|
| Status |
Public on Aug 27, 2023 |
| Title |
Spleen_CK_rep2_Ribo |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Spleen
breed: White Leghorn
age: 7day
genotype: wt
treatment: chicken was inoculated with the same amount of PBS via foot pad injection.Spleen was collected on day 3 after infection.
|
| Treatment protocol |
Group A was the experimental group (ARV), and each chicken was inoculated with 0.1ml 104 TCID50/0.1ml ARV S1133 virus by foot pad injection. Group B was the control group (CON), which was inoculated with the same amount of PBS via foot pad injection. Samples were collected on day 3 after infection.
|
| Growth protocol |
"White Leghorn" SPF chicken eggs were purchased from Beijing Boehringer Ingelheim Vital Biotechnology Co, Ltd. (Beijing, China). Incubation was performed using a fully automated incubator, after which chicks were transferred to an SPF chicken isolator for rearing. Twenty 7-day-old SPF chickens were randomly divided into two groups of 10 chickens and raised aseptically in an SPF chicken isolator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleen tissue from each group was added to lysis buffer, ground at low temperature, and then low concentrations of RNase I were added for digestion. The digested samples were pooled and layered on the surface of 15 ml sucrose buffer (30% sucrose in RB buffer). The ribosomes were pelleted by ultracentrifugation at 42500 rpm for 5 h at 4 °C. RPF extraction was then performed using TRIzol, and ribosomal RNA (rRNA) was depleted using the Ribo-off® rRNA Depletion Kit (Vazyme) following the manufacturer’s instructions.
Sequencing libraries of RPFs were constructed following the VAHTS® Small RNA Library Prep Kit for Illumina (Vazyme). The library was resolved by a 6% polyacrylamide gel. The fraction with an insertion size of ~28 nt was excised and purified from the gel. This fraction was sequenced by an Illumina HiSeq-2000 sequencer for 50 cycles. High-quality reads that passed the Illumina quality filters were kept for sequence analysis.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
total Ribosome protected fiagments
|
| Data processing |
For both mRNA and RPF sequencing data sets, high-quality reads were mapped to the mRNA reference sequence (GRCg6a) through the FANSe2 algorithm with the parameters -E5% --indel -S14.
The expression abundance of mRNA and RPFs was normalized by RPKM (reads per kilobase per million reads)
Differentially expressed genes (DEGs) in RNA-seq and Ribo-seq were identified via the edgeR package with |log2-fold change| > 1 and false discovery rate (FDR) < 0.01.
The quotient of RPFs and mRNA expression abundance is translation efficiency (TE). Differential TE genes (DTEGs) were calculated by a t test with |log2-fold change| > 1 and p value < 0.05.
Bioinformatic analysis was performed using Omicsmart, a real-time interactive online platform for data analysis (http://www.omicsmart.com).
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.
Library strategy: Ribo-seq
|
| |
|
| Submission date |
Aug 22, 2023 |
| Last update date |
Aug 27, 2023 |
| Contact name |
tengda huang |
| E-mail(s) |
2022324065113@stu.scu.edu.cn
|
| Phone |
+8615208155933
|
| Organization name |
sichuan university
|
| Street address |
gaopeng road
|
| City |
chengdu |
| ZIP/Postal code |
610065 |
| Country |
China |
| |
|
| Platform ID |
GPL16133 |
| Series (1) |
| GSE241418 |
Transcriptomic and Translatomic Analyses Reveal Insights into the Signaling Pathways of the Innate Immune Response in the Spleens of SPF Chickens Infected with Avian Reovirus |
|
| Relations |
| BioSample |
SAMN37111163 |
| SRA |
SRX21452564 |
