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| Status |
Public on Nov 08, 2023 |
| Title |
FecB ++ sheep in the luteal phase-2 |
| Sample type |
SRA |
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| Source name |
oviduct
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| Organism |
Ovis aries |
| Characteristics |
phase: luteal
tissue: oviduct
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the stored oviduct tissues with TRIzol reagent. 1.3ug of extracted RNA was used for library construction.
RNA libraries were constructed using an NEBNext® Ultra™ RNA Library Prep Kit (NEB, Ipswich, MA, USA) for Illumina® according to the manufacturer’s recommendations.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
WL2
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| Data processing |
The raw reads in FASTQ format were filtered using fastp to remove low-quality reads containing poly-N, adapters, or poly A, T, C, or G sequences. The obtained clean reads were mapped to the Ovis aries reference genome (Oar_v3.1) using HISAT2.
Coding and non-coding RNAs transcripts were distinguished using Coding-Non-Coding Index (CNCI) , Coding Potential Calculator 2 (CPC2) , and Protein Families database (Pfam) software. StringTie was used to assemble the mRNA transcripts.
The fragments per kilobase per million mapped reads (FPKM) method was used to estimate the expression levels of lncRNA and mRNA transcripts.
Assembly: Oar_v3.1
Supplementary files format and content: text file include FPKM values for each samole
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| Submission date |
Nov 04, 2023 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Weihao Chen |
| Organization name |
Yangzhou University
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| Street address |
88 Daxuenan Rd.
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| City |
Yangzhou |
| ZIP/Postal code |
214000 |
| Country |
China |
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| Platform ID |
GPL19778 |
| Series (1) |
| GSE247022 |
Expression profiles of oviductal mRNAs and lncRNAs in the follicular phase and luteal phase of sheep (Ovis aries) with two fecundity gene (FecB) genotypes |
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| Relations |
| BioSample |
SAMN15887662 |
| SRA |
SRX9604220 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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