Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 26 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)
- Samples
- 26 samples: 12 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
- Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastomaCell reports. Medicine · 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 GSE240506_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 PRJNA1003934 and SRA study SRP454299. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 26 samples.
How we read this: 12 replicated groups read from 26 sample titles; they account for 26 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.
- GSM7699148 BE2C-ctrl-01 BE2C-ctrl
- GSM7699149 BE2C-ctrl-02 BE2C-ctrl
- GSM7699150 BE2C-QCR-01 BE2C-QC
- GSM7699151 BE2C-QCR-02 BE2C-QC
- GSM7699152 BE2C_Ctrl_1 BE2C_Ctrl
- GSM7699153 BE2C_Ctrl_2 BE2C_Ctrl
- GSM7699154 BE2C-QC6352R_1 BE2C-QC6352
- GSM7699155 BE2C-QC6352R_2 BE2C-QC6352
- GSM7699156 GIMEN_RFP_1 GIMEN_RFP
- GSM7699157 GIMEN_RFP_2 GIMEN_RFP
- GSM7699158 GIMEN_MYCN_1 GIMEN_MYCN
- GSM7699159 GIMEN_MYCN_2 GIMEN_MYCN
- GSM7699160 GIMEN_DMSO_1 GIMEN_DMSO
- GSM7699161 GIMEN_DMSO_2 GIMEN_DMSO
- GSM7699162 GIMEN_QC6352_1 GIMEN_QC6352
- GSM7699163 GIMEN_QC6352_2 GIMEN_QC6352
- GSM7699164 SH_SY5Y_DMSO_1 SH_SY5Y_DMSO
- GSM7699165 SH_SY5Y_DMSO_2 SH_SY5Y_DMSO
- GSM7699166 SH_SY5Y_QC6352_1 SH_SY5Y_QC6352
- GSM7699167 SH_SY5Y_QC6352_2 SH_SY5Y_QC6352
- GSM7699168 GEMM_CTRL1 GEMM_CTRL
- GSM7699169 GEMM_CTRL2 GEMM_CTRL
- GSM7699170 GEMM_CTRL3 GEMM_CTRL
- GSM7699171 GEMM_QC6352_1 GEMM_QC6352
- GSM7699172 GEMM_QC6352_2 GEMM_QC6352
- GSM7699173 GEMM_QC6352_3 GEMM_QC6352
- GSE242099 The role of histone lysine demethylases in a genetically defined subset of clonal hematopoiesis 30 samples shares demethylase, histone
- GSE299173 Transcriptomic and epigenetic profiling of adrenergic and mesenchymal neuroblastomas with cell state conversion [RNA-Seq] 0 samples shares neuroblastoma, adrenergic
- GSE181582 IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression 264 samples shares neuroblastoma
- GSE80154 Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma 144 samples shares neuroblastoma
- GSE244123 Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer 103 samples shares neuroblastoma
- GSE251920 Eradicating neuroblastomas by an RBM39 degrader in combination with anti-GD2 immunotherapy regardless of cancer cell state alterations 18 samples shares neuroblastoma
- GSE286396 Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation [ChIP-seq] 12 samples shares demethylase
- GSE251918 Eradicating neuroblastomas by an RBM39 degrader in combination with anti-GD2 immunotherapy regardless of cancer cell state alterations [RNA-seq] 8 samples 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.