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Series GSE249434 Query DataSets for GSE249434
Status Public on Apr 11, 2024
Title Single-cell profiling reveals transcriptome dynamics during bovine oocyte growth
Organism Bos taurus
Experiment type Expression profiling by high throughput sequencing
Summary Mammalian follicle development is characterised by extensive changes in morphology, endocrine responsiveness, and function, providing the optimum environment for oocyte growth, development, and resumption of meiosis. In cattle, the first signs of transcription activation in the oocyte are observed in the secondary follicle, later than during mouse and human oogenesis. While many studies have generated extensive datasets characterising gene expression in bovine oocytes, they are mostly limited to the analysis of fully grown and matured oocytes. The aim of the present study was to apply single-cell RNA sequencing to interrogate the transcriptome of the growing bovine oocyte from the secondary follicle stage through to the mid-antral follicle stage. Single-cell RNA-seq libraries were generated from oocytes of known diameters (<60 to >120 um), and datasets were binned into non-overlapping size groups for downstream analysis. Combining the results of weighted gene co-expression network and Trendy analyses, and differently expressed genes (DEGs) between size groups, we identified a decrease in oxidative phosphorylation and an increase in maternal -genes and transcription regulators across the bovine oocyte growth phase. In addition, around 5,000 genes did not change in expression, revealing a cohort of stable genes. An interesting switch in gene expression profile was noted in oocytes greater than 100 um in diameter, when the expression of genes related to cytoplasmic activities was replaced by genes related to nuclear activities (e.g., chromosome segregation). The highest number of DEGs were detected in the comparison of oocytes 100-109 versus 110-119 um in diameter, revealing a profound change in the molecular profile of oocytes at the end of their growth phase. The current study provides a unique dataset of the key genes and pathways characteristic of each stage of oocyte development, contributing an important resource for a greater understanding of bovine oogenesis.
 
Overall design Bovine (Bos taurus) ovaries were collected at a local abattoir and returned to the laboratory in cold PBS. Fully-grown oocytes (>130 µm diameter) were removed first by aspirating 3-8 mm surface visible follicles. Subsequently, the ovaries were butterflied open, submerged in cold Dissection medium (TCM199 supplemented with 0.4% BSA fraction V, 0.164 mM penicillin, 0.048 mM streptomycin, 1,790 units/L heparin, and 5 μM cilostamide (Barros et al., 2020)), and growing oocytes from late secondary to early antral follicles were liberated by slicing the ovarian cortex. Subsequently, the medium containing the oocytes was filtered through a descending series of mesh filters, including 260 mm mesh, 100 and 40 mm PluriStrainer® filters. Recovered oocytes were washed in cold Dissection medium, denuded by pipetting, and allocated singly to drops of cold PBS, where their diameter was measured under a Nikon Eclipse TE2000-S microscope and NIS Elements BR 5.02.00 64-bit software. Measured oocytes were snap-frozen in 4 mL PBS + 4 mL RTL-Plus buffer (Qiagen) in 0.2 mL PCR microtubes, and kept at -80°C until processed from RNA sequencing.
Web link https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10234-0
 
Contributor(s) Barbosa Latorraca L, Galvão A, Rabaglino M, D'augero JM, Kelsey G, Fair T
Citation(s) 38580918
Submission date Dec 05, 2023
Last update date Apr 11, 2024
Contact name Lais Barbosa Latorraca
E-mail(s) lais_latorraca@hotmail.com
Organization name University College Dublin
Department Agriculture and Food Science
Lab Animal Reproduction
Street address UCD Lyons Farm
City Celbridge
State/province Kildare
ZIP/Postal code W23 ENY2
Country Ireland
 
Platforms (1)
GPL23055 Illumina NextSeq 500 (Bos taurus)
Samples (179)
GSM7947162 A276, <60 μm, replicate 1, scRNAseq
GSM7947163 A277, <60 μm, replicate 1, scRNAseq
GSM7947164 A278, <60 μm, replicate 1, scRNAseq
Relations
BioProject PRJNA1049029

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE249434_RawReadCounts.txt.gz 3.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
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