Transcription profiling of microsporocytes in Arabidopsis Atmcc1.
Ontology highlight
ABSTRACT: Trascriptome analysis of an Arabidopsis mutant with enhanced histone acetylation, Atmcc1, was performed on single microsporocytes using laser microdissection combined with microarray.
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes. Wild type accessions Col-0 were grown on soil at 16M-BM-0C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0RM-BM-.). Three biological replicates were performed for each accession.
Project description:The aim of this study was to investigate the effects of administration of carbon black nanoparticle (CB-NP) to pregnant mice on the development of lymphoid tissues in infantile mice. Pregnant ICR mice were treated with a suspension of CB-NP 95 microg/kg/time) by intranasal instillation, twice, on gestational day 5 and 9. Spleen and thymus were collected from offspring mice at 5 days post-partum. RNA sample was taken from spleen of 5-day-old mouse prenatally received carbon black nanoparticle, while control RNA was taken from control counterpart prenatally received distilled water. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.
Project description:Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in rdm16ros1, ros1, nrpd1ros1 mutants and examine the effect of RDM16 on DNA methylation 4 samples examined: C24 wild type with RD29A-LUC transgene, rdm16ros1 double mutant, ros1 mutant, nrpd1ros1 mutant (all in C24 background with RD29A-LUC transgene)
Project description:The present study aimed to examine the effect of high-fat diet prior to pregnancy on the liver of mouse offspring. Female C57BL/6J mice were fed a normal chow (15.2% fat by energy) (CTR and CTR-PP groups) or a high-fat chow (31.2% fat by energy) (HFD and HFD-PP groups) for 3−4 weeks and then mated with male C57BL/6J mice fed normal chow. Some mothers continued on the same diet until pups reached 21 days of age (CTR and HFD), and others were fed the different chows from gestational day 0 (CTR-PP and HFD-PP) to determine the effects of a high-fat diet during the pre-pregnancy period in HFD-PP/CTR and HFD/CTR-PP comparisons. RNA sample was taken from liver of 3-week-old mouse prenatally received high-fat diet prior to pregnancy, during pregnancy and lactation, or through prior to and during pregnancy and lactation, while control RNA was taken from control counterpart prenatally received normal diet alone. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes. Wild type accessions Col-0, Bur-0 and C24 were grown on soil at 23M-BM-0C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0RM-BM-.). Three biological replicates were performed for each accession.
Project description:This SuperSeries is composed of the following subset Series: GSE24571: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq] GSE38109: Natural variation in Arabidopsis thaliana transcriptomes Refer to individual Series
Project description:The aim of the analysis is to compare the trascriptome of myeloma cells expressing the wt version of novel oncosuppressor FAM46C comparing it with that of cells expressing a mutant variant of the same gene often found in patients (the D90G mutant allele) or to a Mock control. Cells were grown in RPMI media at 500000 cells/ml. After 4 days of culture total RNA was extracted.