Uterus epithelial cells collected from Holstein Friesian cows with or without embryos

Uterus environment is crucial for embryo development. One of fundamental factors affecting uterus condition is presence or absence of embryo. Sample collection were conducted for 3 cows. The data included two groups (Cows were subjected to super ovulation following artificial insemination or the same cows were subjected to super ovulation but injected with saline.) Super ovulation protocol was CIDR injection and Estradiol treatment, 5 days after the treatment, cows were subjected to follicle stimulating hormone treatments (8 times with 12h interval). At the last days of FSH treatments, CIDR was removed and 2 days after CIDR removal artificial insemination was conducted. 7 days after insemination, uterus was flushed to collect embryos and uterus epithelial cells. Presence of normal embryos were confirmed under stereomicroscope. Uterus epithelial cells were centrifuged to collect cellular pellets. The RNA in the cell pellets were extracted using RNAqueous-Micro Total RNA Isolation Kit. RNA quality and concentration were examined using a Bioanalyzer (Agilent technologies, Palo Alto, CA, USA); a cDNA library was constructed using an NEB Ultra RNA prep kit. Clusters were generated on a cBot (Illumina), and one lane of the multiplied samples was sequenced as 100 bp reads (single read) on the HiSeq2500 (Illumina). Image analysis, base calling and quality filtering were performed using the CLC genomic workbench (ver 9.5.4). Sequence data were filtered to discard the adapter sequence, ambiguous nucleotides and low-quality sequences. The remaining sequence data were aligned to the Bos Taurus genome sequence UMD3.1 [URL: ftp://ftp.ensembl.org/pub/release-89/fasta/bos_taurus/dna/] to count sequence reads.