Bovine Ovarian Spheroid RNAseq Under Four Hydrogel Conditions

RNA sequencing data from bovine ovarian cortex samples cultured in four distinct hydrogel matrix formulations for 14 days. The dataset includes data from fresh tissue, pre-embedded spheroids, and spheroid-embedded constructs, with libraries prepared using ultra-low input protocols and sequenced on an Illumina NovaSeq. Author Marcia de Almeida Monteiro Melo Ferraz published the data on figshare under a CC-BY-4.0 license.

Use Cases

• Compare gene expression profiles between fresh ovarian tissue and cultured spheroids based on the described experimental stages.
• Analyze the transcriptional impact of alginate supplementation in collagen and dECM hydrogels based on the four matrix formulations.
• Investigate the relationship between hydrogel mechanical properties (e.g., stiffness characterized by nanoindentation) and cellular response.
• Benchmark alignment and preprocessing pipelines for bovine RNAseq data using the described STAR alignment to the Bos taurus genome.

Strengths

• Includes biological replicates for multiple conditions, with sample counts provided (e.g., n=4 for Col, n=3 for dECM).
• Detailed methodological description covering hydrogel preparation, crosslinking, library construction, and sequencing parameters.
• Hydrogel stiffness was mechanically characterized and reported with specific values (e.g., Col_Alg: 2,905.51 ± 3,242.21 Pa).

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Sample size is small for some conditions (e.g., Col_Alg: n = 1 biological replicate).
• The dataset is small (2.8 MB), which may limit the scope of analysis.

Provenance

Source

figshare

Collection Method

Experimental RNA sequencing of cultured bovine ovarian spheroids, with data processed through a described bioinformatics pipeline.

Freshness

Last updated 2026-04-20 22:51:55; freshness should be verified.