 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 23, 2024 |
| Title |
c_MGKC_2 |
| Sample type |
SRA |
| |
|
| Source name |
ileum
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: ileum
group: MGKC
breed: AA broiler
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (ET101-01-V2, Beijing TransGen Biotech Co., Ltd, Beijing, China). The RNA concentration and integrity were detected using a Fragment Analyzer (Agilent, California, USA). RNA samples that complied with the criteria of having a concentration of more than 40 ng/μL, an integrity value greater than 7.0, and a total content of 1 μg or more were chosen for further experimentation.
Oligo dT beads were employed to enrich mRNA carrying a poly(A) tail. Subsequently, the RNA was fragmented, and first-strand cDNA production was initiated through random N6-primed reverse transcription. This was followed by the synthesis of second-strand cDNA, where dUTP was utilized instead of dTTP. The resulting cDNA then underwent end-repair and subsequent 3’ adenylation. Afterward, adaptors were attached to the termini of these 3’ adenylated cDNA segments. Before initiating PCR amplification, the strand marked with dUTP was selectively degraded using Uracil-DNA-Glycosylase (UDG). The remaining strand was then amplified to create a cDNA library suitable for sequencing. To enrich the purified cDNA template, multiple rounds of PCR amplification were carried out using PCR primers. Heat was used to denature the PCR product, and subsequently, the single-stranded DNA was circularized with the aid of a splint oligo and DNA ligase. Ultimately, DNA nanoball synthesis and sequencing were executed on the DNBSEQ platform in paired-end 150 sequencing mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Description |
ileum from c_MGKC_2
|
| Data processing |
Sequencing data were called raw reads, and quality control was then performed on the raw reads to obtain clean reads. After quality control, the filtered clean reads were aligned to the reference sequence. Then, gene expression quantification, gene difference analysis, and enrichment analysis were performed. Data quality control was completed using SOAPnuke (v1.5.2). Genome alignment was completed using HISAT2 (2.0.4). Transcript quantification and differential comparison were completed via Bowtie2 (v2.2.5) and DESeq2 (v1.2.8), respectively. Genes were considered to be significantly different if they had a q value (adjusted p value) less than 0.05
Assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002315.6/
Supplementary files format and content: gene expression FPKM file, excel
|
| |
|
| Submission date |
Aug 04, 2024 |
| Last update date |
Oct 23, 2024 |
| Contact name |
Jian Wang |
| E-mail(s) |
wangjian0825@sxau.edu.cn
|
| Organization name |
shanxi agricultural university
|
| Street address |
mingxiannanlu 1
|
| City |
Jinzhong |
| ZIP/Postal code |
030801 |
| Country |
China |
| |
|
| Platform ID |
GPL30495 |
| Series (1) |
| GSE273913 |
Dietary supplementation with Bacillus subtilis KC1 alleviates the negative effects of Mycoplasma gallisepticum on growth performance and amino acid metabolism of broiler chickens |
|
| Relations |
| BioSample |
SAMN43024797 |
| SRA |
SRX25595069 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
