Correcting the immune microenvironment disturbed by the overactivation of the neutrophil-driven microglia positive feedback loop efficiently suppressed pathological retinal angiogenesis
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: 4 × Neu group vs 4 × Neu+NETS vs 4 × CTGroups 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 GSE325169_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 PRJNA1438744 and SRA study SRP684573. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 3 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.
- GSM9597092 Neu group 1 Neu group
- GSM9597093 Neu group 2 Neu group
- GSM9597094 Neu group 3 Neu group
- GSM9597095 Neu group 4 Neu group
- GSM9597096 Neu+NETS 1 Neu+NETS
- GSM9597097 Neu+NETS 2 Neu+NETS
- GSM9597098 Neu+NETS 3 Neu+NETS
- GSM9597099 Neu+NETS 4 Neu+NETS
- GSM9597100 CTR 1 CT
- GSM9597101 CTR 2 CT
- GSM9597102 CTR 3 CT
- GSM9597103 CTR 4 CT
- GSE271038 Natural killer cells cooperate with neutrophils to suppress pathological angiogenesis in neovascular age-related macular degeneration 22 samples shares pathological, angiogenesis
- GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares microenvironment
- GSE218173 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [acid] 150 samples shares microenvironment
- GSE259380 TG6050, an oncolytic vaccinia virus encoding interleukin-12 and anti-CTLA-4 antibody induces tumor regression through profound tumor microenvironment remodeling and strong antitumor adaptive immune response [RNA-seq] 149 samples shares microenvironment
- GSE305266 The cortical microenvironment drives early immune organization and controls early osteoclastogenesis in bone healing 90 samples shares microenvironment
- GSE239602 Single-cell and spatial transcriptomics uncovers the role of senescent vascular cells in pathological arterial remodeling during murine atherosclerosis 82 samples shares pathological
- GSE316139 Studying the role of humanized-TLR8 on immune cell dynamics in the placental microenvironment in a spontaneous mouse model of aPL-induced pregnancy loss 57 samples shares microenvironment
- GSE310560 Deep profiling of multiple mouse tumor microenvironments using scRNAseq 56 samples shares microenvironment
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.