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Single-cell sequencing technology demonstrates cellular and functional heterogeneity within the prostate and between the transitional and peripheral zones

ABSTRACT: Single-cell sequencing technology demonstrates cellular and functional heterogeneity within the prostate and between the transitional and peripheral zones

PROVIDER: PRJNA701948 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13712400_1.fastq.gz	Fastqsanger.gz
	SRR13712400_2.fastq.gz	Fastqsanger.gz
	SRR13712401_1.fastq.gz	Fastqsanger.gz
	SRR13712401_2.fastq.gz	Fastqsanger.gz
	SRR13712402_1.fastq.gz	Fastqsanger.gz

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Single-cell sequencing technology demonstrates cellular and functional heterogeneity within the prostate and between the transitional and peripheral zones

Project description:The identification of cellular and functional heterogeneity within the prostate and between the transitional zone (TZ) and peripheral zone (PZ) is critical for understanding the spatial distribution of prostate diseases. Three paired human prostate PZ and TZ tissue samples were used for scRNA-seq.

2024-02-13 | GSE166782 | GEO

Comparison between Gene expression in stroma and glands of the transitional and peripheral zone of the prostate

Project description:To investigate the gene expression differences between the stroma and glands in the transitional and peripheral zones of the prostate Laser microdissection of prostate cancer tissues to separate glands from stroma followed by RNA extraction from the glands and whole Genome Microarray. We have pooled normal glands and stroma out of the transitional and peripheral zones from 10 patients after radical prostatectomy

2011-05-06 | E-GEOD-29090 | biostudies-arrayexpress

Comparison between Gene expression in stroma and glands of the transitional and peripheral zone of the prostate

Project description:To investigate the gene expression differences between the stroma and glands in the transitional and peripheral zones of the prostate

2011-05-06 | GSE29090 | GEO

Microarray analysis of perichondral and reserve growth plate zones

Project description:In the growth plate, the reserve and perichondral zones have been hypothesized to have similar functions, but their exact functions are poorly understood. Our hypothesis was that significant differential gene expression exists between perichondral and reserve chondrocytes that may differentiate the respective functions of these two zones. Normal Sprague-Dawley rat growth plate chondrocytes from the perichondral zone (PC), reserve zone (RZ), proliferative zone (PZ), and hypertrophic zone (HZ) were isolated by laser microdissection and then subjected to microarray analysis. In order to most comprehensively capture the unique features of the two zones, we analyzed both the most highly expressed genes and those that were most significantly different from the proliferative zone (PZ) as a single comparator. Keywords: cell specific expression profiles

2008-03-28 | GSE9537 | GEO

RNA-Seq from human ILC transitional populations

Project description:RNA-Seq from human ILC transitional populations

| PRJNA541317 | ENA

Microarray data from human ILC transitional populations

Project description:Microarray data from human ILC transitional populations

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Regulation of the Alveolar Epithelial Transitional State in Murine and Human Pulmonary Fibrosis

Project description:Idiopathic Pulmonary Fibrosis (IPF) is a progressive scarring disease arising from impaired regeneration of the alveolar epithelium after injury. During regeneration, type 2 alveolar epithelial cells (AEC2s) differentiate into AEC1s via a transitional state that upregulates keratin 8. In IPF, transitional AECs persist with ineffectual AEC1 differentiation. However, whether keratin 8 regulates transitional state persistence and fibrosis is unclear. Here, we isolated AEC2s from WT or keratin 8 KO mice and harvested RNA from freshly isolated cells or from cells cultured for 1, 3, or 7 days. RNAseq was performed.

2023-10-18 | GSE223302 | GEO

RNA-sequencing of the human milk fat layer during colostrum, transitional, and mature stages of lactation

Project description:Human milk fat globules, by enveloping cell contents during their secretion into milk, are a rich source of mammary cell RNA. Here, we pair this non-invasive mRNA source with RNA sequencing technology to probe the milk fat layer transcriptome during three stages of lactation: colostral, transitional, and mature milk production. We find that transcriptional profiles cluster not by postpartum day, but by milk Na:K ratio, indicating that women sampled during the same postpartum time frame could be at markedly different stages of gene expression. Each stage of lactation is characterized by a dynamic range (105-fold) in transcript abundances not previously observed with microarray technology. We discovered that transcripts for isoferritins and cathepsins are strikingly abundant during colostrum production, highlighting the potential importance of these proteins for neonatal health. Two transcripts, encoding M-NM-2-casein (CSN2) and a-lactalbumin (LALBA), make up 45% of the total pool of mRNA in mature lactation. Genes significantly expressed across all stages of lactation are associated with making, modifying, transporting, and packaging milk proteins. Stage-specific transcripts are associated with immune defense during the colostral stage, up-regulation of the machinery needed for milk protein synthesis during the transitional stage, and the production of lipids during mature lactation. We observed strong modulation of key genes involved in lactose synthesis and insulin signaling. In particular, PTPRF may serve as a biomarker linking insulin resistance with insufficient milk supply. This study provides the methodology and reference data set to enable future targeted research on the physiological contributors to sub-optimal lactation in humans. Milk fat mRNA profiles were generated from Day 2 and mature milk samples obtained from lactating mothers

2013-07-22 | E-GEOD-45669 | biostudies-arrayexpress

Tumor formation of prostate cancer cells influenced by stromal cells from the transitional or peripheral zones of the normal prostate.

Project description:This study was designed to investigate the different involvements of prostatic stromal cells from the normal transitional zone (TZ) or peripheral zone (PZ) in the carcinogenesis of prostate cancer (PCa) epithelial cells (PC-3) in vitro and in vivo co-culture models. Ultra-structures and gene expression profiles of primary cultures of human prostatic stromal cells from the normal TZ or PZ were analyzed by electron microscopy and microarray analysis. In vitro and in vivo co-culture models composed of normal TZ or PZ stromal cells and human PCa PC-3 cells were established. We assessed tumor growth and weight in the in vivo nude mice model. There are morphological and ultra-structural differences in stromal cells from TZ and PZ of the normal prostate. In all, 514 differentially expressed genes were selected by microarray analysis; 483 genes were more highly expressed in stromal cells from TZ and 31 were more highly expressed in those from PZ. Co-culture with PZ stromal cells and transforming growth factor-beta1 (TGF-beta1) increased the tumor growth of PC-3 cells in vitro and in vivo, as well as Bcl-2 expression. On the other hand, stromal cells of TZ suppressed PC-3 cell tumor growth in the mouse model. We conclude that ultra-structures and gene expression differ between the stromal cells from TZ or PZ of the normal prostate, and stroma-epithelium interactions from TZ or PZ might be responsible for the distinct zonal localization of prostate tumor formation.

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Klhl6 deficiency impairs transitional B cell survival and differentiation

Project description:Klhl6 belongs to the KLHL gene family, which is composed of an N-terminal BTB-POZ domain and 4 to 6 Kelch motifs in tandem. Several of these proteins function as adaptors of the Cullin3 E3 ubiquitin ligase complex. Here we report that Klhl6 deficiency induces, as previously described, a two-fold reduction in mature B cells. However, we find that this deficit is centered on the inability of transitional T1 B cells to survive and to progress toward the T2 B cell stage, whereas cells that have passed this step generate normal germinal centers upon a T-dependent immune challenge. Klhl6-deficient T1 B cells showed a two-fold over-expression of genes linked with cell proliferation, including most targets of the APC/C complex, a set of genes whose expression is precisely down-modulated upon culture of splenic transitional B cells in presence of BAFF. These results thus suggest a delay in the differentiation process of Klhl6-deficient B cells between the immature and transitional stage. We further show, in the BL2 Burkitt’s lymphoma cell line, that KLHL6 interacts with Cullin3, but also that it binds to HBXIP/Lamtor5, a protein involved in cell cycle regulation and cytokinesis. Finally, we report that KLHL6, which is recurrently mutated in B cell lymphomas, is an off-target of the normal somatic hypermutation process taking place in germinal center B cells in both mice and humans, thus leaving open, whether, in spite of the lack of impact of Klhl6 deficiency on germinal center B cell expansion, mutants could contribute to the oncogenic process.

2018-07-17 | E-MTAB-5928 | biostudies-arrayexpress

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