RNA-sequencing of melanoma celllines compared to normal human melanocytes (NHEMs)
RNA-seq (gene expression) · human · 14 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
- 14 samples: 7 conditions, mostly in duplicateGroups 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
- C-Jun drives melanoma progression in PTEN wild type melanoma cellsCell death & disease · 2019
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 GSE284779_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 PRJNA839865 and SRA study SRP376207. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 7 replicated groups read from 14 sample titles; they account for 14 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.
- GSM8693247 RNA-Seq_human_melanoma_NHEM_76 RNA-Seq_human_melanoma_…
- GSM8693248 RNA-Seq_human_melanoma_NHEM_77 RNA-Seq_human_melanoma_…
- GSM8693249 RNA-Seq_human_melanoma_Sbcl2_64 RNA-Seq_human_melanoma_…
- GSM8693250 RNA-Seq_human_melanoma_Sbcl2_70 RNA-Seq_human_melanoma_…
- GSM8693251 RNA-Seq_human_melanoma_WM3211_65 RNA-Seq_human_melanoma_…
- GSM8693252 RNA-Seq_human_melanoma_WM3211_71 RNA-Seq_human_melanoma_…
- GSM8693253 RNA-Seq_human_melanoma_WM1158_74 RNA-Seq_human_melanoma_…
- GSM8693254 RNA-Seq_human_melanoma_WM1158_68 RNA-Seq_human_melanoma_…
- GSM8693255 RNA-Seq_human_melanoma_WM793_67 RNA-Seq_human_melanoma_…
- GSM8693256 RNA-Seq_human_melanoma_WM793_73 RNA-Seq_human_melanoma_…
- GSM8693257 RNA-Seq_human_melanoma_WM9_69 RNA-Seq_human_melanoma_…
- GSM8693258 RNA-Seq_human_melanoma_WM9_75 RNA-Seq_human_melanoma_…
- GSM8693259 RNA-Seq_human_melanoma_WM1366_66 RNA-Seq_human_melanoma_…
- GSM8693260 RNA-Seq_human_melanoma_WM1366_72 RNA-Seq_human_melanoma_…
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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.