FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [RNA-Seq]
RNA-seq (gene expression) · mouse · 20 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
- Mus musculus (mouse)
- Samples
- 20 samples: 8 conditions, mostly in triplicateGroups 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.
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 GSE247845_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 PRJNA1040817 and SRA study SRP472103. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 8 replicated groups read from 20 sample titles; they account for 20 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.
- GSM7901471 K tumors, replicate 1 K tumors,
- GSM7901472 K tumors, replicate 2 K tumors,
- GSM7901473 K tumors, replicate 3 K tumors,
- GSM7901474 KN tumors, replicate 1 KN tumors,
- GSM7901475 KN tumors, replicate 2 KN tumors,
- GSM7901476 KN tumors, replicate 3 KN tumors,
- GSM7901477 KNF1F2 tumors, replicate 1 KNF1F2 tumors,
- GSM7901478 KNF1F2 tumors, replicate 2 KNF1F2 tumors,
- GSM7901479 KNF1F2 tumors, replicate 3 KNF1F2 tumors,
- GSM7901480 N neoplasias, replicate 1 N neoplasias,
- GSM7901481 N neoplasias, replicate 2 N neoplasias,
- GSM7901482 N neoplasias, replicate 3 N neoplasias,
- GSM7901483 22E-EtOH replicate 1 22E-EtOH
- GSM7901484 22E-EtOH replicate 2 22E-EtOH
- GSM7901485 22E-4OHT replicate 1 22E-4OHT
- GSM7901486 22E-4OHT replicate 2 22E-4OHT
- GSM7901487 KG1A-EtOH replicate 1 KG1A-EtOH
- GSM7901488 KG1A-EtOH replicate 2 KG1A-EtOH
- GSM7901489 KG1A-4OHT replicate 1 KG1A-4OHT
- GSM7901490 KG1A-4OHT replicate 2 KG1A-4OHT
- GSE302857 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [RNA-seq] 81 samples shares reprogramming, epigenomic, rna-seq
- GSE312828 Integrated stress response couples mitochondrial fitness with lineage reprogramming to drive cancer evolution. [RNA-Seq] 24 samples shares reprogramming, lineage, rna-seq
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares foxa1, reprogramming
- GSE268822 Transcriptional landscapes underlying Notch-induced lineage conversion and reprogramming of mammary cells 840 samples shares reprogramming, lineage
- GSE222745 Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [scRNA-Seq] 422 samples shares reprogramming, rna-seq
- GSE248585 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma (ssRNA-Seq) 46 samples shares adenocarcinoma, rna-seq
- GSE300288 Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockade in precancerous phase [scRNA-seq] 31 samples shares adenocarcinoma, rna-seq
- GSE325692 Multi-omic analysis reveals brain-blood concordance and persistent neuroimmune reprogramming with stress and toxicant exposure in a mouse model of Gulf War Illness [RNA-Seq] 30 samples shares reprogramming, rna-seq
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.