RNA-seq profiling of SOX10 overexpression in TADA2B KO A375 melanoma cells
RNA-seq (gene expression) · human · 18 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
- 18 samples: 6 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 GSE319449_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 PRJNA1423302 and SRA study SRP676891. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM9518153 A375_GFPsg_rep1 A375_GFPsg
- GSM9518154 A375_GFPsg_rep2 A375_GFPsg
- GSM9518155 A375_GFPsg_rep3 A375_GFPsg
- GSM9518156 A375_GFPsg_SOX10OE_rep1 A375_GFPsg_SOX10OE
- GSM9518157 A375_GFPsg_SOX10OE_rep2 A375_GFPsg_SOX10OE
- GSM9518158 A375_GFPsg_SOX10OE_rep3 A375_GFPsg_SOX10OE
- GSM9518159 A375_TADA2Bsg1_rep1 A375_TADA2Bsg1
- GSM9518160 A375_TADA2Bsg1_rep2 A375_TADA2Bsg1
- GSM9518161 A375_TADA2Bsg1_rep3 A375_TADA2Bsg1
- GSM9518162 A375_TADA2Bsg1_SOX10OE_rep1 A375_TADA2Bsg1_SOX10OE
- GSM9518163 A375_TADA2Bsg1_SOX10OE_rep2 A375_TADA2Bsg1_SOX10OE
- GSM9518164 A375_TADA2Bsg1_SOX10OE_rep3 A375_TADA2Bsg1_SOX10OE
- GSM9518165 A375_TADA2Bsg2_rep1 A375_TADA2Bsg2
- GSM9518166 A375_TADA2Bsg2_rep2 A375_TADA2Bsg2
- GSM9518167 A375_TADA2Bsg2_rep3 A375_TADA2Bsg2
- GSM9518168 A375_TADA2Bsg2_SOX10OE_rep1 A375_TADA2Bsg2_SOX10OE
- GSM9518169 A375_TADA2Bsg2_SOX10OE_rep2 A375_TADA2Bsg2_SOX10OE
- GSM9518170 A375_TADA2Bsg2_SOX10OE_rep3 A375_TADA2Bsg2_SOX10OE
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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.