SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 13 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
- 13 samples: 13 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
- SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicingJournal of hematology & oncology · 2024
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 GSE256345_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 PRJNA1079234 and SRA study SRP490990. 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 13 sample titles: 13 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.
- GSM8094116 H146 cells, untreated n1 (ATAC-seq)
- GSM8094117 H146 cells, untreated n2 (ATAC-seq)
- GSM8094118 H146 cells, untreated n3 (ATAC-seq)
- GSM8094119 H146 cells, untreated n4 (ATAC-seq)
- GSM8094120 H146 cells, treated n1 (ATAC-seq)
- GSM8094121 H146 cells, treated n2 (ATAC-seq)
- GSM8094122 H146 cells, treated n3 (ATAC-seq)
- GSM8094123 H82 cells, untreated n1 (ATAC-seq)
- GSM8094124 H82 cells, untreated n2 (ATAC-seq)
- GSM8094125 H82 cells, untreated n3 (ATAC-seq)
- GSM8094126 H82 cells, treated n1 (ATAC-seq)
- GSM8094127 H82 cells, treated n2 (ATAC-seq)
- GSM8094128 H82 cells, treated n3 (ATAC-seq)
- GSE300575 Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [ChIP-seq] 22 samples shares rest, transcription
- GSE245175 Neuroblastoma heterogeneity and plasticity over disease progression are rooted in the dynamics of an early sympathetic transcriptional trajectory 79 samples shares transcription, plasticity
- GSE252883 Epiregulon: Inference of single-cell transcription factor activity to dissect mechanisms of lineage plasticity and drug response 38 samples shares transcription, plasticity
- GSE263716 Epigenetic Analysis of SLE Disease Activity in Resting Naive (rN) and Transitional (T1T2) B cells 62 samples shares rest
- GSE300844 Deciphering the functional impact of Alzheimer’s Disease-associated variants in resting and proinflammatory immune cells 192 samples shares rest
- GSE263717 Epigenomic profiles of SLE resting and transitional B cells 150 samples shares rest
- GSE329527 Antigen-restricted Candida albicans Th17 cells link oral-gut immunity and adopt pathogenic features during intestinal inflammation 81 samples shares rest
- GSE278549 PBAF associates with repressed chromatin to enable REST occupancy 61 samples shares rest
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.