Transcrptomic analysis of dysplastic oral keratinocytes infected with Fusobacterium polymorphum strains from patients with leukoplakia
RNA-seq (gene expression) · human · 19 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
- Homo sapiens (human)
- Samples
- 19 samples: 17 distinct titles, 1 of them repeatedGroups 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.
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 GSE324461_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 PRJNA1435191 and SRA study SRP682635. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 19 sample titles: 17 distinct titles with little repetition. 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.
- GSM9577735 DOK infected, Mild dysplasia_derived 139A
- GSM9577736 DOK infected, Severe dysplasia_derived 141A
- GSM9577737 DOK infected, Moderate dysplasia_derived 161A
- GSM9577738 DOK infected, Moderate dysplasia_derived 185A1d
- GSM9577739 DOK infected, OSCC_derived 190Ad
- GSM9577740 DOK infected, Mild dysplasia_derived 199A2d
- GSM9577741 DOK infected, Moderate dysplasia_derived 40A2
- GSM9577742 DOK infected, Severe dysplasia_derived 41A
- GSM9577743 DOK infected, Severe dysplasia_derived 43A3
- GSM9577744 DOK infected, Mild dysplasia_derived 60A2
- GSM9577745 DOK infected, Healthy_derived C44Ad
- GSM9577746 DOK infected, Healthy_derived C47A
- GSM9577747 DOK infected, Healthy_derived C48Bd
- GSM9577748 DOK infected, Healthy_derived C55Bd
- GSM9577749 DOK infected, Healthy_derived C65Bd
- GSM9577750 DOK infected, Healthy_derived C75Bd
- GSM9577751 DOK_uninfected_control_R1
- GSM9577752 DOK_uninfected_control_R2
- GSM9577753 DOK_uninfected_control_R3
- GSE273567 Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer 42 samples shares fusobacterium, infected
- GSE255828 Cytokine stimulated keratinocytes 800 samples shares keratinocytes
- GSE260642 Cytokine stimulated keratinocytes (TCF4 KD) 72 samples shares keratinocytes
- GSE263846 Transcriptional and UV-response regulatory role of PPARb in Normal Human Keratinocytes 48 samples shares keratinocytes
- GSE309699 Interferons inhibit Ebola virus infection of human keratinocytes 44 samples shares keratinocytes
- GSE324594 Transcriptomic changes in primary human keratinocytes following exposure to lamotrigine, lamotrigine-N2-oxide, lamotrigine in combination with valproic acid or interferon-γ, and interferon-γ alone 36 samples shares keratinocytes
- GSE212905 A BNC1-IRF6-AP1 transcriptional network in keratinocytes and Squamous Cell Carcinoma [RNA-Seq] 36 samples shares keratinocytes
- GSE320342 Culturomics reveals Fusobacterium-Prevotella mutualism as a hallmark of nasopharyngeal tumor microbiota [Tissue RNA-seq] 35 samples shares fusobacterium
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.