SMO variants explain the majority of drug resistance in basal cell carcinoma
RNA-seq (gene expression) · human · 107 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
- Basal cell carcinomaThis series is part of our curated briefing on it.
- Samples
- 107 samples: 5 conditions, mostly with about 36 replicates eachGroups 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 GSE58377_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 PRJNA252374 and SRA study SRP043084. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 11 samples read as cases, 17 as controls.
How we read this: 5 replicated groups read from 107 sample titles; they account for 87 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.
- GSM1409314 DNASeq-BCC1-control
- GSM1409315 DNASeq-BCC1-tumor
- GSM1409316 DNASeq-BCC2-tumor
- GSM1409317 DNASeq-BCC2_3-control
- GSM1409318 DNASeq-BCC3-tumor
- GSM1409319 DNASeq-BCC4-tumor
- GSM1409320 DNASeq-BCC4_5-control
- GSM1409321 DNASeq-BCC5-tumor
- GSM1409322 DNASeq-BCC9-control
- GSM1409323 DNASeq-BCC9-tumor
- GSM1409324 DNASeq-BCC10-control
- GSM1409325 DNASeq-BCC10-tumor
- GSM1409326 DNASeq-BCC11-control
- GSM1409327 DNASeq-BCC11-tumor
- GSM1409328 DNASeq-BCC12-control
- GSM1409329 DNASeq-BCC12-tumor
- GSM1409330 DNASeq-BCC13-control
- GSM1409331 DNASeq-BCC13-tumor
- GSM1409332 DNASeq-BCC14-control
- GSM1409333 DNASeq-BCC14-tumor
- GSM1409334 RNASeq_Normal1 RNASeq_Normal
- GSM1409335 RNASeq_Normal2 RNASeq_Normal
- GSM1409336 RNASeq_Normal3 RNASeq_Normal
- GSM1409337 RNASeq_Normal4 RNASeq_Normal
- GSM1409338 RNASeq_Normal5 RNASeq_Normal
- GSM1409339 RNASeq_Normal6 RNASeq_Normal
- GSM1409340 RNASeq_Normal7 RNASeq_Normal
- GSM1409341 RNASeq_Normal8 RNASeq_Normal
- GSM1409342 RNASeq_Resistance1 RNASeq_Resistance
- GSM1409343 RNASeq_Resistance2 RNASeq_Resistance
- GSM1409344 RNASeq_Resistance3 RNASeq_Resistance
- GSM1409345 RNASeq_Resistance4 RNASeq_Resistance
- GSM1409346 RNASeq_Resistance5 RNASeq_Resistance
- GSM1409347 RNASeq_Resistance6 RNASeq_Resistance
- GSM1409348 RNASeq_Resistance7 RNASeq_Resistance
- GSM1409349 RNASeq_Resistance8 RNASeq_Resistance
- GSM1409350 RNASeq_Resistance9 RNASeq_Resistance
- GSM1409351 RNASeq_Sensitive1 RNASeq_Sensitive
- GSM1409352 RNASeq_Sensitive2 RNASeq_Sensitive
- GSM1409353 RNASeq_Sensitive3 RNASeq_Sensitive
+ 67 more — browse all 107 samples with per-sample file links →
- GSE2959 Genome-wide SNP Microarray Mapping in Basal Cell Carcinomas Unveils Uniparental Disomy as a Key Somatic Event. 28 samples same disease briefing · shares basal
- GSE269601 COL10A1 expression distinguishes a subset of cancer-associated fibroblasts present in the stroma of high-risk basal cell carcinoma 21 samples same disease briefing · shares basal
- GSE268728 A neoadjuvant, phase II trial demonstrates efficacy and tolerability of Talimogene laherparepvec in cutaneous basal cell carcinoma (NeoBCC trial) 12 samples same disease briefing · shares basal
- GSE93797 Distinct driver genes and the expression of Hedgehog defines morphoeic basal cell carcinoma 12 samples same disease briefing · shares basal
- GSE266665 Investigating transcriptional programs regulating invasion in basal cell carcinoma 6 samples same disease briefing · shares basal
- GSE337786 Integrated multi-omics reveals the cellular and molecular interactions governing the invasive niche in skin cancer II 2 samples same disease briefing
- GSE264741 Functional Screening and Transcriptomic Analysis Identify Novel Druggable Dependencies and Immunotherapy Targets in Desmoplastic Small Round Cell Tumor 124 samples shares smo, drug
- GSE291147 Mapping convergent regulators of melanoma drug resistance by PerturbFate 320 samples shares resistance, drug
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.