Remodeling of tissue-resident macrophages by MEF2D-expressing cancer precursors primes for liver tumorigenesis [RNA-Seq]
RNA-seq (gene expression) · mouse · 17 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
- 17 samples: 4 × KC1 vs 4 × KC2 vs 3 × Normal_Liver_CtrlGroups 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.
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 GSE278097_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 PRJNA1158494 and SRA study SRP531400. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 3 replicated groups read from 17 sample titles; they account for 11 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.
- GSM8539562 MEF2D_KO1_eHCC
- GSM8539563 MEF2D_KO2_eHCC
- GSM8539564 MEF2D_KO3_eHCC
- GSM8539565 MEF2D_WT1_eHCC
- GSM8539566 MEF2D_WT2_eHCC
- GSM8539567 MEF2D_WT3_eHCC
- GSM8539568 Normal_Liver_Ctrl_1 Normal_Liver_Ctrl
- GSM8539569 Normal_Liver_Ctrl_2 Normal_Liver_Ctrl
- GSM8539570 Normal_Liver_Ctrl_3 Normal_Liver_Ctrl
- GSM8539571 KC1_1 KC1
- GSM8539572 KC1_2 KC1
- GSM8539573 KC1_3 KC1
- GSM8539574 KC1_4 KC1
- GSM8539575 KC2_1 KC2
- GSM8539576 KC2_2 KC2
- GSM8539577 KC2_3 KC2
- GSM8539578 KC2_4 KC2
- GSE239469 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling [RNA-seq] 28 samples shares tumorigenesis, remodeling, rna-seq
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophages, remodeling
- GSE268774 Lymph node macrophages drive immune tolerance and resistance to cancer therapy by expression of the immune-regulatory cytokine IL-33 [RNA-seq] 48 samples shares macrophages, rna-seq
- GSE292815 Diet-induced phospholipid remodeling dictates ferroptosis sensitivity and tumorigenesis in the pancreas 39 samples shares tumorigenesis, remodeling
- GSE337601 XCR1+ and CD11b+ migratory dendritic cells cooperate for the crosspriming of intratumoral CD8+ T cells with a tissue-resident memory phenotype [RNA-Seq] 36 samples shares tissue-resident, rna-seq
- GSE285614 Adipocyte death drives fat redistribution from adipocytes to hepatocytes in steatotic liver disease via S100A8+ macrophages [RNA-seq] 34 samples shares macrophages, rna-seq
- GSE325329 Transcriptomic profiling of macrophages that phagocytosed apoptotic Treg or conventional CD4⁺ T (Tconv) cells under different polarization conditions [RNA-Seq] 28 samples shares macrophages, rna-seq
- GSE237783 Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [RNA-Seq] 28 samples shares macrophages, 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.