PDK1 regulates metabolic balance in osteosarcoma stem cells
RNA-seq (gene expression) · human · 15 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
- OsteosarcomaThis series is part of our curated briefing on it.
- Samples
- 15 samples: 5 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 GSE297211_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 PRJNA1263015 and SRA study SRP585326. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8986368 non-OSC_1 non-OSC
- GSM8986369 non-OSC_2 non-OSC
- GSM8986370 non-OSC_3 non-OSC
- GSM8986371 OSC_1 OSC
- GSM8986372 OSC_2 OSC
- GSM8986373 OSC_3 OSC
- GSM8986374 shCtrl_1 shCtrl
- GSM8986375 shCtrl_2 shCtrl
- GSM8986376 shCtrl_3 shCtrl
- GSM8986377 shPDK1_1_1 shPDK1_1
- GSM8986378 shPDK1_1_2 shPDK1_1
- GSM8986379 shPDK1_1_3 shPDK1_1
- GSM8986380 shPDK1_2_1 shPDK1_2
- GSM8986381 shPDK1_2_2 shPDK1_2
- GSM8986382 shPDK1_2_3 shPDK1_2
- GSE268670 SPRR1A is a potential therapeutic target for osteosarcoma: in vitro and in vivo evaluations using novel generated artificial osteosarcoma cancer stem cell-like cells 3 samples same disease briefing · shares osteosarcoma, stem
- GSE42352 Genome-wide gene expression profiling of mesenchymal stem cells, osteosarcoma cells, and osteosarcoma cell lines. 118 samples same disease briefing · shares osteosarcoma, stem
- GSE207333 Analysis of lncRNA-mRNA co-expression profiles in CD133 positive cancer stem-like cells from osteosarcoma cell line Saos-2 12 samples same disease briefing · shares osteosarcoma, stem
- GSE255956 BRD4 Regulates Gemcitabine Efficacy by Modulating Autophagy Activity in Osteosarcoma Cells [Cell lines] 10 samples same disease briefing · shares osteosarcoma
- GSE255957 BRD4 Regulates Gemcitabine Efficacy by Modulating Autophagy Activity in Osteosarcoma Cells [Patient samples] 6 samples same disease briefing · shares osteosarcoma
- GSE259286 In vitro modeling of nutritional and mitochondrial-targeted therapies for osteosarcoma 98 samples same disease briefing · shares osteosarcoma
- GSE292011 Adaptor protein CIN85 potentiates migration of osteosarcoma cells 12 samples same disease briefing · shares osteosarcoma
- GSE253548 The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma 90 samples same disease briefing · shares osteosarcoma
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.