Project description:CD34+ heamatopoietic stem cells were isolated from the bone marrow of two healthy donors undergoing total hip replacement. Promoter capture Hi-C (PCHi-C) was performed on these cells using the protocol according to Mifsud et al. 2015, with the exception that ligation was performed in situ, and a slightly modified bait capture set was used. Bait positions in hg19 are included as an additional file.
Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in a HiC lib
Project description:Chromatin organisation of trophoblast stem cells (TSC) were compared with that of embryonic stem cells (ESC). The method enriches Hi-C libraries, to detect promoter interactions at restriction fragment level. We prepared Hi-C libraries from TSC and ESC (serum grown) samples and enriched them with a promoter capture bait system that captures ~22.000 promoters. Promoter interactions were then analysed using the GOTHiC pipeline.
Project description:In order to investigate the role of CD34 antigen in haematopoietic commitment, we silenced the CD34 gene expression in CD34+ stem/progenitor cells using a siRNA approach. Experiment Overall Design: To maximize siRNA transfection efficiency, we utilized the NucleofectorTM technology (Amaxa). CD34+ cells were transfected with a mixture of 4 siRNAs targeting CD34 mRNA and with a non-targeting siRNA as a negative control. The expression level of CD34 antigen on control cells (MOCK and negative control treated cells) and CD34siRNA treated cells was assessed by immunofluorescence analysis at 24 and 48h post-nucleofection.
Project description:Erythropoiesis from pluripotent stem cells is very complex, and mirrors that observed in developmental erythropoiesis, with primitive and definitive waves. For a better understanding of their potential for their use in blood transfusion, they were compared to erythropoiesis from cord derived CD34 haematopoietic stem cells. We used microarrays to detail the global programme of gene expression underlying different stages of erythropoiesis from each source, pluripotent or haematopoietic stem cells.
Project description:In situ promoter capture Hi-C on multiple myeloma cell line KMS11 in experimental triplicates. Hi-C libraries were prepared as previously described (Rao et al., 2014, http://dx.doi.org/10.1016/j.cell.2014.11.021). Promoter capture was based on 32,313 biotinylated 120-mer RNA baits (Agilent). Hi-C libraries were sequenced using Illumina HiSeq 2000 technology. The files are in FASTQ format.
Project description:In order to investigate the role of CD34 antigen in haematopoietic commitment, we overexpressed the human CD34 cDNA in human CD34+ cells by retroviral gene transfer. Keywords: treatment comparison