RNA-sequencing analysis of the KYSE150 cells overexpressing caspase-8 mutants (M4, M6, M10, M13) or wild-type caspase-8
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PROVIDER: PRJNA816048 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using RNA sequencing analysis to test the effects of overexpressing caspase-8 mutants or wild-type caspase-8 on the mRNA of KYSE150 cells. Methods: KYSE150 cells were transfected with caspase-8 mutants or wild-type caspase-8 for 48 hours in 1640 medium plus 10% serum. Two independent replicates were plated, transfected in parallel for each caspase-8 mutants or wild-type caspase-8. Results: Log-fold changes of mRNAs between caspase-8 mutants and wild-type caspase-8 group were selected with a significance threshod of p<0.05. There are 3974 overlapping differentially expressed genes in the caspase-8 mutant cells compared to the wild-type caspase-8 cells. Conclusions: Our study determined the mRNA changes of caspase-8 mutant KYSE150 cells compared to the wild-type caspase-8 cells.
2022-03-17 | GSE198569 | GEO
Project description:The transcriptional regulator Mga of Streptococcus pyogenes (the group A streptococcus, GAS) is known to directly activate several virulence genes important for colonization and immune evasion during exponential growth. Transcriptome analysis comparing two mga-1 serotypes (M1 SF370, M6 JRS4) and one mga-2 serotype (M4 GA40634) against their isogenic mga-inactivated strains uncovered a broader Mga regulon profile containing both activated and repressed genes with predicted functions primarily related to the uptake and metabolism of sugars. Although the divergent M1 and M4 Mga profiles were similar in size and content, the M6 JRS4 strain was clearly distinct, even from other M6 strains. Real-time RT-PCR and northern blot analysis validated our microarray results and confirmed that established core Mga regulon genes directly activated by Mga (emm, scpA, sof, fba) exhibited the highest activation levels across all strains tested. A novel ORF (Spy2036) encoding a cytosolic hypothetical protein was highly activated in all three serotypes and was called gene regulated by Mga or grm. Mga was shown to bind directly to Pgrm, which overlaps the Mga-regulated Psof in OF+ strains, suggesting that grm is part of the core Mga regulon and is able to activate two divergently transcribed genes from a single site in a class II background. Both class and serotype specific Mga-regulated genes, such as speB, were apparent. In fact, Mga activated speB as long as it was expressed in the wild type strain, although direct binding of Mga to the PspeB promoter could not be demonstrated. Thus, Mga is able to both directly and indirectly regulate genes shown to be important for virulence and the metabolic homeostasis of GAS. Keywords: Wild-type vs Mga-
2006-08-31 | GSE4598 | GEO
Project description:The transcriptional regulator Mga of Streptococcus pyogenes (the group A streptococcus, GAS) is known to directly activate several virulence genes important for colonization and immune evasion during exponential growth. Transcriptome analysis comparing two mga-1 serotypes (M1 SF370, M6 JRS4) and one mga-2 serotype (M4 GA40634) against their isogenic mga-inactivated strains uncovered a broader Mga regulon profile containing both activated and repressed genes with predicted functions primarily related to the uptake and metabolism of sugars. Although the divergent M1 and M4 Mga profiles were similar in size and content, the M6 JRS4 strain was clearly distinct, even from other M6 strains. Real-time RT-PCR and northern blot analysis validated our microarray results and confirmed that established core Mga regulon genes directly activated by Mga (emm, scpA, sof, fba) exhibited the highest activation levels across all strains tested. A novel ORF (Spy2036) encoding a cytosolic hypothetical protein was highly activated in all three serotypes and was called gene regulated by Mga or grm. Mga was shown to bind directly to Pgrm, which overlaps the Mga-regulated Psof in OF+ strains, suggesting that grm is part of the core Mga regulon and is able to activate two divergently transcribed genes from a single site in a class II background. Both class and serotype specific Mga-regulated genes, such as speB, were apparent. In fact, Mga activated speB as long as it was expressed in the wild type strain, although direct binding of Mga to the PspeB promoter could not be demonstrated. Thus, Mga is able to both directly and indirectly regulate genes shown to be important for virulence and the metabolic homeostasis of GAS. Keywords: Wild-type vs Mga-
2006-08-31 | GSE4597 | GEO
Project description:Escherichia coli M4 strain:M4 Genome sequencing and assembly
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Project description:Arthrobacter sp. M6 strain:M6 Genome sequencing and assembly
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Project description:Sandaracinobacter sp. M6 strain:M6 Genome sequencing and assembly
| PRJNA649658 | ENA
Project description:JRS4 is our wild-type M6 serotype strain and JRS948 is the isogenic covR strain. Keywords: 2-channel
2005-12-19 | GSE3367 | GEO
Project description:Rat iPS M13 cells had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave rat iPS M13 cells unique characteristics which could then be compared with other species' ES cells or iPS cells like human ES cells and mouse ES cells by the homologue genes comparison to show which species' ES cells or iPS cells were more competitive with the other.
2009-04-01 | GSE13360 | GEO
Project description:N6-methyladenosine (m6 A) and alternative polyadenylation (APA) are important regulators of gene expression in eukaryotes. Recently, it was found that m6 A is closely related to APA. However, the molecular mechanism of this new APA regulation remains elusive. Here, we show that YTHDC1, a nuclear m6 A reader, can suppress proximal APA sites and produce longer 3' UTR transcripts by binding to their upstream m6 A sites. YTHDC1 can directly interact with the 3' end processing factor FIP1L1 and interfere with its ability to recruit CPSF4. Binding to the m6 A sites can promote liquid-liquid phase separation of YTHDC1 and FIP1L1, which may play an important role in their interaction and APA regulation. Collectively, YTHDC1 as an m6 A "reader" links m6 A modification with pre-mRNA 3' end processing, providing a new mechanism for APA regulation.
2022-03-11 | GSE198143 | GEO