Differential gene expression in snow crabs (Chionoecetes opilio) in response to different pH treatments
DOI Githup release June 6, 2023
Completed DGE using all 63 samples, updated code to combine forward and reverese sequences in DESeq. Visualized data with:
- Heatmap
- PCA
- Volcano plot
- Rpubs: https://rpubs.com/cskalley/snowcrabs_dge
- Code: https://github.com/course-fish546-2023/courtney_RNAseq_crabs/blob/970eec8fea6298725a453ccc06ac890338e26598/code/snowcrabs_dge.Rmd
- Output: https://github.com/course-fish546-2023/courtney_RNAseq_crabs/tree/main/output
I am working with paired end RNA-Seq data prepared and provided by Laura Spencer.
The ultimate goal of this project is to compare gene expression between snow crabs exposed to low pH levels.
The data is located here, uploaded by LS on 01/12/2022:
https://drive.google.com/drive/u/1/folders/1w7tqjcd-Rabh0TsWpw-JLTcJ2QbWIh3H
Detailed metadeta is located here:
https://docs.google.com/document/d/1HzMTreqnY2BD-oyjEJRA-JECpFE4CXlEoWKkmiaTYis/edit#
Control: samples #1-4
- 5010_1_S1_L003_R2_001.fastq.gz
- 5010_2_S2_L003_R1_001.fastq.gz
- 5010_3_S3_L003_R1_001.fastq.gz
- 5010_4_S4_L003_R1_001.fastq.gz
pH 7.8 (long exposure): samples #39-42
- 5010_39_S39_L003_R1_001.fastq.gz
- 5010_40_S40_L003_R1_001.fastq.gz
- 5010_41_S41_L003_R1_001.fastq.gz
- 5010_42_S42_L003_R1_001.fastq.gz
Hash for samples 1-4 (control):
-
2e862ecd7a241b25980b261eb6829463 5010_1_S1_L003_R1_001.fastq.gz
-
c1d0d493367d748ad825f7c2b4535a7b 5010_1_S1_L003_R2_001.fastq.gz
-
3ba220b8d4e5e128b96fb22a6fdd8e7c 5010_2_S2_L003_R1_001.fastq.gz
-
5c9c5e94000ea696399b8903aafa9b78 5010_2_S2_L003_R2_001.fastq.gz
-
70210dee456eb52ad8362a5603049fb4 5010_3_S3_L003_R1_001.fastq.gz
-
a0c510142e8152e89b85d9d78dbf0b5d 5010_3_S3_L003_R2_001.fastq.gz
-
5960706ab3acbd635c367f02c70ccaad 5010_4_S4_L003_R1_001.fastq.gz
-
b8691b8dcbfac0c3f7a37637fd71bc57 5010_4_S4_L003_R2_001.fastq.gz
Hash for samples 38-41 (long exposure to pH 7.8):
-
d512765b1b412932a78921012be6858a 5010_39_S39_L003_R1_001.fastq.gz
-
960b7db2a6ab538ddc029bf46b1109a3 5010_39_S39_L003_R2_001.fastq.gz
-
5ffc2addd9c17fc5760b8dfcdf2cd2ac 5010_40_S40_L003_R1_001.fastq.gz
-
acdb644ed1172ea3a7817da274d5513f 5010_40_S40_L003_R2_001.fastq.gz
-
0e1e80179a8bf02acba248e7ea91d626 5010_41_S41_L003_R1_001.fastq.gz
-
5efd0698e48a0d0a4e3fe919aba0070f 5010_41_S41_L003_R2_001.fastq.gz