jagannathan-aso-rnaseq-2024-06
RNAseq analysis of ASO modulated splicing of SDCCAG8
Status: In Progress
Project Notes
RNAseq analysis of samples treated with anti-sense oligos (ASOs) designed to rescue splicing of patient SDCCAG8 transcript isoforms. SDCCAG8 (Serologically Defined Colorectal Cancer Antigen 8) is a protein coding gene acting as a SHH signaling and ciliogenesis regulator. Mutations in in SDCCAG8 are associated with Bardet-Biedl Syndrome (BBS) and retinal-renal ciliopathies. BBS primary symptoms include rod/cone dystrophy, polydactyly, obesity, hypogonadism, and kidney dysfunction.
Relevant to this study, patient mutation has affected splicing of SDCCAG8 leading to nonsense mediated decay of transcripts. Therapeutic ASOs were designed to negate abberant splicing.
Samples
- ASO 4_SMG1i_p7_RNA
- ASO 4_DMSO_p7_RNA
- ASO 12_SMG1i_p7_RNA
- ASO 12_DMSO_p7_RNA
- Lipofectamine2000_SMG1i_p7_RNA
- Lipofectamine2000_DMSO_p7_RNA
- RPE-1_p9_RNA
Raw Data
/beevol/home/rbilab/data/jagannathan/20240517_LH00407_0041_B22HKN5LT3
Analysis Notes
Process with standard RNASeq pipeline. Replicates absent for statistical analysis. Acquire exonic coverage to visually examine splicing at the SDCCAG8 locus. Look at TPM values of SDCCAG8 isoforms.
Test out https://nf-co.re/rnaseq/3.14.0
Reference used: GRCh37/hg19
Generate additional plots with Gviz? Heatmaps, coverage, and annotation files both reference and novel?
Utilize StringTie / Ballgown?
Rmats?
Analysis Progress
- Samples processed with nf-core/rnaseq pipeline version 3.14
- Generate coverage tracks
- TPM SDCCAG8 Isoform levels
- Generate custom Gviz SDCCAG8 locus plots
- Splicing specific plots and comparisons
Deliverables
Coverage tracks data: http://amc-sandbox.ucdenver.edu/User64/jagannathan-aso-rnaseq-2024-06/
Reference / Support
https://www.genecards.org/cgi-bin/carddisp.pl?gene=SDCCAG8
https://nf-co.re/rnaseq/3.14.0