Loss of affects gene expression profile in a genome-wide manner in ES cells and liver cells-0

<p><b>Copyright information:</b></p><p>Taken from "Loss of affects gene expression profile in a genome-wide manner in ES cells and liver cells"</p><p>http://www.biomedcentral.com/1471-2164/8/227</p><p>BMC Genomics 2007;8():227-227.</p><p>Published online 10 Jul 2007</p><p>PMCID:PMC1959195.</p><p></p>nes (A) & (B). Horizontal and vertical axes represent expression levels normalized for an individual gene. Each point represents normalized expression data for an individual gene. The genes that showed standard deviation greater than 2.0 in the normalized data of both genotypes (A) were excluded and gene lists were constructed with < 0.05 (B). Fig. 1D–F in the original article [1] remains unchanged and is presented as (C) – (E), respectively

Loss of affects gene expression profile in a genome-wide manner in ES cells and liver cells-1

<p><b>Copyright information:</b></p><p>Taken from "Loss of affects gene expression profile in a genome-wide manner in ES cells and liver cells"</p><p>http://www.biomedcentral.com/1471-2164/8/227</p><p>BMC Genomics 2007;8():227-227.</p><p>Published online 10 Jul 2007</p><p>PMCID:PMC1959195.</p><p></p>gene lists containing the genes that showed a difference at < 0.05 in ES cells. Each heatmap is constructed using GeneSpring GX ver. 7.3.1. Numbers of genes down-(C) or up-(D) regulated in common between ES cells and livers. The numbers of the genes are indicated in Venn diagrams. These genes showed the difference with at least 2-fold between and (< 0.05). Fig. 2B in the original article [1] remains unchanged and is presented as (B). Fig. 2D & F in the original article [1] are removed and Fig. 2C & E were corrected in the original article [1] and are presented as (C) and (D)

Upstream regulator analysis of differentially expressed transcripts between mESC-derived Hb9 control and A2 SMA MNs.

<p>IPA of significantly modified upstream (<b>A</b>) transcriptional regulator, (<b>B</b>) endogenous signaling and (<b>C</b>) drug pathways in upregulated or downregulated transcripts in A2 SMA MNs compared to Hb9 control MNs. Significant upstream regulators were identified as those having an activation z-score greater than or equal to 2.0 for activated regulators or less than or equal to −2.0 for inhibited regulators.</p

Validation of differentially expressed transcripts determined by RNA-Seq using qRT-PCR.

<p>The levels of <i>Crabp1</i>, <i>Crabp2</i>, <i>Isl1</i>, <i>Nkx2.2</i>, <i>Pla2g1b</i>, <i>Smn1</i> and <i>Vim</i> transcripts were measured in total RNAs from control and SMA mESC-derived MNs. (<b>A</b>) The magnitude of change (log₂(fold change)) of selected transcripts in A2 SMA MNs relative to Hb9 control MNs (n = 3/genotype) as determined by RNA-Seq (black bars) or qRT-PCR (grey bars). (<b>B</b>) The magnitude of change of selected transcripts in HB9:eGFP-labeled (black bars) or unlabeled (grey bars) SMA MNs (A2 and E2 cells, respectively) relative to control MNs (Hb9 and C4 cells, respectively; n = 3/genotype).</p

Loss of affects gene expression profile in a genome-wide manner in ES cells and liver cells-3

<p><b>Copyright information:</b></p><p>Taken from "Loss of affects gene expression profile in a genome-wide manner in ES cells and liver cells"</p><p>http://www.biomedcentral.com/1471-2164/8/227</p><p>BMC Genomics 2007;8():227-227.</p><p>Published online 10 Jul 2007</p><p>PMCID:PMC1959195.</p><p></p>gene lists containing the genes that showed a difference at < 0.05 in ES cells. Each heatmap is constructed using GeneSpring GX ver. 7.3.1. Numbers of genes down-(C) or up-(D) regulated in common between ES cells and livers. The numbers of the genes are indicated in Venn diagrams. These genes showed the difference with at least 2-fold between and (< 0.05). Fig. 2B in the original article [1] remains unchanged and is presented as (B). Fig. 2D & F in the original article [1] are removed and Fig. 2C & E were corrected in the original article [1] and are presented as (C) and (D)

Sequences of primers used for qRT-PCR.

<p>Sequences of primers used for qRT-PCR.</p

Relationship between changes in mRNA levels measured by RNA-Seq and protein levels measured by 2D-DIGE or immunoblot (*) of selected genes in normal versus SMA mESC-derived motor neurons.

<p>The protein expression data is taken from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106818#pone.0106818-Wu1" target="_blank">[46]</a>.</p><p>Relationship between changes in mRNA levels measured by RNA-Seq and protein levels measured by 2D-DIGE or immunoblot (*) of selected genes in normal versus SMA mESC-derived motor neurons.</p

Gene network analysis of differentially expressed transcripts between mESC-derived Hb9 control and A2 SMA MNs.

<p>Ingenuity Pathways Analysis (IPA) of biological functions for transcripts (<b>A</b>) upregulated or (<b>B</b>) downregulated in A2 SMA MNs compared to Hb9 control MNs. IPA of canonical pathways for transcripts (<b>C</b>) upregulated or (<b>D</b>) downregulated in A2 SMA MNs compared to Hb9 control MNs. IPA was performed on upregulated or downregulated transcripts with at least a 2-fold change and a p value less than or equal to 0.05. The top 7 canonical pathways or biological functions were shown in the bar graphs. The top canonical pathway for (<b>E</b>) upregulated (Transcriptional Networks in ESCs) or (<b>F</b>) downregulated (Notch Signaling) transcripts in A2 SMA MNs compared to Hb9 control MNs. Downregulated transcripts are green while the upregulated transcripts are red.</p

Loss of affects gene expression profile in a genome-wide manner in ES cells and liver cells-2

<p><b>Copyright information:</b></p><p>Taken from "Loss of affects gene expression profile in a genome-wide manner in ES cells and liver cells"</p><p>http://www.biomedcentral.com/1471-2164/8/227</p><p>BMC Genomics 2007;8():227-227.</p><p>Published online 10 Jul 2007</p><p>PMCID:PMC1959195.</p><p></p>nes (A) & (B). Horizontal and vertical axes represent expression levels normalized for an individual gene. Each point represents normalized expression data for an individual gene. The genes that showed standard deviation greater than 2.0 in the normalized data of both genotypes (A) were excluded and gene lists were constructed with < 0.05 (B). Fig. 1D–F in the original article [1] remains unchanged and is presented as (C) – (E), respectively

RNA-Seq-identified differentially expressed transcripts between mESC-derived Hb9 control and A2 SMA MNs.

<p>(<b>A</b>) Flowchart outlining the analysis of RNA sequencing data. The programs used for each step are shown to the right of the flowchart. (<b>B</b>) Area plot showing the distributions of FPKM values of significant transcripts in Hb9 control (blue) and A2 SMA (orange) MNs. (<b>C</b>) A volcano plot showing the log2-fold difference of statistically significant (p = 0.05) transcripts (shown in blue) between Hb9 control and A2 SMA MNs.</p