Project description:We report the first use of genome-edited human kidney organoids, combined with single-cell transcriptomics, to study APOL1 risk variants at the native genomic locus in different nephron cell types. This approach captures interferon-mediated induction of APOL1 gene expression and cellular dedifferentiation with a secondary insult“second hit” of endoplasmic reticulum stress.
Project description:We have found that MtFTb genes play a role in the response to LD conditions, both under vernalized and non-vernalized conditions. To explore the regulatory gene network downstream of FTb genes on a global scale, we performed RNA sequencing of the gene-edited Mtftb1/b2 vs WT plants. For this, we grew wild-type and gene-edited Mtftb1/2 plants under two different conditions: vernalised long days (VLD), where the plants were vernalized for 14 days and then grown for two weeks under LD photoperiod, with the aim of capture changes in expression profiles in the period in which the plant becomes physiologically committed to flower; the second condition was non-vernalised long days (NVLD), where non-vernalized plants were grown for 60 days, a crucial time point when wild-type plants typically undergo the transition to flowering. This approach allowed us to investigate the gene expression changes in the FTb1/2 mutant independent of vernalization effects.
Project description:We report here NGS RNA-seqencing datasets with wild-type (Chiifu) and GI-edited Chinese cabbage (named gi/CRISPR) grown under optimal temperature (22℃) or treated with high-temperature (37°C for 1 h). Through these RNA-seq analyses, we found differential expression of genes involved in elongated growth between Chiifu and gi/CRISPR plants.
Project description:Oocytes, the irreplaceable gametes for generating a new organism, are matured in the ovary of living female animals. It is unknown whether any genetic manipulations can be applied to oocytes inside the living ovaries. As a proof-of-concept, we here demonstrate genetic amendments of zebrafish immature oocytes within the ovary. Oocyte microinjection in situ (OMIS) stimulates tissue repair responses, but some of microinjected immature oocytes are matured, ovulated and fertilizable. By OMIS-mediated Cas9 approach, ntla and gata5 loci of oocytes arrested at prophase I of meiosis are successfully edited before fertilization. Through OMIS, high efficiency of biallelic mutations in single or multiple loci using Cas9/gRNAs allows immediate manifestation of mutant phenotypes in F0 embryos and multiple transgenes can co-express the reporters in F0 embryos with patterns similar to germline transgenic embryos. Our approach opens a door to efficient modification of the genome and provides a possibility to repair defective oocytes in situ.
Project description:SNV microarray data from eleven family members in a family with high rates of cardiomyopathy Source name refers to patient position in pedigree from "Genome-edited cardiac models reveal combinatorial genetic interactions in human cardiomyopathy" by Deacon et al
Project description:Acute lymphoblastic leukemia harboring the fusion genes involving the MEF2D transcription factor (MEF2D-ALL) is associated with poor clinical outcomes. To explore binding sites in the genome in MEF2D-ALL, we genome-edited a MEF2D-ALL cell line Kasumi-7 so that the fusion is tagged with HA at the carboxyl-terminal and co-expressed with GFP. We used this cell line for ChIP-seq using anti-HA antibody. Pair-end reads for Input and HA ChIP DNA are provided.
Project description:Wild-type (WT) miR-378a-3p or edited miR-378a-3p were expressed in SB2 KD-ADAR1 cells to identify the genes regulated by edited miR-378a-3p vs WT miR-378a-3p. PARVA was one of the genes identified to be regulated by edited miR-378a-3p. We demonstrate that this regulation of PARVA is lost in highly metastatic melanoma cells. Microarray analysis was used to evaluate the robustness and reproducibility of the method used to generate the ex vivo tumor tissue model and confirm its ability to recapitulate the essential features of the original tumor.
Project description:Gene editing using engineered nucleases frequently produces unintended genetic lesions in hematopoietic stem cells (HSCs). Gene-edited HSC cultures thus contain heterogenous populations, the majority of which either do not carry the desired edit or harbor unwanted mutations. In consequence, transplanting edited HSCs carries the risks of suboptimal efficiency and of unwanted mutations in the graft. Here, we present an approach for expanding gene-edited HSCs at clonal density, allowing for genetic profiling of individual clones before transplantation. We achieved this by developing a defined, polymer-based expansion system and identifying long-term expanding clones within the CD201+CD150+CD48-c-Kit+Sca-1+Lin-(KSL) population of pre-cultured HSCs. This dataset compares the gene expression in three different populations: (1) CD201+CD150+CD48-KSL (2) CD201+CD150+CD48+KSL and (3) CD201-KSL cells.
