Pathways significantly represented in oocyte and blastocyst samples with similar molecular signatures.

<p>Listed entries represent transcripts and their respective NCBI accession numbers common to oocyte 1 and 2 relative to oocyte 3 and blastocyst 1 and 2 relative to blastocyst 3. “−” denotes no significantly expressed components were detected in the pathway.</p

Scattergraph plots comparing gene expression of individual human oocytes, 4-cell embryos and blastocysts.

<p>Each of three individual samples at each stage is compared to each of the others. Red dots represent transcripts called Present in both samples, yellow dots represent transcripts absent in both samples and blue dots represent transcripts Present in one sample and not the other. The innermost oblique lines represent 2-fold differentially expressed transcripts. Additional pairs of lines represent transcripts expressed at 5, 10- and 20-fold, respectively. As expected, fewer genes were called Present at the 4-cell stage which reflects the degradation of polyA containing maternal transcripts by the 4-cell stage during EGA.</p

Pathways significantly represented in all oocytes and blastocysts.

<p>Listed entries represent transcripts and their respective NCBI accession numbers that were significantly expressed (P<0.05; q≤0.22) in the appropriate sample(s). “-“ denotes no significantly expressed components were detected in the pathway.</p

Heatmap cluster analysis of individual oocyte and blastocyst gene expression profiles.

<p>Hierarchical clustering was used to compare the gene expression profiles of individual oocytes and blastocysts, with highly expressed genes shown in red, weakly expressed in green. Oocytes show clearly distinct profiles from blastocysts, with oocytes 1 and 2 more similar to each other than to oocyte 3, and blastocyst 1 and 2 more similar to each other than to blastocyst 3. 4-cell embryos were omitted from this analysis based on the low abundance of expressed transcripts.</p

Additional file 1: of Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples

Figure S1. Laser microdissection of FFPE PSCC and ISCC. (DOC 2651 kb

Control of BIRC3 gene expression by GR in ALL.

<p>(A) mRNA expression of BIRC3 in ALL cells treated with Dex, Etop and CM. (B) ChIP analysis was carried out in CEM-C1-15 and (C) CEM-C7-14 cells treated with 1μM Dex for 24hrs. Occupancy on one of the GREs by total GR, and GR phosphorylated on S211 and S226 was analysed. The data is representative of at least three independent experiments. Error bars represent SEM. P-value of less than or equal to 0.05 is indicated by *.</p

Differential recruitment of GR and its phosphoisoforms on the RIPK1 and BECN1 promoters.

<p>Chromatin immuniprecipitation (ChIP) analysis was carried out in CEM-C1-15 and CEM-C7-14 cells treated with 1μM Dex for 24hrs. We identified potential GR binding sites on the (A) RIPK1 and (B) BECN1 promoters and analysed total GR, and GR phosphorylated on S211 and S226 on a subset of sites. The data is representative of at least three independent experiments. Error bars represent SEM. P-value of less than or equal to 0.05 is indicated by *.</p

Microenvironment and chemotherapy effects on ALL cell fate.

<p>(A) Cells were treated with CM (48 hours), 1μM Dex (36 hours) and 10μM Etop (24 hours) in varying combinations. Percentage of cell death was obtained using FACS analysis of PI-stained CEM-C1-15 and CEM-C7-14 cells treated as above. SubG1 phase is shown. (B) Caspase-8 activity was measured in ALL CEM-C7-14 and CEM-C1-15 cells treated as indicated. CEM-C1-15 cells are represented by dark grey bars, CEM-C7-14 by light grey bars. (C) RIPK1 high molecular weight forms were analysed in cells treated with CM and BIRC3 inhibitor AT406 (10μM for 48 hours). Western blot analysis was carried out as described above. The data is representative of at least three independent experiments. Error bars represent SEM. P-value of less than or equal to 0.05 is indicated by *.</p

RIPK1, BECN1 and Caspase-3 protein levels in ALL cells.

<p>(A) CEM-C7-14 and CEM-C1-15 cells were grown in the absence and presence of CM or standard RPMI media for 48h and treated with Dex (1μM) and Etop (10μM) individually or in combination for 24h. Cells were lysed and analysed by SDS PAGE followed by western blot. Blots were probed with antibodies specific for RIPK1, BECN1 and cleaved caspase 3. Actin was used as a loading control. Western blots (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178606#pone.0178606.g002" target="_blank">Fig 2A</a> and data not shown) were densitometrically scanned, normalised to actin and presented as bar charts. (B) RIPK1 protein expression; (C) BECN1 protein expression. The data is representative of at least three independent experiments. Error bars represent SEM. P-value of less than or equal to 0.05 is indicated by *. C is control; CM is conditioned media; D is Dex; DCM is Dex and CM; E is Etop; ECM is Etop and CM; DE is Dex and Etop; DECM is Dex, Etop and CM.</p

Clusters, profiles, and GO groupings of CEM-C7-14 cells.

<p>CEM-C7-14 cells were grown in the absence and presence of CM or standard RPMI media for 48h and treated with Dex (1μM) and Etop (10μM) individually or in combination for 24h. Cells were treated with vehicle (1), CM (2), Dex (3), Etop (4), Dex and Etop (5) or Dex, Etop and CM (6). Identified genes were assigned to one of eight distinct clusters using k-means clustering algorithms. On the left, the data for each cluster are represented as a profile of the z-transformed, log₂ values for the mean of each experimental group/condition. The most significantly overrepresented GO terms are shown for the genes within each cluster.</p