Project description:RNAseq of CD14 cells from 60 female RA patients activated with LPS for 2 hours. Patients were collected crossectionally from the Rheumatology clinic during 2019-2020. Age md 64, range 23-76 years, Disease duration md 10, range 1-45 years.
Project description:RNAseq of CD4 cells from 60 female RA patients activated with aCD3 for 2 hours. Patients were collected crossectionally from the Rheumatology clinic during 2019-2020. Age md 64, range 23-76 years, Disease duration md 10, range 1-45 years.
Project description:Transcriptome profiling of whole proboscis and body wall of the marine Polychaeta Glycera alba, adults, wild population (sex undiscriminated), collected from the muddy-sandy intertidal flats at W Portugal (2020). Transcriptome profiling of glandular and muscular regions of proboscis of the marine Polychaeta Hediste diversicolor, adults, wild population (sex undiscriminated), collected from the muddy-sandy intertidal flats at W Portugal (2019).
Project description:While DNA methylation is an important gene regulatory mechanism in mammals (Razin and Riggs 1980; Moore, Le, and Fan 2013), its function in arthropods remains poorly understood. Studies in eusocial insects have argued for its role in caste development by regulating gene expression and splicing (Elango et al. 2009; Lyko et al. 2010; Bonasio et al. 2012; Flores et al. 2012; Foret et al. 2012; Li-Byarlay et al. 2013; Marshall, Lonsdale, and Mallon 2019; Shi et al. 2013)(Alvarado et al. 2015; Kucharski et al. 2008). However, such findings are not always consistent across studies, and have therefore remained controversial (Arsenault, Hunt, and Rehan 2018; Cardoso-Junior et al. 2021; Harris et al. 2019; Herb et al. 2012; Libbrecht et al. 2016; Oldroyd and Yagound 2021b; Patalano et al. 2015). Here we use CRISPR/Cas9 to mutate the maintenance DNA methyltransferase DNMT1 in the clonal raider ant, Ooceraea biroi. Mutants have greatly reduced DNA methylation but no obvious developmental phenotypes, demonstrating that, unlike mammals (Brown and Robertson 2007; En Li, Bestor, and Jaenisch 1992; Jackson-Grusby et al. 2001; Panning and Jaenisch 1996), ants can undergo normal development without DNMT1 or DNA methylation. Additionally, we find no evidence of DNA methylation regulating caste development. However, mutants are sterile, while in wildtypes, DNMT1 is localized to the ovaries and maternally provisioned into nascent oocytes. This supports the idea that DNMT1 plays a crucial but unknown role in the insect germline (Amukamara et al. 2020; Arsala et al. 2021; Bewick et al. 2019; Schulz et al. 2018; Ventós-Alfonso et al. 2020; Washington et al. 2020).
Project description:About 500 forelimbs were isolated at 10.5 days post coitum, and ChIP-seq was performed using anti-BCL9 (Abcam, ab37305) and anti-TBX3 (Santacruz, sc17871) antibodies. BCL9 is a beta-catenin transcriptional cofactor involved in the transcriptional machinery of Wnt target genes. TBX3 is a transcription factor important in limb development. This experiment identified, in this developmental context, co-occupancy of BCL9 and TBX3 on a genome-wide scale, and at Wnt-related loci, suggesting co-operation between these transcription factors in Wnt-driven limb development (Zimmerli et al. in revision during spring 2020). The following files are available for this experiment: - Raw sequencing data (.fastq) - Genomic enrichment data in bedgraph format (.bdg) which can be used for visualization in a genome browser. - Annotated peak files (.txt) containing high confidence peaks with genomic annotation. NOTE: The raw data relative to the BCL9 ChIP were previously deposited under accession number E-MTAB-7652, and described in Salazar et al. 2019. For simplicity, and to allow easy retrieval, we add the raw data of the entire experiment (including also BCL9) along with the newly generated analyses.
Project description:In the grips of the 2019-2020 SARS-CoV-2 pandemic, the pathogenisis of the virus has been shown to induce sharp responses from the immune system of infected hosts and can result in severe/fatal pulmonary distress. To understand how the virus can provoke such responses in infected hosts we infected golden hamsters with validated SARS-CoV-2 clinical isolates from 5 patients to understand the dynamic changes and functionality of induced gene expression.