Eradicating neuroblastomas by an RBM39 degrader in combination with anti-GD2 immunotherapy regardless of cancer cell state alterations
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- 18 samples: 8 conditions, mostly in duplicateGroups 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
- RBM39 degrader invigorates natural killer cells to eradicate neuroblastoma despite cancer cell plasticitybioRxiv : the preprint server for biology · 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 GSE251920_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 PRJNA1055918 and SRA study SRP479693. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 18 sample titles; they account for 16 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.
- GSM7989951 SKNAS-Naive-H3K27ac-01 SKNAS-Naive-H3K27ac
- GSM7989952 SKNAS-Naive-H3K27ac-02 SKNAS-Naive-H3K27ac
- GSM7989953 SKNAS-IR1-H3K27ac-01 SKNAS-IR1-H3K27ac
- GSM7989954 SKNAS-IR1-H3K27ac-02 SKNAS-IR1-H3K27ac
- GSM7989955 SKNAS-IR2-H3K27ac-01 SKNAS-IR2-H3K27ac
- GSM7989956 SKNAS-IR2-H3K27ac-02 SKNAS-IR2-H3K27ac
- GSM7989957 NB14-ctrl1-H3K27ac-01 NB14-ctrl1-H3K27ac
- GSM7989958 NB14-ctrl1-H3K27ac-02 NB14-ctrl1-H3K27ac
- GSM7989959 NB14-IR1-H3K27ac-01
- GSM7989960 NB14-IR2-H3K27ac-02
- GSM7989976 GEMM CTRL1 GEMM CTRL
- GSM7989977 GEMM CTRL2 GEMM CTRL
- GSM7989978 GEMM Res1 GEMM Res
- GSM7989979 GEMM Res2 GEMM Res
- GSM7989980 NB14 CTRL1 NB14 CTRL
- GSM7989981 NB14 CTRL2 NB14 CTRL
- GSM7989982 NB14 Res1 NB14 Res
- GSM7989983 NB14 Res2 NB14 Res
- GSE164456 Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma 69 samples same disease briefing
- GSE153823 Effect of ASCL1 phosphorylation status on chromatin binding and target regulation in neuroblastoma 52 samples same disease briefing
- GSE120572 A mechanistic classification of clinical phenotypes in neuroblastoma 394 samples same disease briefing
- GSE181582 IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression 264 samples same disease briefing
- GSE12494 SNP data from Neuroblastoma samples 262 samples same disease briefing
- GSE16476 Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma 88 samples same disease briefing
- GSE130612 Multi-omics analysis of neuroblastoma cells reveals a diversity of malignant transformations 64 samples same disease briefing
- GSE112914 Differential gene expression analysis of MYCN-amplified neuroblastoma cells after Doxycycline inducible shRNA knockdown of JMJD6 gene expression 44 samples same disease briefing
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.