Journal: Scientific Reports
Article Title: Selection of optimal extraction and RT-PCR protocols for stool RNA detection of colorectal cancer associated immune genes
doi: 10.1038/s41598-024-78680-0
Figure Lengend Snippet: Study design for RNA extraction and PCR methods. The figure outlines the process used in the study of RNA extraction and PCR methods from stool samples in two cohorts: an evaluation cohort (24 samples: 9 cancer, 8 polyps, 7 controls) and a test cohort (68 samples: 22 cancer, 24 polyps, 22 controls). The evaluation cohort involved multiple RNA extraction methods: Norgen (N), Qiagen (Q), and EasyMAG BioMérieux (EM), with subsequent quality control steps using cel-mir-39 and Oligo-IC mRNA. The PCR methods included two-step RT and GAPDH PCR with a DNA intercalating dye (SYBR green) and TaqMan probes, and one-step GAPDH RT-PCR with TaqMan probes. In the test cohort, RNA extraction was performed using Norgen (N), followed by one-step RT-PCR with TaqMan probes targeting GAPDH, CXCL1, IL18, IL1B, IL6, PTGS2 , and SPP1 .
Article Snippet: 250 ng RNA*. iScript cDNA synthesis kit (Biorad). 20 μl volume. Random hexamer primers. , 2 μl undiluted cDNA (approx. 25 ng) Quantinova SYBR Green PCR Kit (Qiagen) , Two-step RT-PCR. RT: 25° C 5 min, 46 °C, 20 min, 95 °C 1 min. PCR: 40 cycles of 5 Sect. 95 °C, 10 Sect. 60 °C. , SYBR green GAPDH : Origene Qstar NM002046 F: 5’ GTCTCCTCTGACTTCAACAGCG-3 R: 5’ACCACCCTGTTGCTGTAGCCAA-3’ (spans exons 7–8).
Techniques: RNA Extraction, Control, SYBR Green Assay, Reverse Transcription Polymerase Chain Reaction, One Step RT-PCR