|
| Status |
Public on Jun 16, 2023 |
| Title |
CT_1 |
| Sample type |
SRA |
| |
|
| Source name |
ileum of Taiping chicken
|
| Organism |
Gallus gallus |
| Characteristics |
breed: Taiping
diet: CT
tissue: ileum
age: two months
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of the six libraries was extracted using the standard TRIzol™. Agarose gel electrophoresis, Nano Photometer® Spectrophotometer and Bioanalyzer 2100 System were employed to evaluate the quantity and quality of the total RNAs.
About 3 μg total RNA from each sample was used to construct RNA library. Six sequencing libraries were generated using the NEBNext® Multiplex small RNA Library Prep Kit for Illumina®
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were further filtered using fastp(version 0.18.0). After removal of reads containing adapters, containing more than 10% of unknown nucleotides (N) and low quality reads containing more than 50% of low quality (Q-value≤20) bases. The rRNA mapped reads were removed by using Short reads alignment tool Bowtie2
The remaining clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1in a reference-based approach.
The expression abundance and variations of each gene was estimated using abundance and variations by calculated FPKM （fragment per kilobase of transcript per million mapped reads）value. RNAs differential expression analysis was performed by DESeq2 between two different groups
The transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed transcripts.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 19, 2020 |
| Last update date |
Jun 16, 2023 |
| Contact name |
Fang Ma |
| E-mail(s) |
mfang@tsnu.edu.cn
|
| Organization name |
Tianshui normal university
|
| Department |
College of Bioengineering and Technology
|
| Street address |
South Xihe Road
|
| City |
Tianshui |
| State/province |
Qinzhou District |
| ZIP/Postal code |
741000 |
| Country |
China |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE152878 |
RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic and fructo-oligosaccharides |
|
| Relations |
| BioSample |
SAMN15329696 |
| SRA |
SRX8586158 |
