Additional file 9 of Folate regulates RNA m5C modification and translation in neural stem cells

Additional file 9. Source codes used to generate figures

Additional file 6 of Folate regulates RNA m5C modification and translation in neural stem cells

Additional file 6: Table 5. List of high-confidence m5C sites in mouse NSCs

Additional file 2 of Folate regulates RNA m5C modification and translation in neural stem cells

Additional file 2: Table 1. Library statistics

Additional file 1: of RNA-Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas

Table S1. Demographic characteristics of patients with LSCC involved in this study. Table S2. Individual circRNAs detected in the study (please see the attached excel spreadsheet). Table S3. LSCC specific circRNAs detected in the study (please see the attached excel spreadsheet). Figure S1. The representative images of H&E-stained normal laryngeal mucosal and LSCC specimens. Pictures included well differentiated (upper), moderately differentiated LSCC (middle), and normal tissues (lower). From left to right, image magnifications of 40×, 100×, 200×, and 400 × were displayed (scale bar = 100 μm). Figure S2. Gene Ontology annotation analysis for 20 circRNA interacted miRNA and their target gene related significant enriched biological process, cellular components and molecular function. Figure S3. KEGG analysis showing the map of pathway in LSCC using the dysregulated circRNA-miRNA-target genes. (ZIP 8463 kb

Identification process for eligible studies.

<p>Identification process for eligible studies.</p

Forrest plot of the included studies showing relative risk of Mediterranean diet compared to control diet by various outcome measures (Fixed effects model analysis).

<p>Forrest plot of the included studies showing relative risk of Mediterranean diet compared to control diet by various outcome measures (Fixed effects model analysis).</p

Quality assessment of included studies.

<p>Quality assessment of included studies.</p

Characteristics of the studies included in the systematic review and meta-analysis.

<p>Characteristics of the studies included in the systematic review and meta-analysis.</p

Oxygen consumption rates differentially altered upon drug perturbation in sensitive compared to insensitive cells.

<p>(A) NCI-H358 epithelial and mesenchymal lines or (B) NCI-H1703 (BPTES sensitive) and NCI-H1563 (BPTES insensitive) cells were treated with DMSO or 8 µM BPTES and oxygen consumption rate (OCR) was monitored over a 20 hr treatment. Data normalized to OCR at time zero (100%) and presented as mean values +/−SEM. <i>P</i> = 0.024 comparing changes in oxygen consumption with BPTES in the epithelial vs mesenchymal line; <i>P</i> = 0.00017 comparing NCI-H1703 and NCI-H1563 cells. (C) OCR following treatment with the indicated drugs to perturb mitochondrial respiration. Data normalized to OCR measurement prior to oligomycin treatment. (D) Addition of pyruvate to media restores the impaired FCCP response in the mesenchymal line. Average values +/−SEM indicated. Results representative of 2–3 independent experiments.</p

Association between EMT-related markers and BPTES sensitivity in NSCLC lines.

<p>(A) GeneGo analysis indicating four top-ranking mesenchymal signatures correlating with BPTES sensitivity. P-values are calculated within the GeneGo software using the hypergeometric distribution. (B) Anti-correlation between high E-cadherin low vimentin RNA expression levels and sensitivity to BPTES. (C) Mu/mumax values depicted following 72 hr treatment of NSCLC lines with 10 µM BPTES. Equal protein amounts of tumor cell line extracts were electrophoresed, with the group of more sensitive lines on the left and least sensitive on the right, and immunoblotted for the indicated proteins. Histone H3 was used as a loading control. (D) Quantitation of average GAC protein levels relative to PC protein expression (+/−SEM) in BPTES sensitive (n = 7), intermediate (n = 7), and insensitive (n = 7) lines. <i>P</i> = 0.03 comparing GAC/PC protein levels in sensitive compared to insensitive lines; <i>P</i> = 0.06 comparing sensitive to intermediate groups (unpaired 2-tail t-test).</p