Transcriptomics profiling of the effect of inducible knock-down of the melanocyte inducing transcription factor (MITF) in melanoma 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
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × MeWo_0ug_Dox vs 3 × MeWo_1ug_Dox vs 3 × SkMel28_0ug_Dox vs 3 × SkMel28_1ug_DoxGroups 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
- The Lipid Droplet Protein DHRS3 Is a Regulator of Melanoma Cell StatePigment cell & melanoma research · 2025
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 GSE255256_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 PRJNA1074279 and SRA study SRP488664. 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.
- GSM8067674 MeWo_0ug_Dox_R1 MeWo_0ug_Dox
- GSM8067675 MeWo_0ug_Dox_R2 MeWo_0ug_Dox
- GSM8067676 MeWo_0ug_Dox_R3 MeWo_0ug_Dox
- GSM8067677 MeWo_1ug_Dox_R1 MeWo_1ug_Dox
- GSM8067678 MeWo_1ug_Dox_R2 MeWo_1ug_Dox
- GSM8067679 MeWo_1ug_Dox_R3 MeWo_1ug_Dox
- GSM8067680 SkMel28_0ug_Dox_R1 SkMel28_0ug_Dox
- GSM8067681 SkMel28_0ug_Dox_R2 SkMel28_0ug_Dox
- GSM8067682 SkMel28_0ug_Dox_R3 SkMel28_0ug_Dox
- GSM8067683 SkMel28_1ug_Dox_R1 SkMel28_1ug_Dox
- GSM8067684 SkMel28_1ug_Dox_R2 SkMel28_1ug_Dox
- GSM8067685 SkMel28_1ug_Dox_R3 SkMel28_1ug_Dox
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing · shares melanoma
- GSE130956 Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines 12 samples same disease briefing · shares melanoma
- GSE140150 A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo 6 samples same disease briefing · shares melanoma
- GSE317605 A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer [CITE-Seq] 168 samples same disease briefing · shares factor
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing · shares melanoma
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing · shares melanoma
- GSE123728 Clinical and Immunologic Activity of a Single Dose of Neoadjuvant PD-1 Blockade and Predictors of Clinical Outcomes in Resectable Melanoma 24 samples same disease briefing · shares melanoma
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.