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Identification of reproductive performance-related genes in the bovine hypothalamus and pituitary gland and analysis of the regulatory network

GSE160721 Bos taurus RNA-seq (gene expression) 18 samples Submitted 2020/11/04 Platform GPL19172
At a glance

RNA-seq (gene expression) · Bos taurus · 18 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
18 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)
We explored the gene expression patterns of the pituitary gland and hypothalamus of Angus cows at different growth and developmental stages by deep sequencing the transcriptome and identified genes that affect bovine reproductive performance to provide new ideas for improving bovine fertility in production practice. We selected three 6-month-old (weaning period), three 18-month-old (first mating period) and three 30-month-old (early postpartum) Angus cows.
Read the full summary ↓
The physiological statuses of the cows in each group were the same, and their body shapes were similar. After quality control of the sequencing, the transcriptome analyses of 18 samples yielded 129.18 GB of clean data. Clean data for each sample reached 6.30 GB. The GC content was >47.61%, and the base percentage of Q30 was at least 94.19%. We detected 13280 and 13318 expressed genes in the pituitary gland and hypothalamus, respectively, and screened 35 and 50 differential genes for each, respectively. Differential genes in both tissues were mainly concentrated in metabolism, lipid synthesis, and immune-related pathways in the 18-month-old cows compared with those in the 6-month-old cows. The 30-month-old cows presented more regulated reproductive behavior, and pituitary CAMK4 was the main factor regulating the reproductive behavior during this period via the pathways for calcium signaling, longevity, oxytocin, and aldosterone synthesis and secretion.
This dataset
Open GSE160721 in finder → Find more 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 GSE160721_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 PRJNA669304 and SRA study SRP288420. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Samples in this study

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+ 18 more — browse all 18 samples with per-sample file links →

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