Project description:The present study investigated whether maternal periodontal disease modifies the microRNA expression profile in adult offspring. *************************************************************** This study was supported by the São Paulo Research Foundation (FAPESP) [grant #2019/04183-9; #2022/08872-6; #2023/03786-7; #2023/12488-0; #2023/01400-4] and CNPq [grant 151151/2023-7], São Paulo, SP, Brazil. The grants #2019/04183-9; #2023/12488-0; #2023/01400-4 and 151151/2023-7 were awarded to the author Maria Sara de Lima Coutinho Mattera. The grant #2022/08872-6 was awarded to Heloisa Macedo Sampaio. The grant #2023/03786-7 was awarded to Gabriele Fernandes Baliero. ***************************************************************
Project description:To confirm the loss of transcription factor (TF) occupancy at SNP-containing motifs, we performed ChIP-seq for three TFs in the Bl6xSpret hybrid mESC line. This dataset includes cross-link ChIP-seq data for CTCF, KLF4, and SOX2. Two biological replicates were generated for each TF. The protocol was adapted from Trovato et al. (2024), with minor modifications. Chromatin was sheared using a Bioruptor Pico (Diagenode) and incubated overnight at 4 °C with rotation with antibodies against KLF4 (AF3158, R&D Systems), CTCF (07-729, Merck Millipore), or SOX2 (AF2018, R&D Systems). Bead–immunocomplexes were reverse cross-linked after RNA and protein digestion, and DNA was purified using 1.4x SPRI-select beads. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs) and sequenced on an AVITI platform, using Cloudbreak Low 2x150 bp runs (250 M clusters/run) for H3K27Ac and Cloudbreak High 2x75 bp runs (1000 M clusters/run). AVITI and Illumina adapters were trimmed using TrimGalore! v0.6.7 (Krueger et al., 2023). Trimmed reads were competitively aligned to the Bl6 and Spret genomes and filtered to discard reads with allelic mapping bias using a version of WASP extended to include indels (van de Geijn et al., 2015; Sigalova et al., 2025). Finally, duplicate reads were identified and removed using the Picard tool MarkDuplicates v2.15.0. (https://github.com/Krebslabrep/TF-chromatin.git).
Project description:This SuperSeries is composed of the SubSeries listed below to reproduce the data and analyses from Lareau et al. 2023 Nature Genetics
Project description:We profiled the enrichment of the replicative H3.1 and non-replicative H3.3 histone variants using the SNAP-seq assay previously developed in the team (Gatto et al., 2022, Forest et al., 2023). We used KH2 mouse embryonic stem cells (mESCs) bearing doxycycline-inducible H3.1/H3.3-SNAP, which were expressed at low levels following 48h doxycycline treatment. To understand how the variants are distributed cell types of different potencies, we assayed them in pluripotent mESCs and following a 7-day differentiation into neural precursor cells (NPCs).
Project description:In pancreatic cancer, classical and basal-like subtypes are identified as two major PDAC subtypes. Our previous data showed that PDAC tumor cells can switch between the two phenotypes through transcriptional reprogramming particularly in response to inflammatory cues. In this study, we were trying to understand TNFα mediated transcription regulatory network in pancreatic cancer. Hence, we performed RNA-seq in TNFα treated classical cells as well as aqua dest control.
Project description:The Nucleosome Remodeling and Deacetylase (NuRD) complex is essential for development in complex animals but has been refractory to detailed analysis because of its low abundance and resistance to recombinant production. As part of a larger project, absolute quantification using isotopically-labelled AQUA peptides was performed on natively-purified NuRD and six recombinantly-expressed NuRD subcomplexes. This is the first time the NuRD complex has been quantified using the AQUA strategy.
