Ligature-induced periodontitis (LIP) induces rapid alveolar bone loss followed by gingival immunosuppressive conditions
RNA-seq (gene expression) · mouse · 11 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 11 samples: 4 × Removal vs 4 × Naive vs 3 × ligatureGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Epithelial RANKL Limits Experimental Periodontitis via Langerhans CellsJournal of dental research · 2024
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE298066_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1268219 and SRA study SRP588791. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 3 replicated groups read from 11 sample titles; they account for 11 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9006209 ligature 1 ligature
- GSM9006210 ligature 2 ligature
- GSM9006211 ligature 3 ligature
- GSM9006212 Removal 1 Removal
- GSM9006213 Removal 2 Removal
- GSM9006214 Removal 3 Removal
- GSM9006215 Removal 4 Removal
- GSM9006216 Naive 1 Naive
- GSM9006217 Naive 2 Naive
- GSM9006218 Naive 3 Naive
- GSM9006219 Naive 4 Naive
- GSE327719 Estrogen deprivation alters gingival and dentoalveolar complex transcriptomes during ligature-induced periodontitis in mice 24 samples shares ligature-induced, periodontitis, alveolar, gingival
- GSE292710 Traumatic occlusion exacerbates bone resorption by modifying gene expression in the bone tissue of ligature-induced periodontitis in mice 32 samples shares ligature-induced, periodontitis
- GSE309251 Western diet-induced MASH in PWK/PhJ mice identifies disruptions in amino acid and sphingolipid metabolism contributing to cardiac dysfunction 347 samples shares lip
- GSE279388 Inactivation of Atp7b copper transporter in the intestinal epithelial cells is associated with altered lipid processing and cell growth machinery that are independent from hepatic copper accumulation and liver histology severity 76 samples shares lip
- GSE302447 A multi-functional oral small molecule targeting energy and lipid metabolism as a treatment for diet-induced obesity 67 samples shares lip
- GSE313258 Metabolite-driven remodeling of hepatic lipid metabolism by the plasticizer di-isononyl phthalate 54 samples shares lip
- GSE283571 Circadian reprogramming of protein homeostasis and glycolipid metabolism in diabetic nephropathy 47 samples shares lip
- GSE302836 Loss of Hepatocyte PI3Ka Protects Mice from Hepatocellular Carcinoma in association with altered lipid metabolism gene expression 42 samples shares lip
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.