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ABSTRACT: scRNA-seq of ventricular-subventricular zone of preterm and full-term birth mice

PROVIDER: PRJNA944115 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23891550.fastq.gz	Fastqsanger.gz
	SRR23891551.fastq.gz	Fastqsanger.gz
	SRR23891552.fastq.gz	Fastqsanger.gz
	SRR23891553.fastq.gz	Fastqsanger.gz
	SRR23891554.fastq.gz	Fastqsanger.gz

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Project description:scRNA-seq of ventricular-subventricular zone of and term (P28) and preterm (P29) birth mice

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Functional proteome analysis of placenta membrane associated with preterm birth

Project description:In this study, the molecular signature of placenta membrane from preterm birth placenta was assessed and compared to full-term placenta by proteomic profiling with the aim to identify molecules relevant to preterm birth.

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Single-Cell 10x RNA Sequencing of old and young wildtype and interferon receptor knockout mice

Project description:Sequence neural stem cells and related cells of the ventricular-subventricular zone in wildtype mice and mice lacking interferon receptors across ages.

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Transcriptomic and Proteomic Profiling of Human Mesenchymal Stem Cell Derived from Umbilical Cord in the Study of Preterm Birth

Project description:Mesenchymal stem cells (MSCs) hold great therapeutic potential in morbidities associated with preterm birth. However, the molecular expressions of hMSCs in preterm birth infants have not been systematically evaluated. In this study, we presented the dual-omics analyses of umbilical cord (UC) derived hMSCs to identify the dysregulated cellular functions. Materials and methods: The UC-MSCs were collected from 10 full-term and 8 preterm birth infants for transcriptomics and proteomics analyses by using microarray and iTRAQ-based proteome profiling. The integrative analysis of dual-omics data discovered 5,615 commonly identified genes/proteins of which 29 genes/proteins showed consistent up- or down-regulation in preterm birth. The Gene Ontology analysis revealed that the biological processes of mitochondrial translation and cellular response to oxidative stress were mainly enriched in 290 differential expression proteins (DEPs) while the 421 differential expression genes (DEGs) were majorly involved in secondary alcohol metabolic process, cellular response to stress, and mitotic cell cycle in preterm birth. Besides, we identified a 13-protein module involving CUL2 and CUL3, which plays an important role in cullin-RING-based ubiquitin ligase complex, as potential mechanism for preterm birth. The dual-omics data not only provided new insights to the molecular mechanism but also to identify panel of candidate markers associated with preterm birth.

2019-09-26 | PXD013644 | Pride

scRNA-seq of ferret cortical germinal zones from splenial gyrus and lateral sulcus (Borrell lab)

Project description:Diversity of cortical radial glia cells (RGCs) and their complex relationships to generate neurons in species with expanded germinal zones and a folded cortex, remains unclear. We used single-cell RNA sequencing (scRNA-seq) of microdissected cortical germinal layers (ventricular zone (VZ) and outer subventricular zone (OSVZ)), from two cortical regions (splenial gyrus (SG) and neighboring lateral sulcus (LS)) at two critical time points for ferret cortex development (embryonic day (E) 34 and postnatal day (P) 1) to distinguish the molecular diversity of progenitors and newborn neurons, and study their transcriptomic trajectories.

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Gene expression profiling of laser-captured microdissected avascular neocortex in E14.5 neocortical cells were compared by microarray transcription profiling

Project description:Gene expression profiles among avascular region (around ventricular zone), highly vascularized region with honeycomb-patterned vascular plexus (around subventricular zone and intermediate zone), and cortical plate with vertically oriented vessels from laser-captured microdissected E14.5 neocortex were compared by microarray

2019-09-18 | E-MTAB-8359 | biostudies-arrayexpress

Single cell analysis of the postnatal dorsal V-SVZ reveals a role for Bmpr1a-signaling in silencing pallial germinal activity

Project description:The ventricular-subventricular zone (V-SVZ) is the largest neurogenic region of the postnatal forebrain, containing neural stem cells (NSCs) that emerge from both the embryonic pallium and subpallium. Despite of this dual origin, glutamatergic neurogenesis declines rapidly after birth, while gabaergic neurogenesis persists throughout life. We performed single-cell RNA-sequencing (scRNA-Seq) of the postnatal dorsal V-SVZ for unravelling the mechanisms leading to pallial lineage germinal activity silencing. We show that pallial NSCs enter a state of deep quiescence, characterized by high BMP-signaling, reduced transcriptional activity and Hopx expression, whilst in contrast, subpallial NSCs remain primed for activation. Induction of deep quiescence is paralleled by a rapid blockade of glutamatergic neurons production and differentiation. Finally, manipulation of Bmpr1a demonstrates its key role in mediating these effects. Together, our results highlight a central role of BMP-signaling in synchronizing quiescence induction and blockade of neuronal differentiation to rapidly silence pallial germinal activity after birth.

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Quantitative Proteomic Profiling of Cervicovaginal Fluid from Pregnant Women with Term and Preterm Birth

Project description:Preterm birth (PTB) is one of major causes of perinatal mortality and neonatal morbidity, but knowledge of its complex etiology is still limited. Here we present cervicovaginal fluid (CVF) protein profiles of pregnant women who subsequently delivered at spontaneous preterm or term, aiming to identify differentially expressed CVF proteins in PTB and term birth. The CVF proteome of women who sequentially delivered at preterm and term was analyzed using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with two-dimensional nanoflow liquid chromatography-tandem mass spectrometry (2D-nLC-MS/MS). We compared the CVF proteome of PTB (n=5) and control subjects (term birth, n=7) using pooled control CVF (term birth, n=20) as spike-in standard. We identified 1294 CVF proteins, of which 605 were newly identified proteins. Of 990 proteins quantified in both PTB and term birth, 52 proteins were significantly up/down-regulated in PTB compared to term birth. The differentially expressed proteins were functionally associated to immune response, endopeptidase inhibitors and structural constituent of cytoskeleton. Taken together, our study provide quantitative CVF proteome profiles of pregnant women who ultimately delivered at preterm and term. These promising results could help to improve the understanding of PTB etiology and to discover biomarkers for asymptomatic PTB.

2021-09-09 | PXD021401 | Pride

Single cell RNA-sequencing of 75-day old human H1 and H9 embryonic stem cell-derived cerebral organoids

Project description:The scRNA-seq analysis of 75 day old human cerebral organoids grown at the air-liquid interface (ALI-COs) reveals six well-defined major clusters. Cell-type and maturity markers define a (1) distinct population of deep layer subcortical projection neurons, (2) upper layer intracortical (callosal) projection neurons and intermediate progenitors, (3) ventricular and subventricular zone radial glial cells, (4) more mature upper and deep layer neurons, (5) interneurons and (6) actively dividing cells with intermediate progenitor and radial glia markers. In addition, the gene expression profile of these clusters corresponds with their expected functional characteristics appropriate to their maturity. Altogether, our data reflect a full repertoire of cortical neuronal and progenitor identities corresponding with the stages of cortical development in age-matched fetal brains.

2019-02-28 | GSE124174 | GEO

Affymetrix analysis of adult mouse lung exposed to room air or 100% oxygen between postnatal days 0-4

Project description:It is unclear why preterm birth increases risk of cardiovascular disease later in life. Studies in mice indicate excess oxygen used to treat preterm infants causes pulmonary hypertension, cardiac failure, and shortens lifespan. We previously reported neonatal hyperoxia causes pulmonary hypertension in aged mice as defined pathologically by pulmonary capillary rarefaction, dilation of pulmonary arterioles and veins, right ventricular hypertrophy, and reduced lifespan. Here, affymetrix gene arrays were used to identify early transcriptional changes in lungs of young adult mice exposed to room air or 100% oxygen between postnatal days 0-4.

2018-01-01 | E-MTAB-6074 | biostudies-arrayexpress

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