Culturomics reveals Fusobacterium-Prevotella mutualism as a hallmark of nasopharyngeal tumor microbiota [Cell RNA-seq]
RNA-seq (gene expression) · human · 12 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)
- Topic
- Nasopharyngeal carcinomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × HK1, Ctrl vs 3 × HK1, Fn vs 3 × HK1, Pi vs 3 × HK1, MixGroups 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.
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 GSE320343_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 PRJNA1427634 and SRA study SRP679009. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9541204 HK1, Ctrl01 HK1, Ctrl
- GSM9541205 HK1, Ctrl02 HK1, Ctrl
- GSM9541206 HK1, Ctrl03 HK1, Ctrl
- GSM9541207 HK1, Fn01 HK1, Fn
- GSM9541208 HK1, Fn02 HK1, Fn
- GSM9541209 HK1, Fn03 HK1, Fn
- GSM9541210 HK1, Pi01 HK1, Pi
- GSM9541211 HK1, Pi02 HK1, Pi
- GSM9541212 HK1, Pi03 HK1, Pi
- GSM9541213 HK1, Mix01 HK1, Mix
- GSM9541214 HK1, Mix02 HK1, Mix
- GSM9541215 HK1, Mix03 HK1, Mix
- GSE320342 Culturomics reveals Fusobacterium-Prevotella mutualism as a hallmark of nasopharyngeal tumor microbiota [Tissue RNA-seq] 35 samples same disease briefing · shares fusobacterium-prevotella, nasopharyngeal, culturomics, microbiota, mutualism, hallmark, rna-seq
- GSE236418 LINC01770 mediates nasopharyngeal cancer radiation resistance and renders tumor cell vulnerable to ferroptosis [RNA-seq] 6 samples same disease briefing · shares nasopharyngeal, rna-seq
- GSE231572 Development and validation of a microbiota signature to predict prognosis in nasopharyngeal carcinoma 64 samples same disease briefing · shares nasopharyngeal, microbiota
- GSE324767 RNA-Seq quantitative analysis of the regulatory effects of circRBM6 and circMLLT1 on nasopharyngeal carcinoma cell transcriptomes 8 samples same disease briefing · shares nasopharyngeal, rna-seq
- GSE234440 mRNA expression profiling of nasopharyngeal carcinoma cell line HONE1 upon ARNTL2 knockdown [RNA-seq] 6 samples same disease briefing · shares nasopharyngeal, rna-seq
- GSE302204 RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-LR and BALF2-HR overexpress group 6 samples same disease briefing · shares nasopharyngeal, rna-seq
- GSE319431 RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-LR and BALF2-HR overexpress group 6 samples same disease briefing · shares nasopharyngeal, rna-seq
- GSE334187 RNA-seq profiling of FBXO8 knockdown in HONE-1 nasopharyngeal carcinoma cells 6 samples same disease briefing · shares nasopharyngeal, rna-seq
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.