Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22803615.fastq.gz | Fastqsanger.gz | |||
| SRR22803616.fastq.gz | Fastqsanger.gz |
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Project description:Comparison of whole blood DNA methylation in 45 year-old humans with low and high childhood and adulthood socio-economic position Background: Disadvantaged socio-economic position (SEP) in childhood is associated with increased adult mortality and morbidity. We aimed to establish whether childhood SEP was associated with differential methylation of adult DNA. Methods: Forty adult males from the 1958 British Birth Cohort Study were selected from SEP extremes in both early childhood and mid-adulthood. We performed genome-wide methylation analysis on blood DNA taken at 45y using MeDIP (methylated DNA immunoprecipitation). We mapped in triplicate the methylation state of promoters of ~20,000 genes and 400 microRNAs. Probe methylation scores were averaged across triplicates and differential methylation between groups of individuals was determined. Differentially methylated promoter sites of selected genes were validated using pyrosequencing of bisulfite-converted DNA. Results: 9,112 variably methylated probes (from N=223,359 on the microarray) corresponded to 6,176 gene promoters with at least one variable probe. Unsupervised hierarchical clustering of probes obtained from the 500 most variable promoters revealed a cluster enriched with high SEP individuals confirming that SEP differences contribute to overall epigenetic variation. Methylation levels for 1252 gene promoters were associated with childhood SEP vs 545 promoters for adulthood SEP. Functionally, associations with childhood SEP appear in promoters of genes enriched in key cell signalling pathways. The differentially methylated promoters associated with SEP cluster in megabase-sized regions of the genome. Conclusions: Adult blood DNA methylation profiles show more associations with childhood SEP than adult SEP. Organization of these associations across the genome suggests a well-defined epigenetic pattern linked to early socio-economic environment.
2016-05-25 | GSE31713 | GEO
Project description:The MADS genes encode transcription factors (TF) that act as master regulators of plant reproduction and flower development. The SEPALLATA (SEP) MADS subfamily is not only absolutely required for the development of floral organs, but also plays roles in inflorescence architecture and determinacy of the floral meristem. The SEPs act as organizers of MADS complexes and are able to form both heterodimers and heterotetramers in vitro. To date, the MADS TF complexes characterized in angiosperm floral organ development contain at least one SEP TF. Whether DNA-binding by SEP-containing dimeric MADS complexes are sufficient for launching floral organ identity programs, however, is not clear as only defects in floral meristem determinacy were observed in tetramerization impaired SEP mutants. Here we used a combination of genome-wide binding studies, high resolution structural studies of the SEP3-AGAMOUS tetramerisation domain, structure-based mutagenesis and complementation experiments in sep1 sep2 sep3 and sep1 sep2 sep3 ag-4 plants transformed with versions of SEP3 encoding tetramerization mutants. We demonstrate that while SEP3 heterodimers are able to bind DNA both in vitro and in vivo and recognize the majority of SEP3 wild type binding sites genome-wide, tetramerisation is not only required for floral meristem determinacy, but also absolutely required for floral organ identity in the second, third and fourth whorls.
2024-04-30 | GSE227012 | GEO
Project description:To explore chorionic gonadotropin (CG)-regulated gene expression in the primate corpus luteum (CL), adult female rhesus macaques were treated with a model of simulated early pregnancy (SEP). Total RNA was isolated from individual CL and hybridized to AffymetrixM-bM-^DM-" GeneChip Rhesus Macaque Genome Arrays The level of 1192 transcripts changed expression > 2-fold (one-way ANOVA, FDR correction; P<0.05) during SEP when compared to Day 10 untreated controls, and the majority of changes occurred between Days 10 and 12 of SEP. To compare transcript levels between SEP rescued and regressing CL, previously banked rhesus GeneChip array data from the mid- to late and very late luteal phase were analyzed with time-matched intervals in SEP. Comparing RMA-normalized transcripts from the natural cycle with those from luteal rescue revealed 7677 transcripts changing in expression pattern >2 fold (one-way ANOVA, FDR correction; P<0.05) between the two groups. Clustering of samples revealed that the SEP samples possessed the most related transcript expression profiles. Regressed CL (days 18-19, around menses) were the most unlike all other CL. The most affected KEGG pathway was Steroid Biosynthesis, and most significantly absent pathways following SEP treatment includes groups of genes whose products promote cell-death. By further comparing the genome-wide changes in luteal gene expression during rescue in SEP, with those in CL during luteolysis in the natural menstrual cycle, it is possible to identify key regulatory pathways promoting fertility. Simulated early pregnancy (SEP) treatment was begun on day 9 as Duffy and Stouffer (1997) by treatment of females with recombinant human chorionic gonadotropin (hCG; NovarelM-bM-^DM-", Ferring Pharmaceuticals Inc. Parsippany, NJ, USA) in increasing dosages (15, 30,45,90,180,360,720,1440, and 2880 IU) twice daily by intramuscular injection. CL were collected by laparotomy on days 10, 12, 15, and 18, representing 1, 3, 6 and 9 days of hCG treatment (n=4 CL/day). Additionally, luteal day 10 untreated CL were collected to serve as baseline controls for SEP CL. All CL were dissected away from luteal tissue, sectioned, and snap-frozen in liquid nitrogen and stored at -80M-BM-0C until RNA and protein isolation by TRIzolM-BM-. extraction (Invitrogen, Carlsbad, CA, USA) according to manufacturerM-bM-^@M-^Ys protocols.
2011-11-21 | E-GEOD-25335 | biostudies-arrayexpress
Project description:In order to detect the molecular mechanism of seprase involved in tumor metastasis, a comparison of gene expression pattern was made between two groups of human melanoma LOX cell sublines, one is transfected with mock vector expressing GFP only (GUS-1<GSM30738>, GUS-2<GSM30729> and GUS-3<GSM30730>) and the other with pGUS expressing GFP and siRNA targeting mRNA of seprase/FAP alpha (sep-1<GSM30731>, sep-2<GSM30732> and sep-3<GSM30740>).
2008-10-25 | E-GEOD-1773 | biostudies-arrayexpress
Project description:To explore chorionic gonadotropin (CG)-regulated gene expression in the primate corpus luteum (CL), adult female rhesus macaques were treated with a model of simulated early pregnancy (SEP). Total RNA was isolated from individual CL and hybridized to Affymetrix™ GeneChip Rhesus Macaque Genome Arrays The level of 1192 transcripts changed expression > 2-fold (one-way ANOVA, FDR correction; P<0.05) during SEP when compared to Day 10 untreated controls, and the majority of changes occurred between Days 10 and 12 of SEP. To compare transcript levels between SEP rescued and regressing CL, previously banked rhesus GeneChip array data from the mid- to late and very late luteal phase were analyzed with time-matched intervals in SEP. Comparing RMA-normalized transcripts from the natural cycle with those from luteal rescue revealed 7677 transcripts changing in expression pattern >2 fold (one-way ANOVA, FDR correction; P<0.05) between the two groups. Clustering of samples revealed that the SEP samples possessed the most related transcript expression profiles. Regressed CL (days 18-19, around menses) were the most unlike all other CL. The most affected KEGG pathway was Steroid Biosynthesis, and most significantly absent pathways following SEP treatment includes groups of genes whose products promote cell-death. By further comparing the genome-wide changes in luteal gene expression during rescue in SEP, with those in CL during luteolysis in the natural menstrual cycle, it is possible to identify key regulatory pathways promoting fertility.
2011-11-21 | GSE25335 | GEO
Project description:In order to detect the molecular mechanism of seprase involved in tumor metastasis, a comparison of gene expression pattern was made between two groups of human melanoma LOX cell sublines, one is transfected with mock vector expressing GFP only (GUS-1<GSM30738>, GUS-2<GSM30729> and GUS-3<GSM30730>) and the other with pGUS expressing GFP and siRNA targeting mRNA of seprase/FAP alpha (sep-1<GSM30731>, sep-2<GSM30732> and sep-3<GSM30740>). Keywords: other
2008-09-01 | GSE1773 | GEO
Project description:Short open reading frame-encoded peptides (SEP) have been identified across all domains of life and are predicted to be involved in many biochemical processes, however, for the vast majority of SEP their biological function is still unknown. Special methodologies have to be used for the mass spectrometric analysis of SEP, because traditional methods of bottom-up proteomics show a bias against small proteins. Here, we investigated the influence of different staining methods for SDS-PAGE gels prior in-gel digestion following LC-MS/MS analysis for the identification of SEP in the archaeon Methanosarcina mazei. In total, we identified 82 SEP with at least one high confidence (FDR<1 %) unique peptide, of which 45 also met a stricter ion series-based quality criteria. The staining methods provided complementary data that allowed for a range of different SEP to be identified. The highest number of SEP were identified in the samples stained with Coomassie brilliant blue. However, the highest quality of the identified SEP was achieved in the samples without staining. These data demonstrate that in-gel digestion is amenable and well suited for the identification of SEP, and that this classical technique may provide further insights into the world of SEP.
2023-07-06 | PXD018269 | Pride
Project description:HcpR has been shown to be required for growth of Porphyromonas gingivalis in the presence of nitrite (Infect Immun. 2012 Sep;80(9):3319-31. doi: 10.1128/IAI.00561-12. Epub 2012 Jul 9). It also has been shown to regulate the expression of hcp. To define the entire regulon of HcpR RNAseq examination of the wild type and mutant (deficient in HcpR) strains have been used to define the regulon in response to nitrite exposure in bacteria grown in the presence and absence of nitrite. Four biological replicates were prepared for both, wild type and mutant strains grown in the presence and absence of nitrite.
2019-02-14 | GSE117421 | GEO