Entering edit mode
3 months ago
drajangirija
•
0
Hi, I am analyzing RNA-seq samples from 4 different cell lines. The goal is to identify differentially expressed genes (DEGs) between control and treated samples at day 1,3 and day 6. I have 3 replicates for each condition. Given below is the metadata,
| Sample | Cell Line | Day | Treatment | |
|---|---|---|---|---|
| Day1_A_A | A | 1 | Treated | |
| Day1_A_A1 | A | 1 | Treated | |
| Day1_A_A2 | A | 1 | Treated | |
| Day1_A_AC | A | 1 | Control | |
| Day1_A_AC1 | A | 1 | Control | |
| Day1_A_AC2 | A | 1 | Control | |
| Day3_A_A | A | 3 | Treated | |
| Day3_A_A1 | A | 3 | Treated | |
| Day3_A_A2 | A | 3 | Treated | |
| Day3_A_AC | A | 3 | Control | |
| Day3_A_AC1 | A | 3 | Control | |
| Day3_A_AC2 | A | 3 | Control | |
| Day6_A_A | A | 6 | Treated | |
| Day6_A_A1 | A | 6 | Treated | |
| Day6_A_A2 | A | 6 | Treated | |
| Day6_A_AC | A | 6 | Control | |
| Day6_A_AC1 | A | 6 | Control | |
| Day6_A_AC2 | A | 6 | Control | |
| Day1_B_B | B | 1 | Treated | |
| Day1_B_B1 | B | 1 | Treated | |
| Day1_B_B2 | B | 1 | Treated | |
| Day1_B_BC | B | 1 | Control | |
| Day1_B_BC1 | B | 1 | Control | |
| Day1_B_BC2 | B | 1 | Control | |
| Day3_B_B | B | 3 | Treated | |
| Day3_B_B1 | B | 3 | Treated | |
| Day3_B_B2 | B | 3 | Treated | |
| Day3_B_BC | B | 3 | Control | |
| Day3_B_BC1 | B | 3 | Control | |
| Day3_B_BC2 | B | 3 | Control | |
| Day6_B_B | B | 6 | Treated | |
| Day6_B_B1 | B | 6 | Treated | |
| Day6_B_B2 | B | 6 | Treated | |
| Day6_B_BC | B | 6 | Control | |
| Day6_B_BC1 | B | 6 | Control | |
| Day6_B_BC2 | B | 6 | Control | same for cell line C and D. How should I design the experiment for the analysis, and how can I collapse replicates? Thank you. |
From title
Just so we have clarity
A/A1/A2are the same cell line sample library A from day 1 run on three lanes/flowcells? That would be a technical (sequencing) replicate of library for A.But if they are three separate biological replicate sample libraries for "A" then you are not going to want to collapse them. You will be losing valuable information.