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Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE132545 | GEO | 2025/06/11

REPOSITORIES: GEO

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Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout [dataset 2]

Project description:Skin samples from wild type or HIRA knockout mouse embryos were dissociated to give cellular suspensions, then single cell RNA sequencing was performed using the 10X platform. Method: Cellular suspensions of skin cells from wild type and HIRA knockout mice were prepared, then sequencing was performed using the Chromium 10X system. Data were then processed using Cellranger version 2.2.0.

2025-06-11 | GSE132544 | GEO

Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout [dataset 1]

2025-06-11 | GSE132543 | GEO

Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout

Project description:Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout

| PRJNA548326 | ENA

Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout [dataset 2]

Project description:Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout [dataset 2]

| PRJNA548333 | ENA

Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout [dataset 1]

Project description:Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout [dataset 1]

| PRJNA548334 | ENA

Single cell RNA-Seq of Hira-KO and control MII oocytes

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-11-03 | E-GEOD-73382 | biostudies-arrayexpress

The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination.

Project description:Histone chaperones regulate the flow and dynamics of histone variants and ensure their assembly into nucleosomal structures, thereby contributing to the repertoire of histone variants in specialized cells or tissues. To date, not much is known on the distribution of histone variants and their modifications in the dry seed embryo. Here, we bring evidence that genes encoding the replacement histone variant H3.3 are expressed in Arabidopsis dry seeds and that embryo chromatin is characterized by a low H3.1/H3.3 ratio. Loss of HISTONE REGULATOR A (HIRA), a histone chaperone responsible for H3.3 deposition, reduces cellular H3 levels and increases chromatin accessibility in dry seeds. These molecular differences are accompanied by increased seed dormancy in hira-1 mutant seeds. The loss of HIRA negatively affects seed germination even in the absence of HISTONE MONOUBIQUITINATION 1 or TRANSCRIPTION ELONGATION FACTOR II S, known to be required for seed dormancy. Finally, hira-1 mutant seeds show lower germination efficiency when aged under controlled deterioration conditions or when facing unfavorable environmental conditions such as high salinity. Altogether, our results reveal a dependency of dry seed chromatin organization on the replication-independent histone deposition pathway and show that HIRA contributes to modulating seed dormancy and vigor.

| S-EPMC8070706 | biostudies-literature

DNMT1 KNOCKOUT IN MURINE LIVER

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-04-01 | E-GEOD-67771 | biostudies-arrayexpress

Collagen10-Cre;Rosa26-tdTomato e16.5 single cell RNA-sequencing

Project description:In order to assess the descendants of hypertrophic chondrocytes, we utilized Collagen10-Cre;Rosa26-tdTomato mouse total bone isolated at e16.5 by Collagenase II digestion after mechanical digestion and soft tissue removal. After sequencing and downstream analysis using Seurat, we observed clusters of cells with gene profiles matching classically defined chondrocytes, skeletal stem and progenitor cells (SSPCs), and osteoblasts. Trajectory analysis reveals that the SSPCs lie intermediate to the transition of chondrocyte to osteoblast. We conclude that hypertrophic chondrocytes dedifferentiate to this progenitor stage before further differentiation.

2022-02-16 | GSE190616 | GEO

Extraction and sequencing of single nuclei from murine skeletal muscles.

Project description:Single-nucleus RNA sequencing allows the profiling of gene expression in isolated nuclei. Here, we describe a step-by-step protocol optimized for adult mouse skeletal muscles. This protocol provides two main advantages compared to the widely used single-cell protocol. First, it allows us to sequence the myonuclei of the multinucleated myofibers. Second, it circumvents the cell-dissociation-induced transcriptional modifications. For complete details on the use and execution of this protocol, please refer to Dos Santos et al. (2020) and Machado, Geara et al. (2021).

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