RNA-seq of mouse and hamster oocyte and early development
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ABSTRACT:
PROVIDER: PRJEB15293 | ENA |
REPOSITORIES: ENA
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2023-07-20 | PXD034071 | Pride
Project description:To verify the Ribo-seq data of mouse oocyte, we performed MS/MS on mouse fully-grown oocytes. And the results show that our Ribo-seq data well reflect the proteomic dynamics in the fully grown oocytes.
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Project description:This study compares miRNA expression profiles in mouse oocytes as young oocytes vs aged oocytes, and growing oocytes vs small oocytes from primordial follicles. Oocytes were derived from the ovary of young (6-8 week-old) C57BL/6 mice and aged (41-43 week-old) mice and pooled according to whether they were 20 to 50 um or 60 to 80 um in diameter. Of oocytes with the diameter of more than 60um, oocyte from young mice are called ‘young oocytes’ and those from aged mice near the end of their reproductive life span are called ‘aged oocytes’ to analyze the miRNA profiling associated with aging. They were also each called ‘small oocytes’ or ‘large oocytes’ from the size of 60um so as to investigate miRNA profiling associated with growing. Total RNA from oocytes was isolated using mirVana miRNA Isolation Kit (Applied Biosystems). MiRNA expression was profiled using Agilent's Mouse miRNA Microarray Kit (G4472A) annotated against the Sanger miRBASE 10.1 database of miRNAs. This miRNA microarray was provided by Agilent Technologies (Santa Clara, CA). Each sample was run in duplicate.
2012-09-04 | E-GEOD-17966 | biostudies-arrayexpress
Project description:1. The experiment was performed to assess if the newly discovered Syrian hamster specific anti-PD-L1 antibody could induce a biologically relevant change in transcriptome profile in the tumours. This would confirm that the antibody has functional properties. In the larger picture, the Syrian Hamster model is favored over the mouse model for the development of vaccines and testing of oncolytic viruses/immunotherapies. This is because the model is semi permissive to virus replication compared to the mouse model. We can therefore more reliably assess the efficacy of oncolytic virotherapies, mainly oncolysis and promoter specific transgene expression. Moreover, we wanted to test potential improvements to treatment outcomes when combining oncolytic virotherapy and immune checkpoint blockade. However, there are not many commercially available research tools specific to the Syrian Hamster. This is why we developed an in vivo compatible immune checkpoint inhibitor so that we could assess the combination therapy in the Syrian hamster model. Lastly, we also wanted to validate if we could assess the efficacy of the immunotherapies using biopsies from hamsters to remove unnecessary use of animals. 2. To do this, we engrafted one PDAC tumours on the right flank of Syrian hamsters using 5 x10E+6 HapT1 cells grown in culture. When tumours reached 4-5mm in diameter, the hamsters were injected intraperitoneally with either 300ug of IgG2a control or anti-PD-L1 (clone;11B12-1). Hamsters were treated 8 times and a tumour biopsy was taken one day before the last treatment. The biopsy was immediately stored in RNA-later until extraction with RNA mini kit (Qiagen).
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Project description:Here we asked if oocyte proteomes are representative of the transcriptomes, how the abundance of specific genes’ mRNA and protein responds to maternal aging, and if oocyte aging presents the features characteristic of somatic aging. To address these questions on the proteomic level, we employed stable isotope labeling of amino acids in cell culture (SILAC; Geiger et al. 2011) as the method of choice, and performed a SILAC screen of mouse metaphase II (MII) oocytes superovulated at 3, 8+-1 and 58+-10 weeks of maternal age, which correspond to pre-puberty, mature age and climacterium, respectively. We used heavy F9 embryonic carcinoma (EC) cells as internal or "Spike-in" standard for the quantification of oocytes proteins because in contrast to the oocytes they can easily be cultured feeder-free, have stem cell properties and should harbor the majority of all oocyte proteins (although with different relative abundances). The SILAC screen was conducted in parallel with conventional microarray analysis to compare the concordance of protein and transcript levels in these oocytes. Associated microarray data have been deposited to NCBI GEO with accession number GSE42959.
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