Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA sequencing of non-stimulated (non-stim) or lipopolysaccharide (LPS)-stimulated (100 ng/mL, 1 h) wildtype (WT) and mt-tRNAala m.5019A>G mutant murine bone marrow-derived macrophages (BMDMs). Three biological replicates per condition

ABSTRACT: The experiment was designed to examine differentially expressed genes between wildtype BMDMs and BMDMs with a heteroplasmic pathogenic mitochondrial DNA mutation in the mitochondrial tRNA for alanine, which disrupts mitochondrial translation. Both non-stimulated basal state and LPS-stimulated state BMDM transcripts were examined. RNA isolation was carried using RNeasy® Plus kit (74136, Qiagen) following manufacturer’s suggestions and eluted RNA was purified using RNA Clean & Concentrator Kits (Zymo Research). RNA-seq samples libraries were prepared by Cambridge Genomic Services (CGS) using TruSeq Stranded mRNA (Illumina) following the manufacturer’s description. For the sequencing, the NextSeq 75 cycle high output kit (Illumina) was used and samples spiked in with 1% PhiX. The samples were run using NextSeq 500 sequencer (Illumina). Differential Gene Expression Analysis was done using the counted reads and the R package edgeR version 3.26.5 (R version 3.6.1) for the pairwise comparisons.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Dylan Ryan

PROVIDER: E-MTAB-15591 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Primordial follicle assembly is the process by which ovarian primordial follicles are formed. During follicle assembly oocyte nests break down and a layer of pre-granulosa cells surrounds individual oocytes to form primordial follicles. The pool of primordial follicles formed is the source of oocytes for ovulation during a femaleM-bM-^@M-^Ys reproductive life. Complex networks of cellular signaling and gene expression are essential for any biological process. A systems biology experimental approach provides a global view of these gene relationships in a particular developmental process. The current study utilized a systems approach to detect all genes that are differentially expressed in response to seven different growth factor and hormone treatments known to influence primordial follicle assembly in a neonatal rat ovary culture system. One novel growth factor, basic fibroblast growth factor (FGF2), was experimentally determined to inhibit follicle assembly. The different growth factor and hormone treatments were all found to affect the same physiological pathways, but each treatment affected a unique set of differentially expressed genes (signature gene set). A gene bionetwork analysis identified gene modules of coordinately expressed interconnected genes and it was found that different gene modules appear to accomplish distinct tasks during primordial follicle assembly. Unique gene networks were identified for a number of the modules and signature gene sets. Predictions of physiological pathways important to follicle assembly were validated using ovary culture experiments in which ERK1/2 (MAPK1) activity was increased. A number of the highly interconnected genes in these gene networks have previously been linked to primary ovarian insufficiency (POI) and polycystic ovarian disease syndrome (PCOS). Observations have identified novel factors and gene networks that regulate primordial follicle assembly. This systems approach has helped elucidate the molecular control of primordial follicle assembly and provided potential therapeutic targets for the treatment of ovarian disease. We used microarrays to determine genes expressed differentially between control and P0 ovaries treated with 7 growth factors: AMH, CTGF, estradiol (E2), Activin-a, FGF2, progesterone (P4), and TNFa. RNA samples from 7 control samples are compared to 3 growth factor treated ovary samples for each AMH (human Anti-MM-CM-<lerian hormone), CTGF (connective tissue growth factor ), estradiol (E2), TNF (tumor necrosis factor ), FGF2 (fibroblast growth factor 2), Inhba (inhibin, beta A), and 2 samples for progesterone (P4).

Dataset Information

RNA sequencing of non-stimulated (non-stim) or lipopolysaccharide (LPS)-stimulated (100 ng/mL, 1 h) wildtype (WT) and mt-tRNAala m.5019A>G mutant murine bone marrow-derived macrophages (BMDMs). Three biological replicates per condition

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