RNA-Seq of human cutaneous squamous cell carcinoma cell lines and normal human epidermal keratinocytes.
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
- Cutaneous squamous cell carcinomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 6 × UT-SCC vs 3 × NHEKGroups 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
- Clustering of RNA co-expression network identifies novel long non-coding RNA biomarkers in squamous cell carcinomaScientific reports · 2024
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 GSE252347_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 PRJNA1060266 and SRA study SRP480990. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 2 replicated groups read from 12 sample titles; they account for 9 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.
- GSM7999872 UT-SCC12A
- GSM7999873 UT-SCC91 UT-SCC
- GSM7999874 UT-SCC105 UT-SCC
- GSM7999875 UT-SCC111 UT-SCC
- GSM7999876 UT-SCC118 UT-SCC
- GSM7999877 UT-SCC7 UT-SCC
- GSM7999878 UT-SCC59A
- GSM7999879 UT-SCC115 UT-SCC
- GSM7999880 NHEK 59 NHEK
- GSM7999881 NHEK 64 NHEK
- GSM7999882 NHEK 70 NHEK
- GSM7999883 NHEK PC
- GSE319969 Spatial and Bulk Transcriptomic Profiling Defines the Molecular Evolution of Cutaneous Squamous Cell Carcinoma and Reveals Stage-Specific Biomarkers of Clinical Relevance [RNA-Seq] 24 samples same disease briefing · shares cutaneous, squamous, rna-seq
- GSE284467 Multi-omic Sequencing of Intermediate to High-Risk Cutaneous Squamous Cell Carcinoma Identifies Critical Genes and Expression Patterns Associated with Disease and Poor Outcomes 75 samples same disease briefing · shares cutaneous, squamous
- GSE314399 The human Flower isoform hFWE4 facilitates cornification in cutaneous squamous cell carcinoma 23 samples same disease briefing · shares cutaneous, squamous
- GSE326341 Characterization of a Human Cutaneous Squamous Cell Carcinoma Xenograft Mouse Model 20 samples same disease briefing · shares cutaneous, squamous
- GSE260920 Loss of DUSP1 expression creates a cold tumor microenvironment in cutaneous squamous cell carcinoma 17 samples same disease briefing · shares cutaneous, squamous
- GSE200334 Single cell transcriptomes of genetic landscape from actinic keratosis to cutaneous squamous cell carcinoma 14 samples same disease briefing · shares cutaneous, squamous
- GSE292168 SRCAP mutation promotes cutatneous squamous cell carcinoma invasion [RNA-Seq] 8 samples same disease briefing · shares squamous, rna-seq
- GSE341811 Pleckstrin-2 Promotes Cutaneous Squamous Cell Carcinoma by Recruiting Profilin-1 to the Membrane to Destabilize Cytosolic PTEN 6 samples same disease briefing · shares cutaneous, squamous
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.