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. 2017 Sep 15;13(9):e1006997. doi: 10.1371/journal.pgen.1006997

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.