Cytoplasmic ATM restricts oncolytic VSVΔ51 replication by sustaining TBK1-IRF3 signaling in glioblastoma cells
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)
- Topic
- GlioblastomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × LN-18 wild-type mock vs 3 × LN-18 sgATM mock vs 3 × LN-18 wild-type VSVΔ51 vs 3 × LN-18 sgATM VSVΔ51Groups 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 GSE342072_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 PRJNA1505557 and SRA study SRP723061. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9922624 LN-18 wild-type mock rep1 LN-18 wild-type mock
- GSM9922625 LN-18 wild-type mock rep2 LN-18 wild-type mock
- GSM9922626 LN-18 wild-type mock rep3 LN-18 wild-type mock
- GSM9922627 LN-18 sgATM mock rep1 LN-18 sgATM mock
- GSM9922628 LN-18 sgATM mock rep2 LN-18 sgATM mock
- GSM9922629 LN-18 sgATM mock rep3 LN-18 sgATM mock
- GSM9922630 LN-18 wild-type VSVΔ51 rep1 LN-18 wild-type VSVΔ51
- GSM9922631 LN-18 wild-type VSVΔ51 rep2 LN-18 wild-type VSVΔ51
- GSM9922632 LN-18 wild-type VSVΔ51 rep3 LN-18 wild-type VSVΔ51
- GSM9922633 LN-18 sgATM VSVΔ51 rep1 LN-18 sgATM VSVΔ51
- GSM9922634 LN-18 sgATM VSVΔ51 rep2 LN-18 sgATM VSVΔ51
- GSM9922635 LN-18 sgATM VSVΔ51 rep3 LN-18 sgATM VSVΔ51
- GSE112648 SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells 18 samples same disease briefing · shares glioblastoma
- GSE131928 single cell RNA-seq analysis of adult and paediatric IDH-wildtype Glioblastomas 2 samples same disease briefing · shares glioblastoma
- GSE107560 Ivy Glioblastoma Atlas Project 305 samples same disease briefing · shares glioblastoma
- GSE13041 Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age 267 samples same disease briefing · shares glioblastoma
- GSE10878 Integrative Genome-wide Analysis of Glioblastoma. 60 samples same disease briefing · shares glioblastoma
- GSE112650 SOX4/11 Enhances NGN2 Reprogramming Glioblastoma Cells into Neuron Cells by Modulating RhoA and CDC42/RAC1 Pathway Activity 30 samples same disease briefing · shares glioblastoma
- GSE112645 SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells 12 samples same disease briefing · shares glioblastoma
- GSE115459 Exosome-transmitted RVT1 from reactive astrocytes promotes recurrence glioblastoma proliferation 9 samples same disease briefing · shares glioblastoma
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.