Project description:Considerable effort has been devoted to refining experimental protocols having reduced levels of technical variability and artifacts in single-cell RNA-sequencing data (scRNA-seq). We here present evidence that equalizing the concentration of cDNA libraries prior to pooling, a step not consistently performed in single-cell experiments, improves gene detection rates, enhances biological signals, and reduces technical artifacts in scRNA-seq data. In this submission the original single-cell cDNA is from GSE75748 cells labelled EC2 and TB2 in which the cDNA was not equalized prior to library preparation. We performed a set of experiments with the equalization step and provide three count matrices - 1) EQ (equalized cDNA prior to pooling in equal amounts); 2) EQ Vary (same as EQ but pooled at unequal amounts); 3) EQ-75% (equalized cDNA and pooled equally, sequeced to lower total depth).
Project description:We used microarrays to detail the global transcriptional response mediated by ERalpha or ERbeta to the phytoestrogen genistein in the MCF-7 human breast cancer cell model. Experiment Overall Design: MCF-7 human breast cancer cells expressing endogenouse Estrogen Receptor Alpha (ERalpha) were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 20. Cells were then treated with either vehicle control (veh), 6nM 17beta-estradiol (E2), 6nM genistein (LG), 300nM genistein (HG), 300nM S-Equol (EQ), HG+3uM ICI182,780 (IG), EQ+3uM ICI 182,780(IE) for a additional periods of 4h or 24hr before RNA extraction and hybridization on Affymetrix microarrays. We sought to determine if genistein and S-Equol, phytoestrogens selective for the ERbeta can elicit transcriptional response distinctive from those mediated by the ERalpha.
Project description:Sister chromatid cohesion conferred by entrapment of sister DNAs within a tripartite ring formed between cohesinâs Scc1, Smc1, and Smc3 subunits is generated during S and eventually destroyed at anaphase through cleavage of Scc1 by separase. Throughout the cell cycle, cohesinâs association with chromosomes is controlled by opposing activities: loading by the Scc2/4 complex and release by a separase independent releasing activity. Co-entrapment of sister DNAs during replication is accompanied by acetylation of Smc3 by Eco1, which blocks releasing activity and ensures that sisters remain stably connected. Because fusion of Smc3 to Scc1 prevents release and bypasses the requirement for Eco1, we suggested that release is mediated by disengagement of the Smc3/Scc1 interface. We now show that all mutations capable of bypassing Eco1, be they in cohesinâs Smc1, Smc3, Scc1,Wapl, Pds5, or Scc3 subunits, greatly reduce dissociation of N-terminal cleavage fragments of Scc1 (NScc1) from Smc3. We show that this process involves interaction between Smc ATPase heads and is inhibited by Smc3 acetylation Effect of mutations QQ and EQ in Smc3 on cohesin loading onto chromosomes
Project description:This model is based on the publication:
Coletti R, Leonardelli L, Parolo S, Marchetti L. A QSP model of prostate cancer immunotherapy to identify effective combination therapies. Sci Rep. 2020 Jun 3;10(1):9063. doi: 10.1038/s41598-020-65590-0
Comment:
Eq. 3 - no listed species "R", therefore based on Eq. 1 and 2, R_2 used instead.
Eq. 12 - no listed parameter "a_Df" in Table S1, a_Dc used based on parameter description.
Curation Comment:
Simulations are not reproducing manuscript plots. Matlab code is available (Supplementary File 2 of the manuscript publication) but has not been tested, so would be worth reattempting model curation.
