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Single cell gene expression profiling of slow cycling and actively dividing mouse glioblastoma (GBM) cells isolated based on H2B-GFP label retention.

ABSTRACT: Single cell gene expression profiling of slow cycling and actively dividing mouse glioblastoma (GBM) cells isolated based on H2B-GFP label retention.

PROVIDER: PRJNA951632 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24046100_1.fastq.gz	Fastqsanger.gz
	SRR24046100_2.fastq.gz	Fastqsanger.gz
	SRR24046101_1.fastq.gz	Fastqsanger.gz
	SRR24046101_2.fastq.gz	Fastqsanger.gz
	SRR24046102_1.fastq.gz	Fastqsanger.gz

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Single cell gene expression profiling of slow cycling and actively dividing mouse glioblastoma (GBM) cells isolated based on H2B-GFP label retention.

Project description:A slow cycling, dormant cell state is thought to contribute to the therapeutic resistance of GBM tumour cells, yet not much is known about the biology of this slow-cycling cell population in GBM. By using somatic mouse model of GBM, combined with the inducible H2B-GFP label retention system, we isolated dormant tumour cells from their in vivo niches, and characterised them by single cell RNA sequencing.

2023-04-03 | GSE228785 | GEO

Gene expression profiling of infrequently and frequently dividing cells in the mouse epidermis

Project description:Infrequently (LRCs) and frequently (non-LRCs) dividing cells in the mouse epidermis are moleculary distinct. Fluorescence activated cell sorting (FACS) from back skin cells of quadruple-transgenic mice harboring K5-tTA, pTRE-H2B-GFP, K14-CreER and Rosa-tdTomato transgenes.

2016-09-01 | E-GEOD-70523 | biostudies-arrayexpress

Analysis of histone H2BGFP retention in mouse submandibular gland reveals actively dividing stem cell populations.

Project description:The purpose of this study was to use histone 2B-green fluorescent protein (H2BGFP) pulse-chase experiments to provide a broad view of population dynamics in salivary gland and to identify the quiescent stem cells that had previously been suggested to reside in the gland. Two transgenic mouse models in which inducible H2BGFP expression was regulated either by keratin (K)14 promoter or by a ubiquitous promoter were generated. The level of fluorescent label in the submandibular gland induced by a pulse of H2BGFP expression was monitored over a period of 18 weeks of chase. Efficient targeting of H2BGFP label to the relatively undifferentiated ductal cells by K14 promoter did not identify a quiescent population of stem cells. Ubiquitous targeting of all ductal cells identified label-retaining cells but these cells were mapped to the more differentiating ductal compartments. Furthermore, they did not display the major characteristics of quiescent stem cells including the undifferentiated phenotype, mobilization in response to injury, and the clonogenicity in culture. Quantitative assessment of H2BGFP loss in various ductal compartments and short-term lineage tracing of K14(+) ductal cells were consistent with the presence of actively dividing pools of stem/progenitor cells in the intercalated ducts and the basal layer of excretory ducts functioning independently during homeostasis.

| S-EPMC4333511 | biostudies-literature

RNA Sequencing Allows for Differential Gene Expression Analysis of Infrequently Dividing and Frequently Dividing (IDC/FDC) Oral Epithelial Stem Cells

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare palatal epithelial basal cell transcriptomes between infrequently and frequently dividing cells (IDC/FDCs). Methods: RNA was isolated from 200-1000 palatal basal epithelial cells and libraries prepared using the SoLo RNA-Seq library preparation kit (NuGEN). mRNA profiles of 14-day doxycycline chased K5-tTA;tetO-H2B-GFP (containing populations of slow-cycling GFP-HI and fast-cycling GFP-LO) mice were generated with 6 matched samples using an Illumina HiSeq4000. RNA Sequencing Allows for Differential Gene Expression Analysis of infrequently dividing and frequently dividing cells (IDC/FDC). RNA-seq fastq files were trimmed and aligned to the latest mouse genome, mm10 (GRCm38/GCA_000001635.2) using BBMap. A matrix of the data was generated using featureCounts. RNAseq data was analyzed with DESeq2. All statistical analyses were performed using R version 3.4.1 and RStudio version 1.0.143. Validation was performed using lineage tracing and immunofluorescence immunohistochemistry. Results: Using an optimized data analysis workflow, approximately 2% of the transcripts showed differential expression between the GFP-HI and GFO-LO palatal basal epithelial cell with a p value <0.05. Analysis of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to oral epithelial stem cell, such as Lrig1 and Igfbp5 as followed up on in the associated manuscript. Conclusions: Our study represents the first detailed analysis of palatal basal epithelial stem cell transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show GFP-LO infrequently dividing cells are express a distinct transcriptional profile compared to frequently dividing neighbor cells such as Lrig1 and Igfbp5.

2019-10-22 | GSE139146 | GEO

Transcription profiling of CD34+CD38- vs CD34+CD38+ fractions of human umbilical cord blood and comparison of slow-dividing fraction vs the fast dividing fraction of CD34+/CD38- population

Project description:Comparison of the CD34+CD38- versus CD34+CD38+ fractions of human umbilical cord blood and comparison of the slow-dividing fraction versus the fast dividing fraction of the CD34+/CD38- population.

2005-09-08 | E-EMBL-1 | biostudies-arrayexpress

Histone H2B^3-32, H2B K->G, H2B^3-37, and H2B^30-37 mutations

Project description:Histone H2B^3-32, H2B K->G, H2B^3-37, and H2B^30-37 mutations

| PRJNA94007 | ENA

An Intrinsically Disordered Region of Ubp10 Governs its Specificity for Deubiquitinating H2A/H2B Dimers over Nucleosomes

Project description:Histone modifications perform a vast array of functions in regulating gene expression, DNA replication, and repair. Monoubiquitination of histone H2B at K123 in yeast (K120 in humans) is an intriguing modification because it is deposited cotranscriptionally, mediates the installation of several other epigenetic marks, and then disappears; hence, it is associated transiently with actively transcribed chromatin. In yeast, the H2B ubiquitin writer is the E2/E3 pair Rad6/Bre1, and there are two deubiquitinases that can erase it, Ubp8 and Ubp10. Whilst Ubp8 resides within the larger SAGA complex, Ubp10 (USP36 in humans) is a monomeric and constitutively active deubiquitinase, raising questions as to what processes regulate it, given it would be undesirable for H2B to be deubiquitinated prematurely before downstream processes connected to this epigenetic mark occur. Here we show that Ubp10’s activity is regulated by acidic regions within its long N-terminal intrinsically disordered region (IDR), which extensively interact with H2A/H2B dimers, as shown by crosslinking mass spectrometry. These interactions vanish when H2A/H2B is present in nucleosomes. These observations explain why Ubp10 has low baseline activity on nucleosomes, but is activated by FACT, a histone chaperone which evicts H2A/H2B dimers from nucleosomes, thereby generating Ubp10’s preferred substrate, which we demonstrate with single molecule fluorescence experiments. Hence, this work provides a biophysical mechanism for how Ubp10 can provide a housekeeping function to deubiquitinate actively-transcribed DNA, wherein FACT produces a temporary pool of H2A/H2B dimers.

2025-07-16 | PXD051971 | Pride

Histone H2B^3-32, H2B K->G, H2B^3-37, and H2B^30-37 mutations

Project description:Histone H2B was mutated to give H2B^3-32, H2B K->G, H2B^3-37, and H2B^30-37. Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H2B HBR domain. This SuperSeries is composed of the SubSeries listed below.

2006-04-08 | GSE3806 | GEO

Dynamics of actively dividing prokaryotes in the western Mediterranean Sea.

Project description:Microbial community metabolism and functionality play a key role modulating global biogeochemical processes. However, the metabolic activities and contribution of actively growing prokaryotes to ecosystem energy fluxes remain underexplored. Here we describe the temporal and spatial dynamics of active prokaryotes in the different water masses of the Mediterranean Sea using a combination of bromodeoxyuridine labelling and 16S rRNA gene Illumina sequencing. Bulk and actively dividing prokaryotic communities were drastically different and depth stratified. Alteromonadales were rare in bulk communities (contributing 0.1% on average) but dominated the actively dividing community throughout the overall water column (28% on average). Moreover, temporal variability of actively dividing Alteromonadales oligotypes was evinced. SAR86, Actinomarinales and Rhodobacterales contributed on average 3-3.4% each to the bulk and 11, 8.4 and 8.5% to the actively dividing communities in the epipelagic zone, respectively. SAR11 and Nitrosopumilales contributed less to the actively dividing than to the bulk communities during all the study period. Noticeably, the large contribution of these two taxa to the total prokaryotic communities (23% SAR11 and 26% Nitrosopumilales), especially in the meso- and bathypelagic zones, results in important contributions to actively dividing communities (11% SAR11 and 12% Nitrosopumilales). The intense temporal and spatial variability of actively dividing communities revealed in this study strengthen the view of a highly dynamic deep ocean. Our results suggest that some rare or low abundant phylotypes from surface layers down to the deep sea can disproportionally contribute to the activity of the prokaryotic communities, exhibiting a more dynamic response to environmental changes than other abundant phylotypes, emphasizing the role they might have in community metabolism and biogeochemical processes.

| S-EPMC8825817 | biostudies-literature

Histone H2B^30-37

Project description:Histone H2B was mutated to give H2B^30-37. Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H2B HBR domain. Keywords: repeat

2006-04-08 | GSE3805 | GEO

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