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Sample GSM8412822

Query DataSets for GSM8412822

Status

Public on Jul 31, 2024

Title

siUFBP1-3

Sample type

SRA

Source name

Fat body

Organism

Bombyx mori

Characteristics

tissue: Fat body
cell line: BmN

Treatment protocol

he small interfering RNA (siRNA) against BmUFBP1 and siNC (negative control) were designed and synthesized by the Sangon Biotech Company (Sangon, Shanghai, China); the siRNA sequences are shown in Table 1. Thirty larvae on the 3rd day of the 5th instar were used for RNA interference experiments. Each larva was injected with 2.5 µg siNC or siBmUFBP1, and all larvae were administered with 5 µL of BmNPV suspended in water (1 × 106 ODVs/mL) at 12 h post injection of siRNA. Fat body were obtained at 24 h, 48 h and 72 h post injection.

Growth protocol

In a nutshell, the B. mori P50 strain was grown in Anhui Province Key Laboratory of Resource Insect Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei, China. Mulberry leaves were given to the larvae at 26°C and 75% relative humidity.

Extracted molecule

total RNA

Extraction protocol

Following the directions supplied by the manufacturer, RNAiMAX (Thermo Fisher SCIENTIFIC, USA) was used to transfect BmUFBP1 dsRNA or siRNA. For instance, in a 6-well plate, 5 μg of dsRNA was added to a 300 μL volume of serum-free TC100 culture medium for each well, and the mixture was added to an equal volume of RNAiMAX-containing TC100 culture medium, blended thoroughly, and allowed to stand for 15 minutes. The transfection complexes were then added to the BmN cells' supernatant to complete transfection.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

DNBSEQ-T7

Data processing

Bomo_genome_assembly
raw data for splice removal and removal of low quality sequences, The parameter is ~fastp -i sample.R1.fastq -I sample.R2.fastq -o out.R1.fastq -p sample.R2.fastq -q 20-l 100-n 10
The clean reads were mapped to the reference genome using HISAT2
Read count extraction and normalization were performed using Bomo_genome_assembly
Assembly: Bomo_genome_assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

Submission date

Jul 22, 2024

Last update date

Jul 31, 2024

Contact name

Meng hao nan

E-mail(s)

huangshoujun@ahau.edu.cn

Phone

18112808186

Organization name

An hui Agricultural