aging_BalbC
This project is to identify how murine genes in intestine are regulated by microbiota through methylation changes.
Data sotrage and analysis
- All raw data and meta files are stored in RIMLS server. The path is
/ceph/rimlsfnwi/data/cellbio/minoda/aging_BalbC. Please see readmeRawData.md for more information.
- The pre-processed raw data are all stored in the pre-processed repository. Please see readmePreprocessedData.md for more information.
- All the downstream analysis, including DEA (differnetially-expression gene analysis, from bulk RNAseq data), DMR (differentially-methylated regions, from bulk RRBSseq data), and microbiome 16S rRNA profileing, are saved in the result repository. Please see the readmeDownstreamData.md for more information.
Experiments
RNANseq
poly-A mRNA sequencing experiments were conducted at 2018. The experiment included three tissues: SI, LI, CE, two conditions: SPF, GF, and three ages: 3w, 17w, 78w.
RRBS
Two reduced-representation bisulfite sequencing (RRBS-Seq) experiments were conducted. The first experiment included small intestine samples and was conducted at 2018. The second experiment included large intestine sample and was conducted at 2022.
microbiome
16SrDNA sequencing experiments were conducted at 2022-2023. The experiment included three tissues: SI, LI, CE, two conditions: SPF, GF, and three ages: 3w, 17w, 78w. Those files were not analyzed yet.
Change log
- 20240509: update functions. Also update annotated DMR files to DMR_annotated repository. Codes of this repository are also going to public. All data and presentation files are not shown.
- 20240225: re-organize the readme files and scripts.
- 20240224: upload annotated DMR files to DMR_annotated repository.
- 20240218: upload all raw files and temporary results. Re-organized the Results repository.
- 20231118: update DMR.
- 20231117: update 5hmc + 5mc, 5hmc, 5mc.