Additional file 1 of Gene expression profiling unveils the temporal dynamics of CIGB-300-regulated transcriptome in AML cell lines
Creators: name: Vázquez-Blomquist, Dania
name: Ramón, Ailyn C.
name: Rosales, Mauro
name: Pérez, George V.
name: Rosales, Ailenis
name: Palenzuela, Daniel
name: Perera, Yasser
name: Perea, Silvio E.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Diagnostic plots in control cells or CIGB-300 treated OCI-AML3 (O) and HL-60 (H) samples for 3h and 30min. (A) One dimensional hierarchical clustering of all samples (replicates 1, 2, 3), (B) ANOVA R-squared (^2) of covariates (Cell, Time and Treatment) in % (C), Multidimensional Scaling (MDS) of filtered data. Samples from HL60 (H) and OCI-AML3 (O) Untreated or treated with the peptide CIGB-300 for 30min and 3h are indicated. Figure S2. Top 100 differentially up-regulated genes by CIGB-300. (A) Unsupervised Heatmap from the Top 100 most differentially up-expressed genes in HL-60 and OCI-AML3. (B) Pathways analysis in Top 100 up-regulated genes using Enrichr. Figure S3. Top 100 enriched ontology clusters across AML cell lines treated with CIGB-300 for 30min and 3h using Metascape. The most 100 enriched biological processes (-log10(P)) in HL-60 (H) or OCI-AML3 (OCI) after CIGB-300 treatment for 30min and 3h are shown. Figure S4. MCODE in network using Metascape. MCODE was used to identify neighborhoods where proteins are densely connected in network. Network nodes are displayed as pies, where colors in sectors represent the treatment groups according to the legend at the draw corner for HL-60 (H) and OCI-AML3 (OCI) treated with CIGB-300 for 30min and 3h. Figure S5. Predicted Transcription factors from DEGs. TF predicted from regulatory motifs in DEGs in HL-60 and OCI-AML3 after 30min and 3h of CIGB-300 treatment are shown in both panels of the Figure. The Cytoscape on-net analysis plugin iRegulon was used and a NES&gt;3.0 was selected. Figure S6. qPCR validation of genes related to differentiation modulated by CIGB-300. HL-60 and OCI-AML3 cells were treated with 40 μM of CIGB-300 for 30min and 3h. Histogram bars indicate relative mRNA levels ± standard error with respect to a time-matched untreated control, for two independent experiments analyzed in triplicate. All genes were normalized with ABL1, DDX5, and GAPDH genes. Asterisks represent statistically significant changes (p&lt; 0.05) by REST 2009. Figure S7. qPCR validation of the cell cycle related gene CDKN1A/P21 gene modulated by CIGB-300. HL-60 and OCI-AML3 cells were treated with 40 μM of CIGB-300 for 30min, 2h and 8h. Histogram bars indicate relative mRNA levels ± standard error with respect to a time-matched untreated control, for two independent experiments analyzed in triplicate. All genes were normalized with ABL1, DDX5, and GAPDH genes. Asterisks represent statistically significant changes (p&lt; 0.05) by REST 2009. Table S1. Oligonucleotides used for qPCR amplifications. Information of Gene name, oligonucleotide identifiers (ID), Sequence 5´ to 3´ (Sequence 5’…3’), number of bases (# Bases) and Function (Reference or Biomarker) is provided. All were synthesized in Oligonucleotide Synthesis Group (CIGB, Havana).