Project description:Small RNA-Seq analysis of on stool samples from an Italian cohort of 120 healthy individuals with three dietary habits. The cohort includes 72 women and 48 men included an equal proportion of vegetarians, vegans and omnivores.
Project description:Small RNA-Seq analysis of circulating small RNAs performed on plasma samples from an Italian cohort of 120 healthy individuals with three dietary habits. The cohort includes 72 women and 48 men included an equal proportion of vegetarians, vegans and omnivores.
Project description:CTCF ChIP-seq of 39 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011059 (dataset).
Project description:We performed single-nucleus RNA-sequencing on visceral adipose tissue biopsies from 11 Italian donors from the Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA) cohort.
Project description:We performed single-nucleus RNA-sequencing on visceral adipose tissue (VAT) biopsies from 63 Italian donors from the Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA) cohort.
Project description:H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011060 (dataset).
Project description:Embryonic genome activation (EGA) marks the onset of embryonic program and enables the transition toward the first lineage specification. However, the molecular features of EGA and the transcription factors (TFs) orchestrating this process remain unclear. Here, by performing single-cell RNA-seq on bovine embryos, we reveal that major EGA is asynchronously initiated among blastomeres at the 8-cell stage. Integrative analyses reveal distinctive protein accumulation compared to transcription and translation activation during bovine EGA. Furthermore, we investigate the role of SP1, a TF activated at the minor EGA stage, with motifs enriched in accessible chromatin during major EGA stage in bovine and human embryos. SP1 deficiency leads to morula arrest in bovine and impairs EGA in human embryos. Multi-omics analysis demonstrates that SP1 promotes early lineage gene expression by modulating nearby chromatin states in bovine and directly targets key EGA genes in human embryos. Together, our study delineates the dynamics of bovine EGA and uncovers the conserved and species-specific roles of SP1 in regulating EGA and early development in mammals.
Project description:<p>A Genome-wide association study of primary biliary cirrhosis (PBC) with an Italian cohort and loci meeting suggestive criteria were confirmed using a replication dataset from a previous Canadian study. The results confirmed associations for IL12A, IL12RB2, and HLA (peak between DQA1 and DQB1) and identified novel associations with IKZF3/ORMDL3 on chromosome 17, SPIB on chromosome 19, and IRF5 on chromosome. These studies also provided definition of haplotypic associations, differences between the PBC associated chromosome 17 haplotype and that of pediatric asthma and suggested several other genes as candidates for PBC susceptibility including DENND1B.</p>
Project description:We performed a whole-genome DNA methylation analysis using EPIC Illumina BeadArrays on a cohort of 187 “Italian” COVID-19 patients (123 mild and 64 severe) to identify epigenetic markers underlying the worst evolution of the disease (death or Intensive Care Unit admission for mechanical ventilation support).
