Piezoeletric cold atmospheric plasma sensitizes head and neck cancer to chemotherapy and immune checkpoint blockade therapy
RNA-seq (gene expression) · human · 24 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
- Head and neck cancerThis series is part of our curated briefing on it.
- Samples
- 24 samples: 8 conditions, mostly in triplicateGroups 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 GSE235832_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 PRJNA987686 and SRA study SRP445942. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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.
- GSM7510236 Cal27-Control1 Cal27-Control
- GSM7510237 Cal27-Control2 Cal27-Control
- GSM7510238 Cal27-Control3 Cal27-Control
- GSM7510239 Cal27-CAP1 Cal27-CAP
- GSM7510240 Cal27-CAP2 Cal27-CAP
- GSM7510241 Cal27-CAP3 Cal27-CAP
- GSM7510242 A375-Control1 A375-Control
- GSM7510243 A375-Control2 A375-Control
- GSM7510244 A375-Control3 A375-Control
- GSM7510245 A375-CAP1 A375-CAP
- GSM7510246 A375-CAP2 A375-CAP
- GSM7510247 A375-CAP3 A375-CAP
- GSM7510248 Fadu-Control1 Fadu-Control
- GSM7510249 Fadu-Control2 Fadu-Control
- GSM7510250 Fadu-Control3 Fadu-Control
- GSM7510251 Fadu-CAP1 Fadu-CAP
- GSM7510252 Fadu-CAP2 Fadu-CAP
- GSM7510253 Fadu-CAP3 Fadu-CAP
- GSM7510254 Hth83-Control1 Hth83-Control
- GSM7510255 Hth83-Control2 Hth83-Control
- GSM7510256 Hth83-Control3 Hth83-Control
- GSM7510257 Hth83-CAP1 Hth83-CAP
- GSM7510258 Hth83-CAP2 Hth83-CAP
- GSM7510259 Hth83-CAP3 Hth83-CAP
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing
- GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing
- GSE162738 Immune gene signatures in oropharyngeal cancers are associated with inverse prognosis by HPV-status 51 samples same disease briefing
- GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing
- GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing
- GSE114446 Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines 33 samples same disease briefing
- GSE145057 Establishment of a human tongue cancer organoid biobank enables early diagnosis, prognosis, and identification of therapeutic targets 25 samples same disease briefing
- GSE182227 Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma 24 samples same disease briefing
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.