GEO series

The ubiquitin ligase CBL and Fas-associated factor 2 cooperate to regulate the innate immune response to M. tuberculosis

GSE314067 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/02/20 Platform GPL34295

At a glance

RNA-seq (gene expression) · human · 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: Homo sapiens (human)
Samples: 12 samples: 3 × Con_TB vs 3 × Con_mock vs 3 × shCBL_TB vs 3 × shCBL_mockGroups 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: The ubiquitin ligase CBL and Fas-associated factor 2 cooperate to regulate the innate immune response to M. tuberculosisPLoS pathogens · 2026

Summary (written by the submitters)

As a first line of host defense, macrophages must be able to effectively sense and respond to diverse types of pathogens, and while a particular response may be beneficial in some circumstances, it can be detrimental in others. Upon infection, Mycobacterium tuberculosis (Mtb) induces proinflammatory cytokines and activates antibacterial responses.

Read the full summary ↓

Surprisingly, Mtb also triggers antiviral responses that actually hinder the ability of macrophages to restrict Mtb growth. In Mtb-infected macrophages, the ubiquitin ligase CBL suppresses antiviral responses and preserves the antibacterial capacity of the macrophage. However, the mechanisms by which CBL regulates immune signaling are unknown. We found that CBL controls responses to multiple immune stimuli and broadly suppresses the expression of antiviral response genes. We used mass-spectrometry to identify potential CBL substrates, and found, in total, over 46,000 ubiquitylated peptides in Mtb-infected macrophages, including roughly 400 peptides with CBL-dependent ubiquitylation. We then performed genetic interaction analysis of CBL and its putative substrates, and identified the Fas associated factor 2 (FAF2) adapter protein as a key signaling molecule downstream of CBL. Together, these analyses reveal thousands of new ubiquitin-mediated signaling events and identify an important new regulator immune signaling.

Published in

The ubiquitin ligase CBL and Fas-associated factor 2 cooperate to regulate the innate immune response to M. tuberculosis

Truong T, Ray A, Martin K et al. · PLoS pathogens 2026 · PMID 41843626 · doi:10.1371/journal.ppat.1013974

This dataset

Open GSE314067 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 GSE314067_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 PRJNA1389921 and SRA study SRP655936. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41843626) ↗

Study design

3 × Con_TB vs 3 × Con_mock vs 3 × shCBL_TB vs 3 × shCBL_mock

Supports a between-group comparison across 12 samples.

How we read this: 4 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.

Samples in this study

GSM9381014 Con_TB_1 Con_TB
GSM9381015 Con_TB_2 Con_TB
GSM9381016 Con_TB_3 Con_TB
GSM9381017 Con_mock_1 Con_mock
GSM9381018 Con_mock_2 Con_mock
GSM9381019 Con_mock_3 Con_mock
GSM9381020 shCBL_TB_1 shCBL_TB
GSM9381021 shCBL_TB_2 shCBL_TB
GSM9381022 shCBL_TB_3 shCBL_TB
GSM9381023 shCBL_mock_1 shCBL_mock
GSM9381024 shCBL_mock_2 shCBL_mock
GSM9381025 shCBL_mock_3 shCBL_mock

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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.