Raw RNA-seq Count Data from Mycobacterium avium Infected Intestinal Organoids

Paula E. Schweizer's transcriptomic profiling of patient-derived ileal organoids infected with Mycobacterium avium paratuberculosis (MAP) or treated with forskolin over a 48-hour time course. The 13.9 MB dataset, last updated in June 2026, reveals culture-induced transcriptional drift as a primary confounder. Spatial transcriptomics further demonstrated that MAP infection selectively counteracted culture-induced changes in enterocyte gene expression.

Use Cases

• Modeling host-pathogen interactions based on transcriptomic profiling of Mycobacterium avium paratuberculosis infection.
• Analyzing culture-induced transcriptional drift based on time-course gene expression changes over 48 hours.
• Investigating the confounding effects of pharmacological interventions like forskolin treatment on organoid models.
• Studying spatial gene expression patterns in enterocytes based on crypt-villus expression data.

Strengths

• Includes spatial transcriptomics data demonstrating culture-induced changes independent of crypt-villus patterns.
• Provides a 48-hour time-course transcriptomic profile comparing infection and pharmacological treatment.
• Dataset is shared under a CC-BY-4.0 license, facilitating open reuse.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• The 13.9 MB size suggests a relatively small dataset.

Provenance

Source

figshare

Collection Method

Time-course transcriptomic profiling of patient-derived ileal organoids microinjected with Mycobacterium avium paratuberculosis or treated with forskolin.

Freshness

Last updated 2026-06-04 18:00:12; freshness should be verified.