Background
Methods
RNA-sequencing of bovine oocytes
Publicly available annotations
RNA-Seq reads mapping and assembly
LincRNA identification pipeline
Tissue specificity score
RT-PCR analysis of lincRNA expression
Primer name | Primer sequence (5′-3′) | Application |
---|---|---|
lincRNA.41165-F | TGAAGAACCATTGCTCGAGAG | RT-PCR |
lincRNA.41165-R | GTATGGTAACTTATTATCTCAGG | RT-PCR |
lincRNA.25823-F | TTCAATGCCGGTTCTTCATGC | RT-PCR |
lincRNA.25823-R | CAAGTCCCTGCCAAGACATTG | RT-PCR |
lincRNA.2160-F | CCAACAGCTCATCTGTCAATT | RT-PCR |
lincRNA.2160-R | GAACTGTTTCCTGCTGTTTGC | RT-PCR |
lincRNA.17345-F | CAGCTTTGAAGTCACTTCAGG | RT-PCR |
lincRNA.17345-R | AAACATCTTCACTGAGTCTGG | RT-PCR |
lincRNA.25909-F | AGATTGCTGCAAACTCTGCAG | RT-PCR |
lincRNA.25909-R | ATCCAGTAGGCATTCATTGAG | RT-PCR |
RPL19-F | GAAATCGCCAATGCCAACTC | RT-PCR |
RPL19-R | GAGCCTTGTCTGCCTTCA | RT-PCR |
Results
Transcriptome reconstruction of bovine oocytes
RNA-sequencing | |
Number of raw reads | 84,860,000 |
Number of clean reads | 78,250,146 (94%) |
Number of mapped reads | 61,494,822 (78.4%) |
Number of concordant pair alignment | 50,425,754 (82%) |
Number of transcripts in each transfrag class | |
= | 2165 |
1c | 7408 |
j | 7106 |
e | 582 |
i | 4792 |
o | 1699 |
p | 2574 |
u | 8336 |
x | 462 |
s | 4 |
LincRNA identification | |
Number of novel transcripts with multiple exon | 2552 |
Number of transcripts without coding potential | 1627 |
Number of lincRNA (protein domain filter) | 1535 (1183 loci) |
Average length | 782 bp |
Number of average exon | 2.6 |