Project description:Using Affymetrix GeneChips, we analyzed expression profiles of SP cells from EOM and TA. 348 differentially expressed transcripts defined the EOM-SP transcriptome: 229 upregulated in EOM-SP and 119 in TA-SP. Keywords: Expression Profiling Overall design: Six independently separated EOM and six TA SP cell preparations were used for microarray analysis using the Affymetrix® Mouse 430 ver 2.0 GeneChip arrays.
Project description:In rainbow trout, type A spermatogonia can be split into SP cells and non-SP cells by the ability to exclude Hoechst 33342 dye (H33342). The H33342 fluorescence of SP cells are lower than that of non-SP cells, after H33342 staining. To investigate whether SP cells were transcriptomically distinct from non-SP cells, we compared the transcriptome of these cells. We used fluorescence-activated cell sorting (FACS) to isolate SP cells and non-SP cells from the type A spermatogonia in rainbow trout. To compensate unavailability of genetically uniform rainbow trout in independent sampling, SP cells and non-SP cells were collected at 3 times from 3 different parental fish groups. This experimental design allowed us to estimate effects specific to each parental fish genotype on mRNA expression in SP cells by a statistical modeling and to exclude the effects in subsequent analysis.
Project description:Corneal epithelial stem cells reside in the limbus that is the transitional zone between the cornea and conjunctiva, and are essential to maintain the homeostasis of corneal epithelium. However, their characterization is poorly understood. Therefore, we constructed gene expression profiles of limbal epithelial SP and non-SP cell using RNA-sequencing. As a result, limbal epithelial SP cells have immature cell phenotypes with endothelial/mesenchymal cell markers, while limbal epithelial non-SP cells have epithelial progenitor cell markers. Overall design: Examination of rabbit limbal epithelial SP and non-SP cells
Project description:Using Affymetrix GeneChips, we analyzed expression profiles of SP cells from EOM and TA. 348 differentially expressed transcripts defined the EOM-SP transcriptome: 229 upregulated in EOM-SP and 119 in TA-SP. Experiment Overall Design: Six independently separated EOM and six TA SP cell preparations were used for microarray analysis using the Affymetrix® Mouse 430 ver 2.0 GeneChip arrays.
Project description:Sporozoite-specific genes were induced in parasites that express AP2-O whose AP2 domain was swapped with that of AP2-Sp. Overall design: DNA construct encoding AP2 domain of AP2-Sp was introduced into P. bergei schizonts. It was integrated into the locus of the endogenious AP2-O gene, resulting in swap of the AP2-domain (AP2-O::Sp parasites). Gene expression was analyzed in ookinetes cultured for 20h.
Project description:By comparing the gene expression profiling in Anoxybacillus sp. SK 3-4 with and without aluminum exposure, the sets of gene up-regulated and down-regulated by aluminum were identified. The function of genes or proteins induced under these conditions can a reflection of the mechanism of resistance. Transcriptome profiling of Anoxybacillus sp. SK 3-4 treated by aluminum would allow a better understanding of the gene involving in tolerance and removal of aluminum. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure
Project description:Side populations have recently been identified in ovarian cancers and may play an important role in post treatment relapse and resistance to chemotherapeutic drugs. In this study, we aimed to identify the differential expression between IGROV1 SP and NSP on Affymetrix HG-U133plus2 microarrays. We found ovarian tumour SP cells frequently over-express the multi-drug resistance associated P-glycoprotein (ABCB1) by Rank Product (FDR<0.05), and by geneset enrichment analysis, embryonic stem cell-associated ‘NOS’ signature (Notch/Oct4/Sox2 regulated genes) and Polycomb Repressive Complex 2 (PRC2) genes were over-expressed, while PRC2-repressed target genes were significantly under-expressed in the SP from ovarian cell lines compared to non-SP (FDR<10-4). Overall design: Cells were isolated using Hoechst 33342 cell sorting without other treatment. The experiment was carried out in triplicates: 3 SP samples and 3 non-SP samples
Project description:Ribonucleases catalyse maturation of functional RNAs or mediate degradation of cellular transcripts, activities that are critical for gene expression control. Here we identify a previously uncharacterized mammalian nuclease family member NEF-sp (LOC81691) as a testis-specific factor. Recombinant human NEF-sp demonstrates a divalent metal ion-dependent 3′→5′ exoribonuclease activity. This activity is specific to single-stranded RNA substrates and is independent of their length. Presence of a 2′-O-methyl modification at the 3′ end of the RNA substrate is inhibitory. Ectopically-expressed NEF-sp localizes to the nucleolar/nuclear compartment in human cell cultures and this is dependent on an N-terminal nuclear localization signal. Finally, mice lacking NEF-sp are viable and display normal fertility, likely indicating overlapping functions with other nucleases. Taken together, our study provides the first biochemical and genetic exploration of the role of the NEF-sp exoribonuclease in the mammalian genome. Overall design: Testicular transcriptome of Nef-sp-/- and Nef-sp+/- mice was analyzed using RNA-Seq.
Project description:Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results: To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions: The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia. The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions. These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high. Detection of gene expression variance among Frankia HfpCci3 (Cci3) cells grown in ammonium chloride for three days, five days and HfpCci3 cells grown in nitrogen fixing conditions for three days using mRNA-seq