The transcriptome and miRNA expression profiles of SOX10-knockdown uveal melanoma
Non-coding RNA profiling · human · 16 samples
- What it is
- Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
- Organism
- Homo sapiens (human)
- Topic
- Uveal melanomaThis series is part of our curated briefing on it.
- Samples
- 16 samples: 4 × miR_CT_92.1 vs 4 × miR_CT_Mel vs 4 × miR_SOX10KD_92.1 vs 4 × miR_SOX10KD_MelGroups 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 GSE312967_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.
Also filed as BioProject PRJNA1377672 and SRA study SRP653510. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM9357645 miR_CT_92.1_1 miR_CT_92.1
- GSM9357646 miR_CT_92.1_3 miR_CT_92.1
- GSM9357647 miR_CT_92.1_15 miR_CT_92.1
- GSM9357648 miR_CT_92.1_23 miR_CT_92.1
- GSM9357649 miR_CT_Mel_1 miR_CT_Mel
- GSM9357650 miR_CT_Mel_3 miR_CT_Mel
- GSM9357651 miR_CT_Mel_15 miR_CT_Mel
- GSM9357652 miR_CT_Mel_23 miR_CT_Mel
- GSM9357653 miR_SOX10KD_92.1_1 miR_SOX10KD_92.1
- GSM9357654 miR_SOX10KD_92.1_3 miR_SOX10KD_92.1
- GSM9357655 miR_SOX10KD_92.1_15 miR_SOX10KD_92.1
- GSM9357656 miR_SOX10KD_92.1_23 miR_SOX10KD_92.1
- GSM9357657 miR_SOX10KD_Mel_1 miR_SOX10KD_Mel
- GSM9357658 miR_SOX10KD_Mel_3 miR_SOX10KD_Mel
- GSM9357659 miR_SOX10KD_Mel_15 miR_SOX10KD_Mel
- GSM9357660 miR_SOX10KD_Mel_23 miR_SOX10KD_Mel
- GSE228250 Selamectin increases cisplatin sensitivity by inhibiting cisplatin-resistant genes expression and autophagy in uveal melanoma 6 samples same disease briefing · shares melanoma, uveal
- GSE272013 Effect of LINC01315 depletion and overexpression on proliferation of OMM2.3 uveal melanoma cells 6 samples same disease briefing · shares melanoma, uveal
- GSE176474 Transcriptome analysis after CCCP and/or DHA treatment in uveal melanoma cells 4 samples same disease briefing · shares melanoma, uveal
- GSE271497 Transcriptome analysis of 92.1-parental and 92.1-resistant uveal melanoma cells 4 samples same disease briefing · shares melanoma, uveal
- GSE329586 PROS1 expression is regulated by BAP1 in uveal melanocytes and melanomas. 4 samples same disease briefing · shares melanoma, uveal
- GSE227974 MY-COMP, an inhibitor of the transcriptional activity of YAP-B-MYB, identifies NEK2 as a novel mediator of YAP oncogenesis in uveal melanoma cells 29 samples same disease briefing · shares melanoma, uveal
- GSE294950 Epigenetic library screen reveals novel targets for uveal melanoma 24 samples same disease briefing · shares melanoma, uveal
- GSE231396 PRAME induces genomic instability in uveal melanoma 23 samples same disease briefing · shares melanoma, uveal
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.