Project description:To determine the transcriptional targets of HNF1A in human kidney cells, we performed chromatin immunoprecipitation sequencing on D28 kidney organoids generated from WT hPSCs using an established protocol by Morizane et al. (2015) doi: 10.1038/nbt.3392. ChIP-Seq analysis revealed that HNF1A preferentially bound onto the promoter regions of various genes that are predominantly expressed in renal proximal epithelial cells. qRT-PCR validation was performed on various human kidney cell models to confirm that HNF1A binds to promoter regions of selected target genes to regulate their gene expression.
Project description:Somatic mutations of 256 whole-genome sequenced colorectal tumors. 234 MSS, 19 MSI and 3 POLE mutants.
See Katainen R. et al. CTCF/cohesin-binding sites are frequently mutated in cancer, Nature Genetics 2015. doi:10.1038/ng.3335
Project description:RT-PCR of platelet-poor plasma samples per Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, et al. Diverse human extracellular RNAs are widely detected in human plasma. Nat Commun 2016; 7. doi:10.1038/ncomms11106
Project description:Here we used human cortical brain organoids to probe the longitudinal impact of GSK3 inhibition through multiple developmental stages. Chronic GSK3 inhibition increased the proliferation of neural progenitors and caused massive derangement of cortical tissue architecture. Cortical organoids were differentiated as previously described (Paşca et al., 2015, doi: 10.1038/nmeth.3415.).Chronic GSK3 inhibition was performed by adding CHIR99021 (Merck SML1046) to the medium at day 0 (1 microM) and kept throughout the differentiation process until reaching the respective collection timepoints (day 18, day 50, day 100).
Project description:Here we used human cortical brain organoids to probe the longitudinal impact of GSK3 inhibition through multiple developmental stages. Chronic GSK3 inhibition increased the proliferation of neural progenitors and caused massive derangement of cortical tissue architecture. Cortical organoids were differentiated as previously described (Paşca et al., 2015, doi: 10.1038/nmeth.3415.). Chronic GSK3 inhibition was performed by adding CHIR99021 (Merck SML1046) to the medium at day 0 (1 microM) and kept throughout the differentiation process until reaching the respective collection timepoints (day 50, day 100).
Project description:Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 129_rnaseq
EAC expression data - Publication Secrier & Li et al., 2016, Nature Genetics
Project description:To examine the cellular heterogeneity in the PF, in mouse, we used droplet-based single cell RNA sequencing technique developed by Klein et al. 2015, Cell 161, 1187–1201. doi:10.1016/j.cell.2015.04.044.