific Glut2 knockout (rGlut2 KO)

Project description:Glycosuria, whether genetically induced or triggered by SGLT2 inhibitors, activates compensatory glucose-producing pathways that limit glucose lowering in type 2 diabetes. To define these pathways, we studied renal Glut2 knockout mice, which progressively lose Slc5a2 (encoding SGLT2) expression yet maintain normoglycemia despite marked urinary glucose loss. Nuclei were isolated from three pooled flash-frozen kidney samples per group (12-week-old male rGlut2 KO and wild-type control mice) and single-nucleus gene expression and ATAC libraries were constructed using the 10x Chromium Multiome kit (Singulomics Corporation). Libraries were sequenced with ~200 million paired-end reads (PE150) on the Illumina NovaSeq. Reads were aligned to mm10 (2020-A) using Cell Ranger ARC 2.0.2. Downstream analysis used Seurat v5.1.0 and Signac v1.13.0.

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