Long non-coding RNA triplex-dependent regulation of melanoma gene networks
RNA-seq (gene expression) · human · 24 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
- 24 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.
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 GSE302468_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 PRJNA1291051 and SRA study SRP601147. 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 24 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.
- GSM9104561 Empty_Rep1 Empty
- GSM9104562 Empty_Rep2 Empty
- GSM9104563 Empty_Rep3 Empty
- GSM9104564 SLNCR_Full_Length_Rep1 SLNCR_Full_Length
- GSM9104565 SLNCR_Full_Length_Rep2 SLNCR_Full_Length
- GSM9104566 SLNCR_Full_Length_Rep3 SLNCR_Full_Length
- GSM9104567 SLNCR𝛥TFR1_Rep1 SLNCR𝛥TFR1
- GSM9104568 SLNCR𝛥TFR1_Rep2 SLNCR𝛥TFR1
- GSM9104569 SLNCR𝛥TFR1_Rep3 SLNCR𝛥TFR1
- GSM9104570 SLNCR𝛥TFR2_Rep1 SLNCR𝛥TFR2
- GSM9104571 SLNCR𝛥TFR2_Rep2 SLNCR𝛥TFR2
- GSM9104572 SLNCR𝛥TFR2_Rep3 SLNCR𝛥TFR2
- GSM9104573 Empty_Rep1_Batch2
- GSM9104574 Empty_Rep2_Batch2
- GSM9104575 Empty_Rep3_Batch2
- GSM9104576 SLNCR_Full_Length_Rep1_Batch2
- GSM9104577 SLNCR_Full_Length_Rep2_Batch2
- GSM9104578 SLNCR_Full_Length_Rep3_Batch2
- GSM9104579 SLNCR𝛥TFR4_Rep1 SLNCR𝛥TFR4
- GSM9104580 SLNCR𝛥TFR4_Rep2 SLNCR𝛥TFR4
- GSM9104581 SLNCR𝛥TFR4_Rep3 SLNCR𝛥TFR4
- GSM9104582 SLNCR𝛥TFR5_Rep1 SLNCR𝛥TFR5
- GSM9104583 SLNCR𝛥TFR5_Rep2 SLNCR𝛥TFR5
- GSM9104584 SLNCR𝛥TFR5_Rep3 SLNCR𝛥TFR5
- 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
- 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
- GSE91061 Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy 109 samples same disease briefing
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.