RNA-seq analysis of melanoma cell lines with enhancer deletions.
RNA-seq (gene expression) · human · 39 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
- 39 samples: 11 conditions, mostly in triplicateGroups 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 GSE283223_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 PRJNA1192699 and SRA study SRP548573. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 39 samples.
How we read this: 11 replicated groups read from 39 sample titles; they account for 39 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.
- GSM8658218 A_4.2_rep3 A_4.2
- GSM8658219 A_4.2_rep2 A_4.2
- GSM8658220 A_4.2_rep1 A_4.2
- GSM8658221 A_4.1_rep4 A_4.1
- GSM8658222 A_4.1_rep3 A_4.1
- GSM8658223 A_4.1_rep2 A_4.1
- GSM8658224 A_4.1_rep1 A_4.1
- GSM8658225 A_1.2_rep4 A_1.2
- GSM8658226 A_1.2_rep3 A_1.2
- GSM8658227 A_1.2_rep2 A_1.2
- GSM8658228 A_1.2_rep1 A_1.2
- GSM8658229 A_1.1_rep3 A_1.1
- GSM8658230 A_1.1_rep2 A_1.1
- GSM8658231 A_1.1_rep1 A_1.1
- GSM8658232 A_WT_rep4 A_WT
- GSM8658233 A_WT_rep3 A_WT
- GSM8658234 A_WT_rep2 A_WT
- GSM8658235 A_WT_rep1 A_WT
- GSM8658236 W_1.3_rep3 W_1.3
- GSM8658237 W_1.3_rep2 W_1.3
- GSM8658238 W_1.3_rep1 W_1.3
- GSM8658239 W_1.2_rep3 W_1.2
- GSM8658240 W_1.2_rep2 W_1.2
- GSM8658241 W_1.2_rep1 W_1.2
- GSM8658242 W_1.1_rep5 W_1.1
- GSM8658243 W_1.1_rep4 W_1.1
- GSM8658244 W_1.1_rep3 W_1.1
- GSM8658245 W_1.1_rep2 W_1.1
- GSM8658246 W_1.1_rep1 W_1.1
- GSM8658247 W_4.2_rep3 W_4.2
- GSM8658248 W_4.2_rep2 W_4.2
- GSM8658249 W_4.2_rep1 W_4.2
- GSM8658250 W_4.1_rep3 W_4.1
- GSM8658251 W_4.1_rep2 W_4.1
- GSM8658252 W_4.1_rep1 W_4.1
- GSM8658253 W_WT_rep4 W_WT
- GSM8658254 W_WT_rep3 W_WT
- GSM8658255 W_WT_rep2 W_WT
- GSM8658256 W_WT_rep1 W_WT
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- 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
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples same disease briefing · shares lines
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 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.