α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 6 conditions, mostly with about 4 replicates eachGroups 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 GSE99296_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 PRJNA388056 and SRA study SRP108023. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM2640608 ET_w_Gln_rep1 ET_w_Gln
- GSM2640609 ET_w_Gln_rep2 ET_w_Gln
- GSM2640610 ET_w_Gln_rep3 ET_w_Gln
- GSM2640611 ET_w_Gln_rep4 ET_w_Gln
- GSM2640612 ET_w_o_Gln_rep1 ET_w_o_Gln
- GSM2640613 ET_w_o_Gln_rep2 ET_w_o_Gln
- GSM2640614 ET_w_o_Gln_rep3 ET_w_o_Gln
- GSM2640615 ET_w_o_Gln_rep4 ET_w_o_Gln
- GSM2640616 ET_AKG_w_o_Gln_rep1 ET_AKG_w_o_Gln
- GSM2640617 ET_AKG_w_o_Gln_rep2 ET_AKG_w_o_Gln
- GSM2640618 ET_AKG_w_o_Gln_rep3 ET_AKG_w_o_Gln
- GSM2640619 ET_AKG_w_o_Gln_rep4 ET_AKG_w_o_Gln
- GSM2640620 CTRL_rep1 CTRL
- GSM2640621 CTRL_rep2 CTRL
- GSM2640622 IL4_6h_rep1 IL4_6h
- GSM2640623 IL4_6h_rep2 IL4_6h
- GSM2640624 LPS_6h_rep1 LPS_6h
- GSM2640625 LPS_6h_rep2 LPS_6h
- GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares macrophage, activation
- GSE335147 Mitochondrial profiling across macrophage states reveals inhibition of IL-4/IL-13 reprogramming by the integrated stress response 24 samples shares reprogramming, macrophage
- GSE282695 STAT3 regulates pathogen control and clearance in macrophages by reprogramming inflammation-induced microbial defense response 18 samples shares reprogramming, macrophage
- GSE294258 Intracellular iron homeostasis-regulated epigenetic reprogramming contributes to -7/del(7q) leukemia 71 samples shares reprogramming, epigenetic
- GSE276300 EGR2 O-GlcNAcylation Orchestrates the Development of Protumoral Macrophages to Limit CD8+ T Cell Antitumor Responses. 27 samples shares orchestrates, macrophage
- GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares macrophage
- GSE318801 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. 20 samples shares macrophage
- GSE319397 Particle Reprogramming of the TLR–Ferroptosis Axis and Immunometabolic Pathways Inhibits Myeloid Suppression to Improve Checkpoint Blockade in Prostate Cancer 9 samples shares reprogramming
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.