Gene expression data of LT-HSC, MEP and CMP cells from Mx1cre;Atf4 fl/fl mice(cKO) BM and those from controls
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 6 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.
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 GSE233677_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 PRJNA977574 and SRA study SRP440105. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7432279 WT_CMP_rep 1 WT_CMP
- GSM7432280 WT_CMP_rep 2 WT_CMP
- GSM7432281 WT_MEP_rep 1 WT_MEP
- GSM7432282 WT_MEP_rep 2 WT_MEP
- GSM7432283 WT_LT-HSC_rep 1 WT_LT-HSC
- GSM7432284 WT_LT-HSC_rep 2 WT_LT-HSC
- GSM7432285 cKO_CMP_rep 1 cKO_CMP
- GSM7432286 cKO_CMP_rep 2 cKO_CMP
- GSM7432287 cKO_MEP_rep 1 cKO_MEP
- GSM7432288 cKO_MEP_rep 2 cKO_MEP
- GSM7432289 cKO_LT-HSC_rep 1 cKO_LT-HSC
- GSM7432290 cKO_LT-HSC_rep 2 cKO_LT-HSC
- GSE314281 bulkRNA-seq LSKs CMPs MEPs GMPs from bone marrow and spleen 32 samples shares mep, cmp
- GSE276647 Gene expression profile of microglia following traumatic brain injury and nasal anti-CD3 treatment at acute and chronic timepoints 54 samples shares mep
- GSE260482 Gene expression profile at single cell level of CD45+ immune cells from 4TO7 cells (Ctrl or Tim3-KD) liver metastasis at different timepoints 6 samples shares mep
- GSE279249 Effects of depletion of Mel18 on gene expression in mouse long-term hematopoietic stem cells [RNAseq_LT-HSC] 6 samples shares lt-hsc
- GSE261088 Gene expression profile at single cell level of non-parenchymal cells from Fibrosis and Tumor (FAT) Metabolic Dysfunction-Associated Steatohepatitis (MASH) model vs healthy liver at 12- and 24-week timepoints. 4 samples shares mep
- GSE332646 Bulk RNA-seq of juvenile mouse liver following NDMA or saline treatment in WT and Mgmt-/- genotypes across multiple timepoints 214 samples shares mep
- GSE276649 Gene expression profile of microglia following traumatic brain injury and adoptive transfer of Tregs at acute and chronic timepoints 21 samples shares mep
- GSE291047 Role of ATF4 in regulation of kidney gene expressions, signaling pathways and functions [mouse] 17 samples shares atf4
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.