PIKfyve inhibition synergizes with Cisplatin to provoke antitumor immunogenicity in melanoma by alleviating lysosomal degradation of STING
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: 18 samples, each with a distinct title — no replicated groupsGroups 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 GSE218241_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 PRJNA902795 and SRA study SRP408467. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 3 as controls.
How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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.
- GSM6737729 S0_1_MUM2B cells, DMSO, 72hours
- GSM6737730 S0_2_MUM2B cells, DMSO, 72hours
- GSM6737731 S0_3_MUM2B cells, DMSO, 72hours
- GSM6737732 Y_1_MUM2B cells, YM201636, 72hours
- GSM6737733 Y_2_MUM2B cells, YM201636, 72hours
- GSM6737734 Y_3_MUM2B cells, YM201636, 72hours
- GSM6737735 Cis_1_MUM2B cells, Cisplatin, 72hours
- GSM6737736 Cis_2_MUM2B cells, Cisplatin, 72hours
- GSM6737737 Cis_3_MUM2B cells, Cisplatin, 72hours
- GSM6737738 Y_C_1_MUM2B cells, YM201636+Cisplatin, 72hours
- GSM6737739 Y_C_2_MUM2B cells, YM201636+Cisplatin, 72hours
- GSM6737740 Y_C_3_MUM2B cells, YM201636+Cisplatin, 72hours
- GSM6737741 Y_11_Tumor bearing mice，YM201636
- GSM6737742 Y_12_Tumor bearing mice，YM201636
- GSM6737743 Y_13_Tumor bearing mice，YM201636
- GSM6737744 ctr_3_Tumor bearing mice，PBS
- GSM6737745 ctr_4_Tumor bearing mice，PBS
- GSM6737746 ctr_30_Tumor bearing mice，PBS
- GSE91061 Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy 109 samples same disease briefing
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing
- GSE130956 Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines 12 samples same disease briefing
- 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
- GSE300877 Diverse roles of SERPINE1 in regulating cellular proliferation and invasion 6 samples same disease briefing
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples same disease briefing
- GSE317605 A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer [CITE-Seq] 168 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.