← BioTransfer GEO Dataset Finder
GEO series

Transcriptomic responses in the host during mosquito-transmitted and blood passaged Plasmodium chabaudi infections.

GSE178515 Mus musculus (mouse) RNA-seq (gene expression) 87 samples Submitted 2024/06/12 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 87 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
87 samples: 30 conditions, mostly in triplicateGroups 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.
Summary (written by the submitters)
Plasmoidium chabuadi AS infections initiated by mosquito transmitted infections give rise to an attenuated blood-stage infection when compared to serially blood passaged parasites. Furthermore, Plasmoidium chabuadi CB infections have an increased virulence as compared with Plasmoidium chabuadi AS. We compared the immune response in the spleens induced by these two types of parasites and two types of infection routes in order to determine what may cause this attenuation. Spleens were taken at several timepoints during the blood-stage infection and RNA-seq analysis was performed.
This dataset
Open GSE178515 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE178515_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA739466 and SRA study SRP324748. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
30 conditions, mostly in triplicate
Mosquito Transmitted P. chabaudi AS Infection… ×4 Serially Blood Passaged P. chabaudi CB Infect… ×4 Mosquito Transmitted P. chabaudi CB Infection… ×4 Serially Blood Passaged P. chabaudi AS Infect… ×3 Serially Blood Passaged P. chabaudi AS Infect… ×3 Serially Blood Passaged P. chabaudi AS Infect… ×3 Serially Blood Passaged P. chabaudi AS Infect… ×3 Serially Blood Passaged P. chabaudi AS Infect… ×3 +22 more

Supports a between-group comparison across 87 samples.

How we read this: 30 replicated groups read from 87 sample titles; they account for 87 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.

Samples in this study

+ 47 more — browse all 87 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.