RNA-sequencing of Oral Squamous Cell carcinoma cells, PE/CA-PJ41, treated with human plasma or platelet-rich-plasma (PRP)
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
- Head and neck cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 4 × OSCC PECA_PJ41 Control vs 4 × OSCC PECA_PJ41 Plasma vs 4 × OSCC PECA_PJ41 PRPGroups 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 GSE296894_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 PRJNA1261931 and SRA study SRP584712. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 3 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.
- GSM8979548 OSCC PECA_PJ41 Control_1 OSCC PECA_PJ41 Control
- GSM8979549 OSCC PECA_PJ41 Control_2 OSCC PECA_PJ41 Control
- GSM8979550 OSCC PECA_PJ41 Control_3 OSCC PECA_PJ41 Control
- GSM8979551 OSCC PECA_PJ41 Control_4 OSCC PECA_PJ41 Control
- GSM8979552 OSCC PECA_PJ41 Plasma_1 OSCC PECA_PJ41 Plasma
- GSM8979553 OSCC PECA_PJ41 Plasma_2 OSCC PECA_PJ41 Plasma
- GSM8979554 OSCC PECA_PJ41 Plasma_3 OSCC PECA_PJ41 Plasma
- GSM8979555 OSCC PECA_PJ41 Plasma_4 OSCC PECA_PJ41 Plasma
- GSM8979556 OSCC PECA_PJ41 PRP_1 OSCC PECA_PJ41 PRP
- GSM8979557 OSCC PECA_PJ41 PRP_2 OSCC PECA_PJ41 PRP
- GSM8979558 OSCC PECA_PJ41 PRP_3 OSCC PECA_PJ41 PRP
- GSM8979559 OSCC PECA_PJ41 PRP_4 OSCC PECA_PJ41 PRP
- GSE176077 RNA-seq profiling of salivary transcriptome reveals potential diagnostic RNAs and oral microbial dysbiosis in oral squamous cell carcinoma 28 samples same disease briefing · shares squamous, oral
- GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares squamous
- GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares squamous
- GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 samples same disease briefing · shares squamous
- 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
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.