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SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity [GEX]

GSE239450 Homo sapiens (human) RNA-seq (gene expression) 26 samples Submitted 2024/10/30 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 26 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
Homo sapiens (human)
Samples
26 samples: 26 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
SARS-CoV-2 infection elucidates features of pregnancy-specific immunityCell reports · 2024
Summary (written by the submitters)
Pregnancy is a risk factor for increased severity of SARS-CoV-2 and other respiratory infections. The mechanisms underlying this risk have not been well-established, partly due to limited understanding of how pregnancy shapes and modulates immune responses. To gain insight into the roles of pregnancy in shaping the immune responses we collected peripheral blood mononuclear cells (PBMC) from 17 non-pregnant and 9 pregnant donors with various COVID severities and compared their immunological profiles.
Published in
SARS-CoV-2 infection elucidates features of pregnancy-specific immunity
Oh DS, Kim E, Normand R et al. · Cell reports 2024 · PMID 39504241 · doi:10.1016/j.celrep.2024.114933
This dataset
Open GSE239450 in finder → Find more human 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 GSE239450_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 PRJNA999323. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39504241) ↗
Study design
26 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 26 sample titles: 26 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.

Samples in this study
Datasets on a similar topic

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