RNA-sequencing of primary human glioblastoma resected tissue before and after a personalized, neoantigen-based vaccine plus poly-ICLC (NeoVax); tissues from a Phase 1 clinical trial
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × Subject_1_pre_NeoVax_region vs 3 × Subject_2_pre_NeoVax_region vs 2 × Subject_3_pre_NeoVax_region vs 2 × Subject_4_pre_NeoVax_regionGroups 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.
- Paper
- Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed GlioblastomaClinical cancer research : an official journal of the American Association for Cancer Research · 2024
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 GSE237936_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 PRJNA997267 and SRA study SRP450776. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 10 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.
- GSM7656652 Subject_1_pre_NeoVax_region_1 Subject_1_pre_NeoVax_re…
- GSM7656653 Subject_1_pre_NeoVax_region_2 Subject_1_pre_NeoVax_re…
- GSM7656654 Subject_1_pre_NeoVax_region_3 Subject_1_pre_NeoVax_re…
- GSM7656655 Subject_2_pre_NeoVax_region_1 Subject_2_pre_NeoVax_re…
- GSM7656656 Subject_2_pre_NeoVax_region_2 Subject_2_pre_NeoVax_re…
- GSM7656657 Subject_2_pre_NeoVax_region_3 Subject_2_pre_NeoVax_re…
- GSM7656658 Subject 3_pre_NeoVax_region_1
- GSM7656659 Subject_3_pre_NeoVax_region_2 Subject_3_pre_NeoVax_re…
- GSM7656660 Subject_3_pre_NeoVax_region_3 Subject_3_pre_NeoVax_re…
- GSM7656661 Subject_3_post_NeoVax
- GSM7656662 Subject_4_pre_NeoVax_region_1 Subject_4_pre_NeoVax_re…
- GSM7656663 Subject_4_pre_NeoVax_region_2 Subject_4_pre_NeoVax_re…
- GSE263588 Comprehensive transcriptomic profiling of glioblastoma patient-derived primary tumor cell lines using bulk RNA-sequencing 49 samples shares rna-sequencing, glioblastoma, primary
- GSE255626 Next generation sequencing from primary glioblastoma patient tissues (Total RNA-seq) 109 samples shares glioblastoma, primary
- GSE254145 Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence [seq] 79 samples shares glioblastoma, primary
- GSE264695 Neoadjuvant anti-PD1 immunotherapy for surgically accessible recurrent glioblastoma: clinical and molecular outcomes of a stage 2 single-arm expansion cohort 20 samples shares glioblastoma, clinical
- GSE301688 Preclinical Evaluation of the Efficacy of a Cyclin-dependent Kinase Inhibitor Ribociclib in Combination with Letrozole Against Patient-Derived Glioblastoma Cells 18 samples shares glioblastoma, clinical
- GSE266210 Bulk RNA-sequencing results of p16INK4A-high and -low glioblastoma, IDH-wild type, grade 4. 11 samples shares rna-sequencing, glioblastoma
- GSE279852 Single-cell RNA-sequencing of undifferentiated pleomorphic sarcoma, myxofibrosarcoma, and liposarcoma samples from patients participating in a clinical trial studying BO-112 plus Nivolumab and hypofractionated pre-operative radiotherapy. 10 samples shares rna-sequencing, clinical
- GSE238012 Integrating multisector molecular characterization into personalized peptide vaccine design for patients with newly diagnosed glioblastoma. 16 samples shares glioblastoma, personalized
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.