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Genome-wide DNA access sites in ventilated preterm lamb lungs [ATAC-seq]

ABSTRACT: 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

ORGANISM(S): Ovis aries

PROVIDER: GSE163807 | GEO | 2021/06/30

REPOSITORIES: GEO

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RNA expression in ventilated preterm lamb lungs [RNA-seq]

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

Genome-wide DNA access sites in ventilated preterm lamb lungs [ATAC-seq]

Project description:Genome-wide DNA access sites in ventilated preterm lamb lungs [ATAC-seq]

| PRJNA687665 | ENA

RNA expression in ventilated preterm lamb lungs [RNA-seq]

Project description:RNA expression in ventilated preterm lamb lungs [RNA-seq]

| PRJNA687664 | ENA

Proteomics analysis of preterm lung tissue with mass spectrometry to understand the impact of tidal volume strategy at birth

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

Next Generation Sequencing Facilitates Quantitative Analysis of ventilated and unventilated preterm lambs and normal full-term lambs.

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of ventilated and unventilated preterm lambs and normal full-term lambs.

| PRJNA687876 | ENA

Suckling lamb perirenal fat transcriptome

Project description:The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf= 8, Churra= 6) was used for the RNA-Seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes. The differential expression analysis performed identified 373 differentially expressed genes (DEGs) between the two compared breeds. In Assaf lambs, DEGs were enriched in Gene Ontology (GO) biological processes related to fatty-acid oxidation, while in Churra lambs, the majority of the significantly enriched GO terms were related to cholesterol synthesis, which suggests that upregulated DEGs in Assaf lambs are implicated in fat burning, while the Churra upregulated DEGs are linked to fat accumulation.

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2020-05-28 | GSE149490 | GEO

miRNA expression in tracheal aspirates [ICS-BPD vs. ICS-BPD-PH]

Project description:Tracheal aspirate (TAs) samples were collected from intubated preterm infants with hemodynamically significant intracardiac shunt (ICS), and a diagnosis of ICS-BPD/ICS-BPD-PH. 36 TA samples were analyzed. Small RNAs were extracted and the expression miRNAs was detected with PCR arrays.

2023-08-02 | GSE239868 | GEO

miRNA transcriptome and myofiber characteristics of lamb skeletal muscle during hypertrophic growth

Project description:Longissimus muscle samples were collected from lambs at 6 developmental time points (prenatal gestational d 85, 110, 133, and postnatal d 42, 65, and 243). Muscle samples were examined to determine the impact of myofiber hypertrophy on the miRNA profile.

2022-07-22 | GSE207055 | GEO

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