Type I IFN Dynamics Orchestrate Protective ICAM1⁺ Neutrophil Heterogeneity as an Early Checkpoint for Survival in Lethal Viral Infection [ICAM1 RNAseq]
RNA-seq (gene expression) · mouse · 19 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
- 19 samples: 6 × day1BMsurvived vs 6 × day1BMdied vs 3 × day1ICAM1positive vs 3 × day1ICAM1negativeGroups 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 GSE313167_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 PRJNA1378717 and SRA study SRP653991. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 4 replicated groups read from 19 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.
- GSM9359236 Circulating cells from day0,1,5 after VSV infection
- GSM9363161 day1BMsurvived_1 day1BMsurvived
- GSM9363162 day1BMsurvived_2 day1BMsurvived
- GSM9363163 day1BMsurvived_3 day1BMsurvived
- GSM9363164 day1BMsurvived_4 day1BMsurvived
- GSM9363165 day1BMsurvived_5 day1BMsurvived
- GSM9363166 day1BMsurvived_6 day1BMsurvived
- GSM9363167 day1BMdied_1 day1BMdied
- GSM9363168 day1BMdied_2 day1BMdied
- GSM9363169 day1BMdied_3 day1BMdied
- GSM9363170 day1BMdied_4 day1BMdied
- GSM9363171 day1BMdied_5 day1BMdied
- GSM9363172 day1BMdied_6 day1BMdied
- GSM9363173 day1ICAM1positive_1 day1ICAM1positive
- GSM9363174 day1ICAM1positive_2 day1ICAM1positive
- GSM9363176 day1ICAM1positive_3 day1ICAM1positive
- GSM9363179 day1ICAM1negative_1 day1ICAM1negative
- GSM9363181 day1ICAM1negative_2 day1ICAM1negative
- GSM9363184 day1ICAM1negative_3 day1ICAM1negative
- GSE313732 Type I IFN Dynamics Orchestrate Protective ICAM1⁺ Neutrophil Heterogeneity as an Early Checkpoint for Survival in Lethal Viral Infection [RNA-Seq] 78 samples shares icam1, ifn, heterogeneity, orchestrate, protective, neutrophil, checkpoint, dynamics
- GSE280164 An IFN/STAT1/CYBB Axis Defines Protective Plasmacytoid DC to Neutrophil Crosstalk in Aspergillus fumigatus Infected mice [RNA-seq] 24 samples shares ifn, protective, neutrophil
- GSE293493 Transcriptional effects of co-culture on the spatiotemporal dynamics of T cell motility and cancer-T cell interactions [bulk_seq_IFN] 10 samples shares ifn, dynamics
- GSE325703 PAX3-SIX2 muscle stem cell heterogeneity drives muscle-specific repair dynamics diversification 12 samples shares heterogeneity, dynamics
- GSE283255 Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [ATAC-seq2] 14 samples shares heterogeneity, orchestrate
- GSE283256 Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [ATAC-seq1] 10 samples shares heterogeneity, orchestrate
- GSE326200 Absence of Clec1a in murine cDC1s decrease IFN responses to necrotic cells 237 samples shares ifn
- GSE309564 IFNg shapes macrophage inflammatory responses by STAT1 isoform-specific epigenetic and transcriptional mechanisms [RNA-Seq] 72 samples shares ifn
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.