The pandemic dilemma

Pairwise overlaps of TAD boundaries. The pairwise overlaps of TAD boundaries are shown for all samples of this study, after calling boundaries using hicratio (all reads, d = 0500). Before TAD calling, the Hi-C matrices were either unprocessed (filtered) or corrected using iterative correction (IC) (resolution = 40 kb). (PDF 3847 kb

Additional file 3: Table S2. of HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

HiC-bench input-output objects. The table summarizes the inputs and outputs of the TAD-calling task using three different methods with parameter values stored in the params files (column 2). The first column describes the tree structure of the input directories that are essentially the different Hi-C matrices for each sample, before (filtered) and after matrix correction using different methods (e.g., IC). The second column lists all the different parameter scripts and the third column corresponds to the tree structure of the generated output objects. (XLSX 10 kb

El Diario de Pontevedra : periódico liberal: Ano XXVII Número 7776 - 1910 abril 11

Supplementary material 2. (DOCX 128 kb

image_2_The Transcription Factor Zfx Regulates Peripheral T Cell Self-Renewal and Proliferation.jpeg

<p>Peripheral T lymphocytes share many functional properties with hematopoietic stem cells (HSCs), including long-term maintenance, quiescence, and latent proliferative potential. In addition, peripheral T cells retain the capacity for further differentiation into a variety of subsets, much like HSCs. While the similarities between T cells and HSC have long been hypothesized, the potential common genetic regulation of HSCs and T cells has not been widely explored. We have studied the T cell-intrinsic role of Zfx, a transcription factor specifically required for HSC maintenance. We report that T cell-specific deletion of Zfx caused age-dependent depletion of naïve peripheral T cells. Zfx-deficient T cells also failed to undergo homeostatic proliferation in a lymphopenic environment, and showed impaired antigen-specific expansion and memory response. In addition, the invariant natural killer T cell compartment was severely reduced. RNA-Seq analysis revealed that the most dysregulated genes in Zfx-deficient T cells were similar to those observed in Zfx-deficient HSC and B cells. These studies identify Zfx as an important regulator of peripheral T cell maintenance and expansion and highlight the common molecular basis of HSC and lymphocyte homeostasis.</p

image_4_The Transcription Factor Zfx Regulates Peripheral T Cell Self-Renewal and Proliferation.jpeg

<p>Peripheral T lymphocytes share many functional properties with hematopoietic stem cells (HSCs), including long-term maintenance, quiescence, and latent proliferative potential. In addition, peripheral T cells retain the capacity for further differentiation into a variety of subsets, much like HSCs. While the similarities between T cells and HSC have long been hypothesized, the potential common genetic regulation of HSCs and T cells has not been widely explored. We have studied the T cell-intrinsic role of Zfx, a transcription factor specifically required for HSC maintenance. We report that T cell-specific deletion of Zfx caused age-dependent depletion of naïve peripheral T cells. Zfx-deficient T cells also failed to undergo homeostatic proliferation in a lymphopenic environment, and showed impaired antigen-specific expansion and memory response. In addition, the invariant natural killer T cell compartment was severely reduced. RNA-Seq analysis revealed that the most dysregulated genes in Zfx-deficient T cells were similar to those observed in Zfx-deficient HSC and B cells. These studies identify Zfx as an important regulator of peripheral T cell maintenance and expansion and highlight the common molecular basis of HSC and lymphocyte homeostasis.</p

Additional file 2: Table S2. of N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration

Primer sequences used for qRT-PCR, RACE, siRNAs, and vector construction in this study. (XLSX 11 kb