Additional file 8: Estimation of biological variations

Slides:

Advertisements

Similar presentations

Supplementary Fig. S1: Hierarchical clustering of AUX/IAA genes, showing significant differential expression under at least one abiotic stress condition.

Advertisements

Figure SOM1. Functional roles of the genes affected in zmet2-m1 mutants. Although the genes localized on the intracellular membranes were slightly over-represented.

Cell lineXY11q WM WM793-P WM793-P Lu ABAB WM793:WM793-P2WM793:1205-Lu WM793 WM793:WM793-P1 Supplemental.

Supplemental Figure 1. Levels of nitrate, carbohydrates and metabolites involved in nitrate assimilation, and the medium pH. Starch and the sum of Glucose,

Distinguishing active from non active genes: Main principle: DNA hybridization -DNA hybridizes due to base pairing using H-bonds -A/T and C/G and A/U possible.

Supplementary Figure 1 List of top 50 most abundantly expressed lncRNAs and mRNAs in HP and PFC from RNAseq. Expression abundance of lncRNAs and mRNAs.

Figure S1 P. stipitis TRC1 N. crassa PDR-1 A. niger RhaR

From: Expression of the HSF4 DNA Binding Domain-EGFP Hybrid Gene Recreates Early Childhood Lamellar Cataract in Transgenic Mice Invest. Ophthalmol. Vis.

Figure 1. Gene expression analysis

Figure S2 A B Log2 Fold Change (+/- cAMP) Transcriptome (9hr)

S8 Figure. Expression of genes determined by qPCR matches expression determined from transcriptome assembly. Genes encoding adenylate cyclase, triacylglycerol.

Figure S7: RT-qPCR expression patterns of 11 candidate NTSR contigs

M. Fu, G. Huang, Z. Zhang, J. Liu, Z. Zhang, Z. Huang, B. Yu, F. Meng

Sensitivity of RNA‐seq.

Influence of RNA Labeling on Expression Profiling of MicroRNAs

Volume 11, Issue 11, Pages (June 2015)

Chloroplast Signaling Gates Thermotolerance in Arabidopsis

Regulation of gene expression by FACT.

Figure 4. (A) Scatterplot of RPC4 T statistic (between TP0 and TP36) for the indicated groups of isolated tRNA genes (RPC4 peak only, n = 35; RPC4 + H3K4me3.

Volume 44, Issue 3, Pages (November 2011)

Steven J. Petesch, John T. Lis Cell

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters by Pascal Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke-Andersen,

SAGA Is a General Cofactor for RNA Polymerase II Transcription

Dynamics and variability of SMAD2 signaling in single cells

The ribozyme approach distinguishes RNA-dependent and RNA-independent functions of lincRNA genes. The ribozyme approach distinguishes RNA-dependent and.

Volume 21, Issue 11, Pages (November 2014)

Analysis of total and polysomal RNA clk-1(qm30) and clk-1(qm30)+WT.

Gene-Expression Variation Within and Among Human Populations

Genome-wide expression screen identifies novel hypoxia-regulated genes

Reversing the TERT promoter mutation to WT reverses the active chromatin marks and alters long-range chromatin interactions. Reversing the TERT promoter.

Andrew D. Bosson, Jesse R. Zamudio, Phillip A. Sharp Molecular Cell

Volume 11, Pages (January 2019)

Magnitude of mRNA fold change is best predictor of mRNA-to-protein correlation. Magnitude of mRNA fold change is best predictor of mRNA-to-protein correlation.

Biased Allelic Expression in Human Primary Fibroblast Single Cells

Volume 16, Issue 8, Pages (August 2016)

Volume 7, Issue 9, Pages (September 2014)

The DHX15–CMTR1 interaction inhibits translation of a subset of genes.

Laura S. Bisogno, Matthew B. Friedersdorf, Jack D. Keene

Volume 26, Issue 1, Pages (April 2007)

Volume 16, Issue 4, Pages (November 2004)

Volume 88, Issue 4, Pages (November 2015)

Volume 44, Issue 3, Pages (November 2011)

Volume 9, Issue 5, Pages (November 2017)

Volume 8, Issue 2, Pages (February 2017)

Volume 23, Issue 7, Pages (May 2018)

Volume 11, Issue 11, Pages (June 2015)

Limited transcriptomic changes upon HOTAIR RNA overexpression in MDA‐MB‐231 breast cancer cells Limited transcriptomic changes upon HOTAIR RNA overexpression.

RNA-seq results at the SAM

Xin Xie, Tomas Venit, Nizar Drou, Piergiorgio Percipalle

A multitiered approach to characterize transcriptome structure.

Antisense expression associates with larger gene expression variability. Antisense expression associates with larger gene expression variability. (A–D)

Comparison of N. gonorrhoeae gene expression in infected men in vivo and isolates grown in vitro. Comparison of N. gonorrhoeae gene expression in infected.

Volume 10, Issue 2, Pages (August 2011)

Volume 15, Issue 12, Pages (June 2016)

UPF1 depletion specifically up-regulates components of the PERK/IRE1 ER stress response pathways. UPF1 depletion specifically up-regulates components of.

Differential protein, mRNA, lncRNA and miRNA regulation by p53.

Analyzing Fission Yeast Multidrug Resistance Mechanisms to Develop a Genetically Tractable Model System for Chemical Biology Shigehiro A. Kawashima,

Additional file 4: Comparison of RNA-Seq and RT-qPCR expression analyses of candidate genes between RIL165 and RIL387.

Volume 17, Issue 3, Pages (October 2016)

(A) Western blot probing nuclear extract from wild-type (wt) and the newly generated ACF1 mutant (AcfC) embryos (0–16 h). (A) Western blot probing nuclear.

Validation and pathway enrichment analysis of genes rescued by DM-α-KG treatment of rho0 cells based on microarray experiments. Validation and pathway.

Enrichment of miRNAs among DPAR genes and their relative expression under dietary restriction. Enrichment of miRNAs among DPAR genes and their relative.

RNA Polymerase II Collision Interrupts Convergent Transcription

Fig. 3 The rs risk enhancer is a hub for intrachromosomal and interchromosomal interactions. The rs risk enhancer is a hub for intrachromosomal.

Correlation of miR-21 expression levels with DEGs in 28 bladder cancer cell lines. Correlation of miR-21 expression levels with DEGs in 28 bladder cancer.

Cell Sorting of Induced SE-like Cells Using SEOR1pro:SEOR1-YFP.

SY-1425 induces maturation in RARA-high AML

Differential Expression of RNA-Seq Data

Transcriptomic Analysis of GmSIN1 OE-1 Transgenic Soybean.

Cxxc1-deficient TH17 cells exhibit a Treg cell–like expression profile

Presentation transcript:

Additional file 8: Estimation of biological variations Additional file 8: Estimation of biological variations. The log2 fold changes of expression in Zinc (A) and Cadmium (B) treated cells as compared to the Control TY cells for the Heavy–metal-translocating P-type ATPase encoding gene cadA (MESS2v1_740030), the periplasmic binding protein of the ABC type transporter encoding gene znuC (MESS2v1_300037) and the putative Signal peptidase II encoding gene (MESS2v1_740019) were calculated using the reference genes recA (MESS2v1_330003) and glnA (MESS2v1_390006) for STM 2683. The RNAseq differential expression values are shown as black bars. Blue bars (two independent replicates) show the relative log2 fold changes (Metal / Control) as analyzed by qPCR using pooled RNA samples, and error bars correspond to three technical replicates. The three red bars (three independent replicates) show the relative log2 fold changes (Metal / Control) as analyzed by qPCR using RNA samples corresponding to biological replicates, and error bars correspond to three biological replicates. The scatter plot (C) shows the average log2 fold changes (Metal / Control) from the two replicates on pooled RNA samples (X Axis ) against the mean from three replicates on RNA samples from 3 biological replicates (Y Axis) which was used to calculate the correlation factors (R2) indicated on the graph.