Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 5 × B vs 5 × PGroups 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
- Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent mannerNPJ biofilms and microbiomes · 2024
Read the full summary ↓
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 GSE269171_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 PRJNA1120449 and SRA study SRP512034. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8307446 B1 B
- GSM8307447 B2 B
- GSM8307448 B3 B
- GSM8307449 B4 B
- GSM8307450 B5 B
- GSM8307451 P1 P
- GSM8307452 P2 P
- GSM8307453 P3 P
- GSM8307454 P4 P
- GSM8307455 P5 P
- GSE270467 Antibiotics damage the colonic mucus barrier in a microbiota-independent manner 50 samples shares independent, manner
- GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares independent, manner
- GSE260592 Antibiotics damage the colonic mucus barrier in a microbiota-independent manner I 28 samples shares independent, manner
- GSE270466 Antibiotics damage the colonic mucus barrier in a microbiota-independent manner II 22 samples shares independent, manner
- GSE275003 CTCF tunes gene expression in a loop-dependent and -independent manner 172 samples shares independent, manner
- GSE274792 CTCF tunes gene expression in a loop-dependent and -independent manner [ChIP-Seq] 30 samples shares independent, manner
- GSE274789 CTCF tunes gene expression in a loop-dependent and -independent manner [ATAC-Seq] 24 samples shares independent, manner
- GSE300428 Rbm24 promotes outer hair cell survival through Insm1 repression while independently regulating hair bundle morphogenesis 163 samples shares independent
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.