Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticity
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 86 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- NeuroblastomaThis series is part of our curated briefing on it.
- Samples
- 86 samples: 86 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.
- Paper
- Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticityThe EMBO journal · 2024
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 GSE240593_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1004275 and SRA study SRP454510. 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 86 sample titles: 86 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.
- GSM7703126 IMR32_DMSO_24h, rep1 [ATAC-seq]
- GSM7703127 IMR32_DMSO_24h, rep2 [ATAC-seq]
- GSM7703128 IMR32_ACBI1_24h, rep1 [ATAC-seq]
- GSM7703129 IMR32_ACBI1_24h, rep2 [ATAC-seq]
- GSM7703130 BE(2)C_DMSO_24h, rep1 [ATAC-seq]
- GSM7703131 BE(2)C_DMSO_24h, rep2 [ATAC-seq]
- GSM7703132 BE(2)C_ACBI1_24h, rep1 [ATAC-seq]
- GSM7703133 BE(2)C_ACBI1_24h, rep2 [ATAC-seq]
- GSM7703134 IMR5_siCtrl_48h, rep1 [ATAC-seq]
- GSM7703135 IMR5_siCtrl_48h, rep2 [ATAC-seq]
- GSM7703136 IMR5_siSMA4-5_48h, rep1 [ATAC-seq]
- GSM7703137 IMR5_siSMA4-5_48h, rep2 [ATAC-seq]
- GSM7703138 IMR5_siSMA4-7_48h, rep1 [ATAC-seq]
- GSM7703139 IMR5_siSMA4-7_48h, rep2 [ATAC-seq]
- GSM7703140 IMR32_DMSO_24h, input
- GSM7703141 IMR32_ACBI1_24h, input
- GSM7703142 IMR32_DMSO_24h, HAND2, ChIP
- GSM7703143 IMR32_ACBI1_24h, HAND2, ChIP
- GSM7703144 IMR32_DMSO_24h, PHOX2B, ChIP
- GSM7703145 IMR32_ACBI1_24h, PHOX2B, ChIP
- GSM7703146 IMR32_DMSO_24h, GATA3, ChIP
- GSM7703147 IMR32_ACBI1_24h, GATA3, ChIP
- GSM7703148 IMR32_DMSO_24h, MYCN, ChIP
- GSM7703149 IMR32_ACBI1_24h, MYCN, ChIP
- GSM7703150 IMR32_DMSO_24h, H3K27ac, ChIP
- GSM7703151 IMR32_ACBI1_24h, H3K27ac, ChIP
- GSM7703152 IMR32_siCtrl_72h, input
- GSM7703153 IMR32_siSMARCA4-5_72h, input
- GSM7703154 IMR32_siCtrl_72h, HAND2, ChIP
- GSM7703155 IMR32_siSMARCA4-5_72h, HAND2, ChIP
- GSM7703156 IMR32_siCtrl_72h, PHOX2B, ChIP
- GSM7703157 IMR32_siSMARCA4-5_72h, PHOX2B, ChIP
- GSM7703158 IMR32_siCtrl_72h, GATA3, ChIP
- GSM7703159 IMR32_siSMARCA4-5_72h, GATA3, ChIP
- GSM7703160 IMR32_siCtrl_72h, MYCN, ChIP
- GSM7703161 IMR32_siSMARCA4-5_72h, MYCN, ChIP
- GSM7703162 IMR32_siCtrl_72h, H3K27ac, ChIP
- GSM7703163 IMR32_siSMARCA4-5_72h, H3K27ac, ChIP
- GSM7703164 IMR5 cells, DMSO, 8h, rep1 [RNA-seq]
- GSM7703165 IMR5 cells, DMSO, 8h, rep2 [RNA-seq]
+ 46 more — browse all 86 samples with per-sample file links →
- GSE183729 Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity 18 samples same disease briefing · shares neuroblastoma, plasticity
- GSE164456 Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma 69 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
- 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
- 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
- GSE167478 MYCN directly regulates TET1 expression to control 5-hmC distribution and enhance neuroblastoma cell migration in hypoxia 22 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.