Expression profiling of HPV+ Patient Derived Xenografts (PDXs) by high throughput sequencing
RNA-seq (gene expression) · human · 21 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)
- Samples
- 21 samples: 21 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.
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 GSE193388_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 PRJNA796005 and SRA study SRP354301. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 21 sample titles: 21 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.
- GSM5799452 OPBT25-Biological replicate 1 [18170XR.01.04]
- GSM5799453 OPBT25-Biological replicate 2 [18170XR.01.05]
- GSM5799454 OPBT25-Biological replicate 3 [18170XR.01.06]
- GSM5799455 OPTT59-Biological replicate 1 [18170XR.01.07]
- GSM5799456 OPTT59-Biological replicate 2 [18170XR.01.08]
- GSM5799457 OPTT59-Biological replicate 3 [18170XR.01.09]
- GSM5799458 OPTT61-Biological replicate 1 [18170XR.01.10]
- GSM5799459 OPTT61-Biological replicate 2 [18170XR.01.11]
- GSM5799460 OPTT61-Biological replicate 3 [18170XR.01.12]
- GSM5799461 OPBT75-Biological replicate 1 [18170XR.01.13]
- GSM5799462 OPBT75-Biological replicate 2 [18170XR.01.14]
- GSM5799463 OPBT75-Biological replicate 3 [18170XR.01.15]
- GSM5799464 OPTT82-Biological replicate 1 [18170XR.01.16]
- GSM5799465 OPTT82-Biological replicate 2 [18170XR.01.17]
- GSM5799466 OPTT82-Biological replicate 3 [18170XR.01.18]
- GSM5799467 OPTT88-Biological replicate 1 [18170XR.01.19]
- GSM5799468 OPTT88-Biological replicate 2 [18170XR.01.20]
- GSM5799469 OPTT88-Biological replicate 3 [18170XR.01.21]
- GSM5799470 OPTT98-Biological replicate 1 [18170XR.01.22]
- GSM5799471 OPTT98-Biological replicate 2 [18170XR.01.23]
- GSM5799472 OPTT98-Biological replicate 3 [18170XR.01.24]
- GSE306800 Extracellular matrix-myCAF signatures correlate with resistance to neoadjuvant aPD-L1 immune checkpoint inhibition with durvalumab + metformin in HPV+ HNSCC 18 samples shares hpv
- GSE226620 CD161 expression of TRM cells counteracts the HPV-associated clinical benefit in oropharyngeal cancer immunotherapy 30 samples shares hpv
- GSE262419 Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes 4558 samples shares derived
- GSE263588 Comprehensive transcriptomic profiling of glioblastoma patient-derived primary tumor cell lines using bulk RNA-sequencing 49 samples shares derived
- GSE268014 Spatial transcriptomic analysis of tumor heterogeneity in HPV+ and HPV- Head and Neck Squamous Cell Carcinoma 39 samples shares hpv
- GSE217649 Bulk RNA sequencing for gene expression profileing of primary liver sinusoidal endothelial cells and iPSC-derived hepatic endoderm, septum mesenchymal cells, endothelial cells, and liver bud organoids 26 samples shares derived
- GSE333738 Genome-wide mapping of human H4K20me3 in the HN-SCC-151 HPV-negative head and neck squamous cell carcinoma cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs. 24 samples shares hpv
- GSE299997 Integrated profiling of iPSC-derived motor neurons carrying C9orf72, FUS, TARDBP, or SOD1 mutations 156 samples shares derived
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.