RNA sequencing of neuroblastoma cells treated with selinexor or with XPO1 knockdown
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
- NeuroblastomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × IMR5 - dmso vs 3 × IMR5 - selinexor vs 3 × IMR5 - sicontrol vs 3 × IMR5 - siXPO1-10Groups 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
- Combining selinexor with alisertib to target the p53 pathway in neuroblastomaNeoplasia (New York, N.Y.) · 2022
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 GSE178937_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 PRJNA741521 and SRA study SRP325661. 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.
- GSM5401545 IMR5 - dmso_rep1 IMR5 - dmso
- GSM5401546 IMR5 - dmso_rep2 IMR5 - dmso
- GSM5401547 IMR5 - dmso_rep3 IMR5 - dmso
- GSM5401548 IMR5 - selinexor_rep1 IMR5 - selinexor
- GSM5401549 IMR5 - selinexor_rep2 IMR5 - selinexor
- GSM5401550 IMR5 - selinexor_rep3 IMR5 - selinexor
- GSM5401551 IMR5 - sicontrol_rep1 IMR5 - sicontrol
- GSM5401552 IMR5 - sicontrol_rep2 IMR5 - sicontrol
- GSM5401553 IMR5 - sicontrol_rep3 IMR5 - sicontrol
- GSM5401554 IMR5 - siXPO1-10_rep1 IMR5 - siXPO1-10
- GSM5401555 IMR5 - siXPO1-10_rep2 IMR5 - siXPO1-10
- GSM5401556 IMR5 - siXPO1-10_rep3 IMR5 - siXPO1-10
- GSE112914 Differential gene expression analysis of MYCN-amplified neuroblastoma cells after Doxycycline inducible shRNA knockdown of JMJD6 gene expression 44 samples same disease briefing · shares neuroblastoma, knockdown
- GSE183729 Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity 18 samples same disease briefing · shares neuroblastoma
- GSE275538 Identification of EPLIN as a novel MYCN-independent target in neuroblastoma and medulloblastoma 1 samples same disease briefing · shares neuroblastoma
- GSE130612 Multi-omics analysis of neuroblastoma cells reveals a diversity of malignant transformations 64 samples same disease briefing · shares neuroblastoma
- GSE120572 A mechanistic classification of clinical phenotypes in neuroblastoma 394 samples same disease briefing · shares neuroblastoma
- GSE181582 IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression 264 samples same disease briefing · shares neuroblastoma
- GSE12494 SNP data from Neuroblastoma samples 262 samples same disease briefing · shares neuroblastoma
- GSE16476 Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma 88 samples same disease briefing · shares neuroblastoma
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.