Integrated Metagenomics and Transcriptomics Analysis Reveals Pathways Associated with Oral Periapical Lesions Formation and Progression
RNA-seq (gene expression) · human · 16 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
- 16 samples: 4 × Abscess vs 4 × Cyst vs 4 × Granuloma vs 4 × Healthy controlGroups 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
- Integrated metagenomics and transcriptomics analysis reveals pathways associated with oral periapical lesions formation and progressionCurrent research in microbial sciences · 2025
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 GSE299006_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 PRJNA1272096 and SRA study SRP589930. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM9030359 Abscess11 Abscess
- GSM9030360 Abscess12 Abscess
- GSM9030361 Abscess13 Abscess
- GSM9030362 Abscess14 Abscess
- GSM9030363 Cyst8 Cyst
- GSM9030364 Cyst9 Cyst
- GSM9030365 Cyst10 Cyst
- GSM9030366 Cyst11 Cyst
- GSM9030367 Granuloma8 Granuloma
- GSM9030368 Granuloma9 Granuloma
- GSM9030369 Granuloma10 Granuloma
- GSM9030370 Granuloma11 Granuloma
- GSM9030371 Healthy control7 Healthy control
- GSM9030372 Healthy control8 Healthy control
- GSM9030373 Healthy control9 Healthy control
- GSM9030374 Healthy control10 Healthy control
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- GSE275870 Expression profiling of primary and metastatic oral squamous cell carcinoma identifies progression-associated transcriptome changes and therapeutic vulnerabilities 108 samples shares progression, oral
- GSE180791 Proteogenomic characterization reveals that lipid droplet formation promotes esophageal squamous cell cancer progression 102 samples shares progression, formation
- GSE339456 Integrated bulk and spatial transcriptomic analysis identifies progression-associated molecular signatures in biopsy-proven hypertensive nephropathy [RNA-seq] 35 samples shares progression, integrated
- GSE261171 High-Resolution Single-Cell RNA Sequencing Uncovers Disparate Neutrophil Populations within Metastatic Cancer Lesions Linked to Progression Free Survival in Multiple Myeloma Patients 28 samples shares progression, lesions
- GSE267104 Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA [RNAseq] 17 samples shares integrated, formation
- GSE271703 Integrated ChIP-seq and Transcriptomic Profiling of Histone Modifications Across Breast Cancer Progression in MCF10A-Derived Cell Lines [ChIP-Seq] 60 samples shares progression, integrated
- GSE267239 Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA 57 samples shares integrated, formation
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.