Differential gene expression analysis for S.pyogenes SP-STK(-) mutant
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ABSTRACT:
ORGANISM(S): Streptococcus pyogenes
PROVIDER: GSE10914 | GEO | 2013/02/28
SECONDARY ACCESSION(S): PRJNA107211
REPOSITORIES: GEO
Similar Datasets
Project description:This analysis revealed ~17.% of all ORFs (292 out of a total 1697 ORFs) differed by at least 1.5 fold (Log2 +0.6) between the mutant and wild-type strains. Of these, ~45% of the ORFs (130 out of 292 ORFs) revealed at least 2-fold (Log2 +1) differences. The complete spectrum of differentially expressed genes in the muatnt strain revealed almost equal number of genes up (143, 49%) or down-regulated (149, 51%). However, at a higher stringency (at least 2-fold), this distribution revealed slightly more leaning towards down-regulated genes (74 out of 130, 57%) indicating the lack of SP-STK results into down regulation of several genes. Amongst the genes belonging to different functional categories, the most notable genes that were affected by the absence of SP-STK were those correspond to Carbohydrate transport and metabolism (57 out of 292, 20% at low stringency and 32 out of 130 ,~25% at high stringency), phage (28, ~10% at low stringency and 24, ~18% at high stringency), and virulence (5-6% irrespective of stringency level). Almost 20-25% of differentially expressed genes revealed at two stringencies were found to be either with unknown or undefined functions. Keywords: knockout mutant This analysis is based on a total of three independent prearations of total RNA from the wild-type S. pyogenes M1SF370 and the isogenic knockout mutant lacking SP-STK (SPy1625). First two preparations included dyeswap experiment and hence repeated twice (exp1-4). The third preparation done only one (Exp#5). Thus, the present analysis is based on five separate experiments
2013-02-28 | E-GEOD-10914 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from the SEEDSTICK mutant in Arabidopsis with a wild type, to unveil the role of this transcription factor in seed development and decipher the impact of this factor in PAs metabolism Methods: Total RNA was extracted from two biological replicates from both wild-type and stk mutant inflorescences and siliques until 5 DAP with the Qiagen Kit according to the manufacturer's instructions. DNA contaminations were removed using the PROMEGA RQ1 RNase-Free DNase according to the manufacturer's instructions. RNA quality integrity was analyzed by electrophoresis gel and was validated on a Bioanalyzer 2100 (Aligent, Santa Clara, CA); RNA Integrity Number (RIN) values were greater than 7 for all the samples. In order to confirm that in stk mutant samples STK was not expressed, STK expression was checked by real time PCR with primer RT 780 (5â??-TGCGATGCAGAAGTTGCGCTC-3â??) and RT 781 (5â??-AGTACGCGGCATTGATTTCTTG-3â??). Sequencing libraries were prepared according to the manufacturerâ??s instructions by TruSeq RNA Sample Prep kit (Illumina Inc.) and sequenced on Illumina HiSeq2000 in one lane single-read 50bp. The processing of fluorescent images into sequences, base-calling and quality value calculations were performed using the Illumina data processing pipeline (version 1.8). Raw reads were filtered to obtain high-quality reads by removing low-quality reads containing more than 30% bases with Q < 20. Finally, a quality control of the raw sequence data was performed using FastQC [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/]. Results: A total of 102,278,242 reads passed a quality filter and 85% were mapped back to the Arabidopsis TAIR10 genome. Approximately 90% mapped uniquely to only one location and could be assigned to a single annotated TAIR10 gene. Normalization of expression values was performed using RPKM values. All other parameters were kept at default levels. The CLC Genomic Workbench was also further used to determine all differentially expressed transcripts found in each cDNA library. Baggerley's test and a FDR correction were used for statistical analysis of samples. Our analysis revealed that 156 genes were upregulated, whereas for 90 genes a reduction in their mRNA level was observed in the stk mutant when compared to wild-type . Data analysis revealed a significant enrichment for terms related to the phenylpropanoid metabolic process, flavonoid biosynthetic process as well as cellular amino acid derivative metabolic process. Conclusion: Our genome-wide transcriptomic analysis suggests that the ovule identity factor STK is involved in the regulation of several metabolic processes providing a strong connection between cell fate determination, development and metabolism. In particular we characterize, through phenotypic, genetic, biochemical and transcriptomic approaches, the role of STK in PAs biosynthesis. Our results indicate that STK exerts this role through the direct regulation of the gene encoding for BANYULS/ANTHOCYANIDIN REDUCTASE (BAN/ANR), which converts anthocyanidins into their corresponding 2,3-cis-flavan-3-ols. Our study also demonstrates that the levels of H3K9ac chromatin modification directly correlate with the active state of BAN in an STK-dependent way. This supports the theory that MADS-domain proteins control the expression of their target genes through the modification of the chromatin states. STK might recruit or negatively regulate histone modifying factors to control their activity. Moreover, we show that STK controls through a complex regulatory network not only directly BAN but also other regulators of this key gene in tannin production mRNA profiles from both Arabidopsis wild-type and stk mutant inflorescences and siliques until 5 DAP were generated by deep sequencing, in duplicate according to the manufacturerâ??s instructions by TruSeq RNA Sample Prep kit (Illumina Inc.) and sequenced on Illumina HiSeq2000 in one lane single-read 50bp. In order to confirm that in stk mutant samples STK was not expressed, STK expression was checked by real time PCR with primer RT 780 (5â??-TGCGATGCAGAAGTTGCGCTC-3â??) and RT 781 (5â??-AGTACGCGGCATTGATTTCTTG-3â??).
2014-12-17 | E-GEOD-59637 | biostudies-arrayexpress
Project description:STK-17, a kinase that responses to azoles transcriptionally, is required for azole resistance. By analyzing and comparing the transcriptomes from samples of N. crassa Wild Type, stk-17ko and stk-17com strain treated with or without ketoconazole, the biological processes that would be affected by stk-17 deletion was revealled.
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Project description:In this work, we reported that STK-12 functions as a novel repressor of cellulase expression. The stk-12 disruption strain not only displayed enhanced cellulase production but also retained a steady state, with high expression levels of cellulase genes, for longer than the wild type strain.
2022-03-05 | GSE129410 | GEO
Project description:Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from the SEEDSTICK mutant in Arabidopsis with a wild type, to unveil the role of this transcription factor in seed development and decipher the impact of this factor in PAs metabolism Methods: Total RNA was extracted from two biological replicates from both wild-type and stk mutant inflorescences and siliques until 5 DAP with the Qiagen Kit according to the manufacturer's instructions. DNA contaminations were removed using the PROMEGA RQ1 RNase-Free DNase according to the manufacturer's instructions. RNA quality integrity was analyzed by electrophoresis gel and was validated on a Bioanalyzer 2100 (Aligent, Santa Clara, CA); RNA Integrity Number (RIN) values were greater than 7 for all the samples. In order to confirm that in stk mutant samples STK was not expressed, STK expression was checked by real time PCR with primer RT 780 (5’-TGCGATGCAGAAGTTGCGCTC-3’) and RT 781 (5’-AGTACGCGGCATTGATTTCTTG-3’). Sequencing libraries were prepared according to the manufacturer’s instructions by TruSeq RNA Sample Prep kit (Illumina Inc.) and sequenced on Illumina HiSeq2000 in one lane single-read 50bp. The processing of fluorescent images into sequences, base-calling and quality value calculations were performed using the Illumina data processing pipeline (version 1.8). Raw reads were filtered to obtain high-quality reads by removing low-quality reads containing more than 30% bases with Q < 20. Finally, a quality control of the raw sequence data was performed using FastQC [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/]. Results: A total of 102,278,242 reads passed a quality filter and 85% were mapped back to the Arabidopsis TAIR10 genome. Approximately 90% mapped uniquely to only one location and could be assigned to a single annotated TAIR10 gene. Normalization of expression values was performed using RPKM values. All other parameters were kept at default levels. The CLC Genomic Workbench was also further used to determine all differentially expressed transcripts found in each cDNA library. Baggerley's test and a FDR correction were used for statistical analysis of samples. Our analysis revealed that 156 genes were upregulated, whereas for 90 genes a reduction in their mRNA level was observed in the stk mutant when compared to wild-type . Data analysis revealed a significant enrichment for terms related to the phenylpropanoid metabolic process, flavonoid biosynthetic process as well as cellular amino acid derivative metabolic process. Conclusion: Our genome-wide transcriptomic analysis suggests that the ovule identity factor STK is involved in the regulation of several metabolic processes providing a strong connection between cell fate determination, development and metabolism. In particular we characterize, through phenotypic, genetic, biochemical and transcriptomic approaches, the role of STK in PAs biosynthesis. Our results indicate that STK exerts this role through the direct regulation of the gene encoding for BANYULS/ANTHOCYANIDIN REDUCTASE (BAN/ANR), which converts anthocyanidins into their corresponding 2,3-cis-flavan-3-ols. Our study also demonstrates that the levels of H3K9ac chromatin modification directly correlate with the active state of BAN in an STK-dependent way. This supports the theory that MADS-domain proteins control the expression of their target genes through the modification of the chromatin states. STK might recruit or negatively regulate histone modifying factors to control their activity. Moreover, we show that STK controls through a complex regulatory network not only directly BAN but also other regulators of this key gene in tannin production
2014-12-17 | GSE59637 | GEO
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2012-10-20 | GSE41705 | GEO
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2011-07-31 | E-GEOD-28881 | biostudies-arrayexpress
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