Table 1. Details of the tissues and cell types sequenced to generate the TxBF RNA-Seq dataset for the sheep gene expression atlas.
| Subset | Tissue Type | Library Type | Sequencing Depth | Total Number of Libraries | Number of Individuals |
|---|---|---|---|---|---|
| Core Atlas | Liver, spleen, ovary, testes, hippocampus, kidney medulla, bicep muscle, reticulum, ileum, thymus, left ventricle | Total RNA-Seq | >100 million paired-end reads per sample | 59 (~10 per individual) | 3 adult males and 3 adult females |
| Core Atlas | GI tract, reproductive tract, brain, endocrine, cardiovascular, lymphatic, musculo-skeletal-system, immune cells | mRNA-Seq | >25 million paired-end reads per sample | 202 (~45 per individual) | 3 adult males and 3 adult females |
| LPS Time Course (Core Atlas) |
BMDM 0h (-LPS) and 7h (+LPS) | Total RNA-Seq | >100 million paired-end reads per sample | 12 (2 time points per individual) | 3 adult males and 3 adult females |
| LPS Time Course (Core Atlas) |
BMDM 0h, 2h, 4h, 7h, 24h post LPS treatment | mRNA-Seq | >25 million paired-end reads per sample | 30 (3 time points per individual) | 3 adult males and 3 adult females |
| GI Tract Time Series | Gastro-intestinal tract | mRNA-Seq | >25 million paired-end reads per sample | 108 (~12 tissues per individual) | 9 lambs (3 at birth, 3 at one week and 3 at 8 weeks) |
| Early Development (blastocysts) |
Day 7 blastocysts (3 pools of 8) | Nu Gen Single Cell Ovation Kit | >66 million paired-end reads per sample | 3 | 3 pools |
| Early Development (day 23) |
Day 23 whole embryos | Total RNA-Seq | >100 million paired-end reads per sample | 3 | 3 embryos (all male) |
| Early Development (day 35) | Liver, brain, embryonic fibroblasts | mRNA-Seq | >25 million paired-end reads per sample | 7 | 3 embryos (two female and one male) |
| Early Development (day 100) | Liver, ovary | mRNA-Seq | >25 million paired-end reads per sample | 5 | 3 female (liver) 2 female (ovary) |
| Maternal Reproductive Time Series (days 23, 35 and 100) | Placenta and ovary | mRNA-Seq | >25 million paired-end reads per sample | 12 | 2 females per time point |
Tissues and cells were chosen to cover all major organ systems. All libraries were Illumina 125bp paired end stranded libraries. See S2 Table for a detailed list of the tissues and cell types sequenced.