GEO series

Persistent effects on bovine granulosa cell transcriptome after resolution of uterine disease

GSE128697 Bos taurus RNA-seq (gene expression) 16 samples Submitted 2019/03/22 Platform GPL21659

At a glance

RNA-seq (gene expression) · Bos taurus · 16 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: Bos taurus
Samples: 16 samples
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.

Summary (written by the submitters)

Metritis is associated with reduced fertility in dairy cows, but the mechanisms are unclear because the disease resolves several weeks before insemination. One hypothesis is that metritis causes persistent changes in granulosa cells during follicle development, which might be evident in the transcriptome of granulosa cells from dominant follicles weeks after parturition.

Read the full summary ↓

To test this hypothesis we collected follicular fluid and granulosa cells from dominant follicles 63 days post partum from cows previously diagnosed with metritis, at least 6 weeks after resolution of the disease, and from cows not diagnosed with metritis (control cows). Bacterial lipopolysaccharide was detected in follicular fluid, and concentrations were associated with follicular fluid IL-8 and glucose concentrations. Transcriptome analysis using RNAseq revealed 177 differentially expressed genes in granulosa cells collected from cows that had metritis compared with control cows. The most upregulated genes were ITLN1, NCF2, CLRN3, FSIP2 and ANKRD17, and the most downregulated genes were ACSM1, NR4A2, GHITM, CBARP and NR1I3. Pathway analysis indicated that the differentially expressed genes were involved with immune function, cell-cell communication, cell cycle and cellular metabolism. Predicted upstream regulators of the differentially expressed genes included NFκB, IL-21 and lipopolysaccharide, which are associated with infection and immunity. Our data provide evidence for a persistent effect of metritis on the transcriptome of granulosa cells in ovarian follicles after the resolution of disease

This dataset

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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 GSE128697_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 PRJNA528510 and SRA study SRP189109. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 16 more — browse all 16 samples with per-sample file links →

Datasets on a similar topic

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GSE42535 Gene expression in cultured bovine ovarian granulosa 15 samples shares granulosa, bovine
GSE94541 Identification of potential biomarkers in donor cows for in vitro embryo production by granulosa cells transcriptomics 24 samples shares granulosa
GSE255879 Change in the ability of granulosa cells to elongate transzonal projections during follicle development 24 samples shares granulosa
GSE11495 Regulation of granulosa and theca cell transcriptomes during ovarian antral follicle development. 12 samples shares granulosa
GSE72038 Effects of Intramuscular Administration of Folic Acid and Vitamin B12 on Granulosa Cells Gene Expression in Postpartum Dairy Cow 6 samples shares granulosa
GSE54138 Effect of maternal age on the granulosa cell transcriptome of preovulatory dominant follicle in cattle 6 samples shares granulosa

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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.