Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 54 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
- 54 samples: 54 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
- Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acidNature communications · 2025
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 GSE253786_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 PRJNA1067130 and SRA study SRP484940. 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 54 sample titles: 54 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.
- GSM8027907 CHP-134, DMSO, Replicate1, RARA ChIP
- GSM8027908 CHP-134, DMSO, Replicate2, RARA ChIP
- GSM8027909 CHP-134, DMSO, RARA ChIP, input
- GSM8027910 CHP-134, 1day 2uM ATRA, Replicate1, RARA ChIP
- GSM8027911 CHP-134, 1day 2uM ATRA, Replicate2, RARA ChIP
- GSM8027912 CHP-134, 1day 2uM ATRA, RARA ChIP, input
- GSM8027913 CHP-134, DMSO, Replicate1, SMAD9 ChIP
- GSM8027914 CHP-134, DMSO, Replicate2, SMAD9 ChIP
- GSM8027915 CHP-134, DMSO, SMAD9 ChIP, input
- GSM8027916 CHP-134, 1day 2uM ATRA, Replicate1, SMAD9 ChIP
- GSM8027917 CHP-134, 1day 2uM ATRA, Replicate2, SMAD9 ChIP
- GSM8027918 CHP-134, 1day 2uM ATRA, SMAD9 ChIP, input
- GSM8027919 CHP-134, 3day 2uM ATRA, Replicate1, SMAD9 ChIP
- GSM8027920 CHP-134, 3day 2uM ATRA, Replicate2, SMAD9 ChIP
- GSM8027921 CHP-134, 3day 2uM ATRA, SMAD9 ChIP, input
- GSM8027922 CHP-134, 6day 2uM ATRA, Replicate1, SMAD9 ChIP
- GSM8027923 CHP-134, 6day 2uM ATRA, Replicate2, SMAD9 ChIP
- GSM8027924 CHP-134, 6day 2uM ATRA, SMAD9 ChIP, input
- GSM8027925 CHP-134, DMSO, Replicate1, SMAD4 ChIP
- GSM8027926 CHP-134, DMSO, Replicate2, SMAD4 ChIP
- GSM8027927 CHP-134, DMSO, SMAD4 ChIP, input
- GSM8027928 CHP-134, 1day 2uM ATRA, Replicate1, SMAD4 ChIP
- GSM8027929 CHP-134, 1day 2uM ATRA, Replicate2, SMAD4 ChIP
- GSM8027930 CHP-134, 1day 2uM ATRA, SMAD4 ChIP, input
- GSM8027931 TGW, DMSO, Replicate1, RARA ChIP
- GSM8027932 TGW, DMSO, Replicate2, RARA ChIP
- GSM8027933 TGW, DMSO, RARA ChIP, input
- GSM8027934 TGW, 1day 2uM ATRA, Replicate1, RARA ChIP
- GSM8027935 TGW, 1day 2uM ATRA, Replicate2, RARA ChIP
- GSM8027936 TGW, 1day 2uM ATRA, RARA ChIP, input
- GSM8027937 TGW, 3day 0.5uM ATRA, Replicate1, RARA ChIP
- GSM8027938 TGW, 3day 0.5uM ATRA, Replicate2, RARA ChIP
- GSM8027939 TGW, 3day 0.5uM ATRA, RARA ChIP, input
- GSM8027940 TGW, DMSO, Replicate1, SMAD4 ChIP
- GSM8027941 TGW, DMSO, Replicate2, SMAD4 ChIP
- GSM8027942 TGW, DMSO, SMAD4 ChIP, input
- GSM8027943 TGW, 1day 2uM ATRA, Replicate1, SMAD4 ChIP
- GSM8027944 TGW, 1day 2uM ATRA, Replicate2, SMAD4 ChIP
- GSM8027945 TGW, 1day 2uM ATRA, SMAD4 ChIP, input
- GSM8027946 TGW, 3day 2uM ATRA, Replicate1, SMAD4 ChIP
+ 14 more — browse all 54 samples with per-sample file links →
- 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, protein
- 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
- GSE130612 Multi-omics analysis of neuroblastoma cells reveals a diversity of malignant transformations 64 samples same disease briefing · shares neuroblastoma
- GSE153823 Effect of ASCL1 phosphorylation status on chromatin binding and target regulation in neuroblastoma 52 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
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.