Additional file 4 of Characterization of distinct circular RNA signatures in solid tumors
Creators: name: Wang, Chengdi
name: Liu, Wen-Rong
name: Tan, Shuangyan
name: Zhou, Jian-Kang
name: Xu, Xiaomin
name: Ming, Yue
name: Cheng, Jian
name: Li, Jiao
name: Zeng, Zhen
name: Zuo, Yuanli
name: He, Juan
name: Peng, Yong
name: Li, Weimin
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 4: Figure S1. Characterization of protein-coding gene profiles in normal tissues. Figure S2. Bioinformatics validation of tissue-specifically expressed genes using the GTEx dataset. Gene expression was measured in transcripts per million (TPM). Figure S3. The genes with tissue-specific expression patterns were generally enriched in the physiological processes (A) and signaling pathways (B) that were specific to the corresponding tissue. Figure S4. The tissue-specific expression patterns of circRNAs were confirmed by the circAtlas database. Figure S5. The tissue specificity of a subset of circRNAs was governed by their cognate genes. Examples of tissue-specific circRNAs corresponding to their host gene expression. B-D Bioinformatics validation of brain-specifically expressed SLAIN1 using FANTOM5 (B), GTEx (C) and HPA (D) datasets. Figure S6. Brain-specifically expressed hsa_circ_0073539 was regulated by the brain-specific splicing factor QKI. A Brain-specific expression of hsa_circ_0111312 was independent of its host gene (MAN2A1) expression. B The Pearson correlation coefficients between brain-specific hsa_circ_0073539 and the splicing factor QKI. Figure S7. The distribution of uniquely mapped reads (A) and the number of identified upregulated and downregulated circRNAs (B) in each cancer sample. The p-value was calculated using the Wilcoxon rank-sum test, ns denotes no significance, * denotes p &lt; 0.05, ** denotes p &lt; 0.01, *** denotes p &lt; 0.001. Figure S8. Expression patterns of dysregulated circRNAs in cancer. A,B The expression profiles of hsa_circ_0077837 (A) and hsa_circ_0001681 (B) in different cancers. The p-value was calculated using the Wilcoxon rank-sum test, ns denotes no significance, * denotes p &lt; 0.05, ** denotes p &lt; 0.01, *** denotes p &lt; 0.001. Figure S9. Comparison of expression changes between differentially expressed circRNAs and their parental genes among different cancers. Based on circRNA fold-change versus its linear transcript fold-change, circRNAs were divided into four groups. Figure S10. Aberrant expression of circRNAs in cancers may be regulated by the host genes or RBPs. A Expression of hsa_circ_0099329 and its host gene PPFIA2 in tested cancers. B The splicing factor RBFOX1 was exclusively downregulated in GBM. C The Pearson correlation coefficients between RBFOX1 and hsa_circ_0111312 in GBM. The p-value was calculated using the Wilcoxon rank-sum test, ns denotes no significance, * denotes p &lt; 0.05, ** denotes p &lt; 0.01, *** denotes p &lt; 0.001. D Expression of hsa_circ_0111312 and its host gene RASAL2 in tested cancers. Figure S11. circLIFR expression in solid tumors and cells. A Quantification of circLIFR by RT-qPCR in solid tumors (LUAD, CRC, GC, THCA, GBM) and their matched adjacent normal tissues, and circLIFR expression was normalized to U6 mRNA levels. N, normal tissues; T, tumor tissues. B Identification of the circularization site of circLIFR in KYSE150 and HCT-116 cells by RT-PCR and Sanger sequencing. C,D Cellular distribution of circLIFR in KYSE150 and HCT-116 cells, determined by cell nucleus/cytoplasm fractionation and RT-qPCR analyses (C) and fluorescence in situ hybridization (D). β-actin mRNA and U6 RNA represent cytoplasmic and nuclear RNAs, respectively. Western blotting confirmed the efficiency of nuclear/cytoplasmic isolation. Data are shown as the mean ± SD. Figure S12. Effects of circLIFR on cell migration and motility in KYSE150 and HCT-116 cells.