RNA expression in ventilated preterm lamb lungs [RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA687664 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goal of this study was to measure by RNA-seq the impact of preterm birth and invasive mechanical ventilation verses noninvasive respiratory support on the lung transcriptome Methods: Lung mRNA profiles were generated for: 1) Unventilated preterm lamb, 2) preterm lambs delivered at gd131 and intubated and mechanically ventilated for 3 days, 3) preterm lambs delivered at gd131 and not intubated and resuscitated by placing a face mask over the nose and mouth and controlling O2 delivery via a computer-controlled electronic blower device, 4) unventilated naturally delivered full-term lambs. Results: Using an optimized data analysis workflow, we mapped between 61 and 81 million sequence reads per sample to the sheep genome Oar_v3.1/oviAri3 Conclusions: Our study represents the first detailed analysis of ventilated preterm lung transcriptomes, with biologic replicates, generated by RNA-seq
2021-06-30 | GSE163806 | GEO
Project description:Purpose: ATAC-seq was performed on preterm lambs that were ventilated by invasive mechanical ventilation or noninvasive respiratory support utilizing a mask and compared to gestation-age-matched preterm lambs that were not ventilated and naturally delivered term lambs. Methods: Lung chromatin access profiles were generated for: 1) Unventilated preterm lamb, 2) preterm lambs delivered at gd131 and intubated and mechanically ventilated for 3 days, 3) preterm lambs delivered at gd131 and not intubated and resuscitated by placing a face mask over the nose and mouth and controlling O2 delivery via a computer-controlled electronic blower device, 4) unventilated naturally delivered full-term lambs. Results: Using an optimized data analysis workflow, we mapped between 76 and 96 million sequence reads per sample to the sheep genome Conclusions: Our study represents the first detailed analysis of ventilated preterm lung chromatin access, with biologic replicates, generated by ATAC-seq
2021-06-30 | GSE163807 | GEO
Project description:Genome-wide DNA access sites in ventilated preterm lamb lungs [ATAC-seq]
| PRJNA687665 | ENA
Project description:This study aimed to use a lamb model of preterm birth to investigate the impact of different tidal volume strategies, applied during positive pressure ventilation, on lung injury development. Preterm lambs were ventilated for a total of 15 minutes, followed by a 30 minute ‘rest’ period where lambs were supported via the intact placenta. A group of lambs was also euthanised at birth to act as an unventilated control group. At post-mortem lung tissue was sampled for proteomic analysis. Lung tissue samples were analysed by mass spectrometry-based proteomics using a TMT-11plex labelling approach, followed by nano-liquid chromatography coupled to an Q Exactive HF-X benchtop Orbitrap mass spectrometer in a data-dependent acquisition mode.
2023-10-09 | PXD041917 | Pride
Project description:This project focuses both on the separate and combined effects of large tidal volume ventilation and hyperoxia on gene expression in the lungs of anesthetized rats. Rats were either mechanically or spontaneously ventilated at either 21 or 100% oxygen and expression levels were evaluated on RG_U34 GeneChips.
2007-10-10 | E-GEOD-489 | biostudies-arrayexpress
Project description: Not available
| S-EPMC3289264 | biostudies-literature
Project description:We compared fetal membrane tissue from preterm labor deliveries to fetal tissue from preterm labor with preterm prelabor rupture of membranes (PPROM) deliveries to further explore the concept that spontaneous preterm birth can result from the initializing of two separate but overlapping pathological events. Chorioamnion, separated into amnion and chorion, was collected from gestationally age-matched cases and controls within 15 minutes of birth, and analyzed using RNA sequencing. In our study, transcriptome analysis of preterm fetal membranes revealed distinct differentially expressed genes for PPROM, separate from preterm labor. This study is the first to report transcriptome data that reflects the individual pathophysiology of amnion and chorion tissue from PPROM deliveries.
2024-03-13 | GSE243831 | GEO
Project description:Background: Intratracheal budesonide mixed with surfactant has been investigated as an alternative to decrease lung injury and prevent bronchopulmonary dysplasia in preterm infants. However, possible systemic effects are not known. Our goal was identify systemic effects of intra-tracheal instilled budesonide by transcriptome analysis of the brain and lung in a preterm lamb model of mechanical ventilation. Methods: We performed RNA-sequencing of the fetal periventricular white matter and liver from preterm sheep after treatment with intratracheal budesonide mixed with surfactant or surfactant alone followed by mechanical ventilation. Unventilated animals were used as controls. mRNA profiles were generated from polyA selected RNA using Illumina platform. Read sequences were aligned to the sheep genome (Oar 4.0) using Bowtie2 followed read counts using featureCounts. We performed differential expression analysis using EdgeR. Results: We identified large and significant gene expression genes both in the liver and in the priventricular white matter in animals treated with budesonide+surfactant compared to surfactant alone and unventilated animals. There were complexes synergies and antagonism of effect of ventilation and budesonide on gene expression. Ventilation induced inflammatory signaling in the periventricular white matter and liver which was partially antagonized by budesonide. Budesonide also suppressed developmental pathways in the periventricular white matter. Conclusions: Intratracheal budesonide had systemic effects including suppression of developmental pathways in the brain. These effects could have clinical implication in affecting the neurodevelopmental outcomes of preterm newborns.
2019-11-26 | GSE131195 | GEO
Project description:Preterm birth is often predisposed by chorioamnionitis (CA) and CA affects the fetal gut and lungs via intra-amniotic (IA) inflammation, thus accentuating the proinflammatory effects of preterm birth. It is not known if IA inflammation also affects other perfusion-sensitive organs (e.g., kidneys) before and after preterm birth. Using preterm pigs as model for preterm infants, we hypothesized that CA induces fetal and neonatal renal dysfunctions that can intially be detected via plasma proteome, partly explaining the frequent renal dysfunction in preterm infants. Fetal pigs (88% gestation) were given an IA dose of lipopolysaccharide (LPS, 1 mg/kg, n=28), delivered preterm by cesarean section three days later, and compared with controls (CON, n=26) at birth and postnatal day five. Plasma proteome and protein markers of inflammatory pathways were evaluated.
2021-03-25 | PXD014619 | Pride
Project description:Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed phenotypic differences in histochemical and metabolic parameters related to meat quality among different muscles. Utilizing RNA Sequencing, this study characterized the whole transcriptome of nine lamb muscles: Semimembranosus (SM), Semitendinosus (ST), Gluteobiceps (GB), Gluteus medius (GM), Rectus femoris (RF), Supraspinatus (SS), Longissimus lumborum (LL), Adductor (AD) and Psoas major (PS).
2018-03-30 | GSE112500 | GEO