Table 1. Summary of reads from raw data to cleaned sequences for small RNAs in Receptive Versus Pre-receptive Endometrium in goat.
| Item | R library (receptive endometrium) | P library (pre-receptive endometrium) | ||
|---|---|---|---|---|
| Total (%) | Unique (%) | Total (%) | Unique (%) | |
| Raw reads | 7717603(100%) | 1028383(100%) | 6307668(100%) | 401202(100%) |
| 3’ADT&length | 2461440(31.89%) | 618853(60.18%) | 589698(9.35%) | 215293(53.66%) |
| Junk reads | 6783(0.09%) | 3180(0.31%) | 1778(0.03%) | 1188(0.3%) |
| Rfam | 801419(10.38%) | 41322(4.02%) | 274894(4.36%) | 21723(5.41%) |
| mRNA | 236734(3.07%) | 80731(7.85%) | 62332(0.99%) | 24153(6.02%) |
| Repeats | 104302(1.35%) | 12589(1.22%) | 39894(0.63%) | 5197(1.3%) |
| rRNA | 601798(7.8%) | 17270(0.22%) | 191856(3.04%) | 9341(0.15%) |
| tRNA | 96971(1.26%) | 6847(0.09%) | 38937(0.62%) | 2487(0.04%) |
| snoRNA | 23920(0.31%) | 6185(0.08%) | 17307(0.27%) | 4362(0.07%) |
| snRNA | 20979(0.27%) | 4648(0.06%) | 7101(0.11%) | 2284(0.04%) |
| other Rfam RNA | 57751(0.75%) | 6372(0.08%) | 19693(0.31%) | 3249(0.05%) |
| Clean reads | 4233874(54.86%) | 284622(%) | 5386427(85.39%) | 139040(34.66%) |
Notes: 3’ADT & length filter: reads removed due to 3ADT not found and length with<18 and >26 were remove (for animals). Junk: > = 2N, > = 7A, > = 8C, > = 6G, > = 7T, > = 10 Dimer, > = 6 Trimer, or > = 5 Tetramer. Rfam: Collection of many common non-coding RNA families except micro RNA; http://rfam.janelia.org. mRNA: http://goat.kiz.ac.cn/GGD/download.htm; Repeats: Prototypic sequences representing repetitive DNA from different eukaryotic species; http://www.girinst.org/repbase, there is overlap in mapping of reads with rRNA, tRNA, snRNA, snoRNA and repeats.