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

(A) Absolute numbers of BM cells in polyI-polyC–injected control (Fbw7, MxCre) and CKO (Fbw7, MxCre) mice 2 wk after polyI-polyC deletion are shown

(B) Lin BM cells were stained for c-kit and Sca-1 to mark the LSK population (dot plot), and absolute LSK numbers (histogram) were calculated (also at 2 wk after polyI-polyC). (C) Quantitation of peripheral (spleen) LSKs 2 wk after polyI-polyC injection. P < 0.05. (D and E) Absence of enhanced rates of apoptosis as defined by a combination of 7-AAD/annexin V staining in either total BM of LSK cells (3 wk after polyI-polyC injection). (F) LSK cells were analyzed by FACS for CD34 expression to separate long-term (LT, CD34) from short-term (ST, CD34) HSCs. (G) MPs (Lin/Sca-1/c-kit) were analyzed by FACS for CD34 and FcγRII/III expression to show common MPs (CMP, CD34/ FcγRII/III; bottom right gate), granulocyte/macrophage progenitors (GMP, CD34/ FcγRII/III; top right gate), and megakaryocyte/erythroid progenitors (MEP, CD34 / FcγRII/III; bottom left gate). (H) Absolute number of mature (IgM/B220) and immature (IgM/B220) BM B cells are shown (2 wk after polyI-polyC). Error bars show the SD. Numbers indicate the percentage of cells in each gate. *, P < 0.05; **, P < 0.005. For all experiments, = 8.<p><b>Copyright information:</b></p><p>Taken from "Control of hematopoietic stem cell quiescence by the E3 ubiquitin ligase Fbw7"</p><p></p><p>The Journal of Experimental Medicine 2008;205(6):1395-1408.</p><p>Published online 9 Jun 2008</p><p>PMCID:PMC2413036.</p><p></p

(A) Western blot detecting expression of Notch1-IC, uncleaved membrane Notch1 (Notch1-TM), c-Myc, cyclin E, and b-actin in total BM extracts

(B) Expression of c-Myc in cytokine-stimulated BM progenitors. LineageIL-7RαSca-1c-kit cells from control and CKO (Mx-creFbw7) mice were cultured for 48 h in the presence of cytokines. c-Myc expression was quantified using densitometry and actin normalization. Phospho–c-Myc (T58/S62) and actin levels are also shown. A representative of three experiments is shown. (C) Quantitative RT-PCR quantifying expression of Fbw7 and c-Myc in the cells used in B. Expression is normalized using b-actin.<p><b>Copyright information:</b></p><p>Taken from "Control of hematopoietic stem cell quiescence by the E3 ubiquitin ligase Fbw7"</p><p></p><p>The Journal of Experimental Medicine 2008;205(6):1395-1408.</p><p>Published online 9 Jun 2008</p><p>PMCID:PMC2413036.</p><p></p