Impact of autoimmune inflammation on HSPC and monocyte gene expression
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 24 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
- A distinct metabolic and epigenetic state drives trained immunity in HSC-derived macrophages from autoimmune miceCell stem cell · 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 GSE215003_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 PRJNA888067 and SRA study SRP401500. 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 24 sample titles: 24 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.
- GSM6619873 GMP, Control, replicate 1 [control_GMP_1]
- GSM6619874 GMP, Control, replicate 2 [control_GMP_2]
- GSM6619875 GMP, Control, replicate 3 [control_GMP_3]
- GSM6619876 SLAM, Control, replicate 1 [control_HSC_1]
- GSM6619877 SLAM, Control, replicate 2 [control_HSC_2]
- GSM6619878 SLAM, Control, replicate 3 [control_HSC_3]
- GSM6619879 BM Mon, Control, replicate 1 [control_monocyte_1]
- GSM6619880 BM Mon, Control, replicate 2 [control_monocyte_2]
- GSM6619881 BM Mon, Control, replicate 3 [control_monocyte_3]
- GSM6619882 MPPG/M, Control, replicate 1 [control_MPP3_1]
- GSM6619883 MPPG/M, Control, replicate 2 [control_MPP3_2]
- GSM6619884 MPPG/M, Control, replicate 3 [control_MPP3_3]
- GSM6619885 GMP, Pristane, replicate 1 [lupus_GMP_1]
- GSM6619886 GMP, Pristane, replicate 2 [lupus_GMP_2]
- GSM6619887 GMP, Pristane, replicate 3 [lupus_GMP_3]
- GSM6619888 SLAM, Pristane, replicate 1 [lupus_HSC_1]
- GSM6619889 SLAM, Pristane, replicate 2 [lupus_HSC_2]
- GSM6619890 SLAM, Pristane, replicate 3 [lupus_HSC_3]
- GSM6619891 BM Mon, Pristane, replicate 1 [lupus_monocyte_1]
- GSM6619892 BM Mon, Pristane, replicate 2 [lupus_monocyte_2]
- GSM6619893 BM Mon, Pristane, replicate 3 [lupus_monocyte_3]
- GSM6619894 MPPG/M, Pristane, replicate 1 [lupus_MPP3_1]
- GSM6619895 MPPG/M, Pristane, replicate 2 [lupus_MPP3_2]
- GSM6619896 MPPG/M, Pristane, replicate 3 [lupus_MPP3_3]
- GSE313869 Impact of Fc engineering on the transcriptional profile of monocytes and interstitial macrophages in the lungs of Hu-FcgR Tg mice after MA30 infection 36 samples shares monocyte, impact
- GSE326335 Bulk RNA Sequencing of Chimera-Derived Monocyte-Derived Macrophages Targeted for Mitochondrial ROS During Peak Experimental Autoimmune Encephalomyelitis 14 samples shares autoimmune, monocyte
- GSE261266 TPO stimulation midulates gene expression of iKMT2A-MLLT3 HSPC 34 samples shares hspc
- GSE274860 RNA sequestration in P-bodies sustains myeloid leukemia [HSPC_RNAseq] 24 samples shares hspc
- GSE271146 Inflammation Impacts Androgen Receptor Signaling in Basal Prostate Stem Cells Through Interleukin 1 Receptor Antagonist 282 samples shares impact
- GSE286217 Transcriptional and epigenetic programs of in vitro-expanded HSPCs and their T cell progenitors progeny 59 samples shares hspc
- GSE263945 Inflammation Rewires the Enteric Nervous System Through Neurogenic Monocyte Recruitment 33 samples shares monocyte
- GSE228455 Gene expression profile at single cell level of monocytes sorted from C57BL/6J mouse ear tissue at 3 weeks post Leishmania major infection [scRNA-seq] 218 samples shares monocyte
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.