Project description:Over recent decades, it has been proposed that DNA interactions between mammalian chromosomes play an important role in the regulation of gene expression and cell fate determination. To study how DNA interactions change between cell types, high throughput chromosome confirmation capture (Hi-C) profiles were collected from CD4+ T cells, CD8+ T cells and B cells from mice.
Project description:Over recent decades, it has been proposed that DNA interactions between mammalian chromosomes play an important role in the regulation of gene expression and cell fate determination. To study how DNA interactions change between cell types, high throughput chromosome confirmation capture (Hi-C) profiles were collected from CD4+ T cells, CD8+ T cells and B cells from human subjects.
Project description:CD4+ T cells and CD8+ T cells were isolated from the peripheral blood of two human donors and were cultured to induce activation. High-throughput chromosome confirmation capture (Hi-C) was used to examine DNA interactions between chromosomes.
Project description:To evaluate the impact of -165-kb Zeb2 enhancer deletion on 3D chromatin structure, we performed in situ Hi-C analysis of WT and Zeb2 –165–/– splenic CD8+ T cells, which showed no significant global changes on the structure of chromosome 2
Project description:We generated an interaction map using capture in situ Hi-C in human iPSC-derived cardiomyocytes Differentiation of cardiomyocytes from iPSC followed by capture in situ Hi-C
Project description:During an immune response, CD8 T cells fall along a gradient of memory potential, but the regulators of these fate decsisions are not well understood. We utlized Id3-GFP and Id2-YFP reporter mice to elucidate the role of Id3 and Id2 during early CD8 T cell differentiation by gene expression. Id3-GFP hi Id2-YFP int or Id3-GFP lo Id2-YFP hi OT-I cells were sorted into trizol at day 6 of VSV-OVA infection and analyzed by microarray
Project description:Naïve CD44-lo/CD62L-hi/CD8+ T cells from C3H.SW mice were compared to CD44-hi/CD82L-lo/CD8+ effector memory T cells and CD44-lo/CD62L-hi/CD8+ postmitotic T cells, using 3 biological replicates of each type of sample. The later two cells types were highly purified at day 14 after transplantation from GVHD B6/SJL mice receiving donor C3H.SW mouse-derived naive CD44-lo/CD62L-hi/CD8+ T cells and T cell-depleted bone marrow. Recipient mice had first been lethally irradiated at a dose of 10Gy in two fractions. This is a MHC-identical minor histocompatibility antigen-mismatched mouse GVHD model of human allogeneic hematopoietic stem cell transplantation. Naive T cell samples were from pools of 2 mice each, while effector memory and postmitotic T cell samples were purified from pools of T cells from 4 mice each. After RNA extraction and cleanup, biotin labeled cRNA was prepared from 600 ng total RNA, using two rounds of in vitro transcription, and hybridized to Affymetrix Mouse Genome 430A 2.0 arrays using standard techniques. Keywords: Cell type comparison 9 samples were analyzed on 9 Affymetrix microarrays to assay mRNA levels. There were 3 biological replicates of each of 3 different cell types.