Project description:RCH-ACV cells was depleted for SETDB2 by shRNA lentivirus construct co-expressing mCherry fluorescent. After sorting of mCherry positive cells, the cells were cultured and expanded and total RNA was extracted for Microarray experiment.
Project description:Study of BLaER1 cell line epigenetic changes induced throughout transdifferentiation. The Illumina Infinium MethylationEPIC Beadchip was used to obtain genomewide methylation profiles of BLaER1 cells at 7 different times throughout transdifferentiation treatment (0h, 3h, 12h, 24h, 48h, 72h and 168h). As a reference, the parental RCH-ACV cell line at 168h of treatment and anonymous donor blood derived macrophages were also profiled.
Project description:The NSD2 p.E1099K (EK) mutation has been shown to be enriched in patients with relapsed ALL indicating a role in clonal evolution and drug resistance. We previously demonstrated that the impact of EK is highly cell context dependent. To uncover 3D chromatin architecture-related mechanisms underlying drug resistance, we performed Hi-C on three B-ALL cell lines heterozygous for NSD2 EK (RS4;11, RCH-ACV, SEM) and assessed changes upon knockdown.
Project description:REST is a master regulator of genes that are involved in the acqusition of neuronal fate. The role of REST is not well understood so we attempted to investigate the role of REST in the development of neural cells by analysing the genes that are upregulated when REST is knocked down via shRNA We used microarrays to assess the genes which were up and down regulated after REST is knocked down E12.5 NSP cells were infected with either control or REST shRNA expressing lentiviruses and collected after 6 days for RNA extraction
Project description:BLaER1 is a human B cell precursor leukemia cell line derived from the RCH-ACV cells. These cells are stably infected with a construct that overexpresses the transcription factor C/EBPa fused with the estrogen receptor hormone binding domain (ER) and GFP. Upon induction with beta-estradiol, C/EBP is internalized into the nucleus, promoting massive transcriptional changes and inducing the transdifferentiation of these pre-B cells into functional macrophages. This process, that lasts 7 days, can be monitored by the detection of specific B cell and macrophage surface markers by flow cytometry. With the goal of understanding the interplay between chromatin and transcription, we have generated transcriptomic data by RNA-Seq in twelve time points along the transdifferentiation process, in two biological replicates.