SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [RNA-seq]
RNA-seq (gene expression) · human · 13 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Small cell lung cancerThis series is part of our curated briefing on it.
- 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 GSE256347_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1079237 and SRA study SRP491005. 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.
- GSM8094134 H146 cells, untreated n1 (RNA-seq)
- GSM8094135 H146 cells, untreated n2 (RNA-seq)
- GSM8094136 H146 cells, untreated n3 (RNA-seq)
- GSM8094137 H146 cells, treated n1 (RNA-seq)
- GSM8094138 H146 cells, treated n2 (RNA-seq)
- GSM8094139 H146 cells, treated n3 (RNA-seq)
- GSM8094140 H146 cells, treated n4 (RNA-seq)
- GSM8094141 H82 cells, untreated n1 (RNA-seq)
- GSM8094142 H82 cells, untreated n2 (RNA-seq)
- GSM8094143 H82 cells, untreated n3 (RNA-seq)
- GSM8094144 H82 cells, treated n1 (RNA-seq)
- GSM8094145 H82 cells, treated n2 (RNA-seq)
- GSM8094146 H82 cells, treated n3 (RNA-seq)
- GSE239702 Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation 27 samples same disease briefing · shares neuroendocrine, transcription, factors
- GSE272002 LSD1 inhibitor, TAS1440, disrupts INSM1-LSD1 complex activating tumor-suppressive pathways via transcriptional reprogramming in neuroendocrine SCLC 324 samples same disease briefing · shares neuroendocrine, transcription
- GSE307259 c-JUN Enhances CRISPR Knock-In anti-B7-H3 CAR T-cell Function for Treatment of Small Cell Lung Cancer and thoracic SMARCA4-deficient undifferentiated tumors 12 samples same disease briefing · shares smarca4
- GSE280219 ONECUT2 reprograms neuroendocrine fate and is an actionable therapeutic target in small cell lung cancer. 24 samples same disease briefing · shares neuroendocrine
- GSE303770 ISL1: A Novel Neuroendocrine Subtype in Small Cell Lung Cancer Predicts Durable Response to Lurbinectedin 24 samples same disease briefing · shares neuroendocrine
- GSE330338 Multi-Omics Integration Identifies Critical Molecular Drivers and Alternative Splicing Events in Small Cell Lung Cancer 16 samples same disease briefing · shares splicing
- GSE274458 Crosstalk between cancer-associated fibroblasts and non-neuroendocrine tumor cells in small cell lung cancer involves in glycolysis and antigen-presenting features 15 samples same disease briefing · shares neuroendocrine
- GSE267310 Microenvironment Shapes Small Cell Lung Cancer Neuroendocrine States and Presents Therapeutic Opportunities 12 samples same disease briefing · shares neuroendocrine
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.