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IFIT2-induced transcriptomic changes in Mycobacterium tuberculosis infected macrophages

GSE297207 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/06/16 Platform GPL32271
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 8 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.
Paper
IFIT2-induced transcriptomic changes in Mycobacterium tuberculosis infected macrophagesFrontiers in cellular and infection microbiology · 2025
Summary (written by the submitters)
Interferon-induced protein with tetratricopeptide repeat 2 (IFIT2) is known for its antiviral activity and has recently been implicated in the defense against Mycobacterium tuberculosis (M. tb). This study employed global transcriptomics to investigate the downstream effects of IFIT2 induction in THP-1 macrophages infected with R179 M.
Read the full summary ↓
tb, aiming to elucidate its role and downstream contributing factors that aid it in intracellular M. tb killing. Using a vector-based overexpression approach, IFIT2 expression was induced in THP-1 cells infected with R179 M. tb, followed by RNA extraction 12 hours postinfection and AmpliSeq-based targeted transcriptome sequencing. Bioinformatics analysis identified 282 differentially expressed genes (DEGs), of which 189 were upregulated and 90 were downregulated (FDR <0.05). Filtering for highly significant DEGs (|log2(fold change) | > 1.5) yielded 70 genes, predominantly upregulated, with functional enrichment in pathways such as defense response to viruses and cytokine-mediated signaling. Signaling pathway impact analysis highlighted pathway activation and inhibition of the tuberculosis (TB) pathway. RT-qPCR validation confirmed the upregulation of selected DEGs (ISG15, CMPK2, RSAD2, IFI44L, IFI44), corroborating the AmpliSeq data. This study provides comprehensive insights into the transcriptomic profile induced by IFIT2 in TB, revealing critical downstream contributors and pathways that underpin IFIT2’s ability to combat M. tb infection.
Published in
IFIT2-induced transcriptomic changes in Mycobacterium tuberculosis infected macrophages
Manful EE, Pietersen RD, Baker B · Frontiers in cellular and infection microbiology 2025 · PMID 40463504 · doi:10.3389/fcimb.2025.1536446
This dataset
Open GSE297207 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 GSE297207_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 PRJNA1262999 and SRA study SRP585283. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40463504) ↗
Study design
8 conditions, mostly in triplicate
THP-1 Cells-Infected, IFIT2-induced,12hrs, ×3 THP-1 Cells-Infected-Untreated, Control, 12hr… ×3 THP-1 Cells-Infected, CKB-induced, 12hrs, ×3 THP-1 Cells -Uninfected-Untreated, Control, 1… ×3 THP-1 Cells-Infected-Untreated, Control, 4hrs, ×3 THP-1 Cells-Infected-EmptyVector-induced, 12h… ×3 THP-1 Cells-Uninfected-Untreated, Control, 4h… ×3 THP-1 Cells-Uninfected, IFIT2-induced, 12hrs, ×2 +1 more

Supports a between-group comparison across 23 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 23 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
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