|
| Status |
Public on May 09, 2022 |
| Title |
CON 5 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Ros 308
tissue: Hypothalamus
age: Posthatch day 42
treatment: Basal diet + 24oC
|
| Treatment protocol |
Birds were fed two dietary treatments; basal diets or 1% L-Citrulline supplemented diets. At 28 days old. Birds were allocated to thermoneutral (TNZ- 24oC, 60% RH) or high temperature (HS-35oC, 60% RH) environments. The study had four (4) treatments comprising of CON (TNZ + basal diet); A (TNZ + L-Cit diet); B (HS + basal diet); C (HS+ L-Cit diet). Each treatment had 6 replicates of 12 chickens each.
|
| Growth protocol |
The chicks were reared at 32oC for the first 3 days and the temperature was reduced by 2oC at 3 days interval until 24oC. Each chamber had three battery cages with double-tiers and a total of 8 cages per battery cage. The cage dimension was 38 × 47 × 35 cm and three birds were housed per cage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The hypothalamic samples (n =6/group) were lysed using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for RNA extraction in accordance to the manufacturer's protocol. The concentration and purity were detected and the quality of the library was tested by Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw data provided by the sequencing platform (Fastq files) were filtered for quality check.
The filtered reads were aligned to the chicken reference genome (assembly Gallus gallus_4.0) and annotated transcripts of the Ensembl gene annotation using an upgraded version of hisat2 with tophat
The htseq statistics (https://htseq.readthedocs.io/en/release_0.9.1/) was applied to compare the read count value of each gene as the original expression of the gene
RSeQC was used to analyze the expression saturation of the sequencing results and calculated the expression levels of all genes
The DE-Seq R package (http://www.bioconductor.org/packages/release/bioc/html/DESeq.html) was used to analyze and screen the differential expression of genes among groups
Assembly: Gallus_gallus.GRCg6a.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: excel table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 02, 2022 |
| Last update date |
May 09, 2022 |
| Contact name |
Victoria Anthony Uyanga |
| E-mail(s) |
uyangava@sdau.edu.cn
|
| Phone |
+8615069857298
|
| Organization name |
Shandong Agricultural University
|
| Department |
Animal Nutrition and Feed Science
|
| Lab |
Animal EcoNutrition Lab
|
| Street address |
61 Daizong Street, China
|
| City |
Taian |
| State/province |
Please select |
| ZIP/Postal code |
271000 |
| Country |
China |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE202003 |
Transcriptomics of hypothalamic responses of broiler chickens fed L-citrulline supplemented diets under different ambient temperatures |
|
| Relations |
| BioSample |
SAMN28027660 |
| SRA |
SRX15104786 |
