Radiosensitizing effect of THBS1 knockdown in radioresistant head and neck carcinoma cell lines
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: 3 × Cal27 control vs 3 × Cal27 siTHBS1 vs 3 × Detroit562 control vs 3 × Detroit562 siTHBS1Groups 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 GSE305473_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 PRJNA1306054 and SRA study SRP608934. 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.
- GSM9177647 Cal27 control replicate 1 Cal27 control
- GSM9177648 Cal27 control replicate 2 Cal27 control
- GSM9177649 Cal27 control replicate 3 Cal27 control
- GSM9177650 Cal27 siTHBS1 replicate 1 Cal27 siTHBS1
- GSM9177651 Cal27 siTHBS1 replicate 2 Cal27 siTHBS1
- GSM9177652 Cal27 siTHBS1 replicate 3 Cal27 siTHBS1
- GSM9177653 Detroit562 control replicate 1 Detroit562 control
- GSM9177654 Detroit562 control replicate 2 Detroit562 control
- GSM9177655 Detroit562 control replicate 3 Detroit562 control
- GSM9177656 Detroit562 siTHBS1 replicate 1 Detroit562 siTHBS1
- GSM9177657 Detroit562 siTHBS1 replicate 2 Detroit562 siTHBS1
- GSM9177658 Detroit562 siTHBS1 replicate 3 Detroit562 siTHBS1
- GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares head, neck
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing · shares head, neck
- GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares head, neck
- GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 samples same disease briefing · shares head, neck
- GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing · shares head, neck
- GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing · shares head, neck
- GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing · shares head, neck
- GSE173161 Comparative analysis of gene expression after Oct4 or Scrambled siRNA knockdown in HNSCC cell lines 18 samples same disease briefing · shares knockdown, lines
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.