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| Status |
Public on Nov 30, 2021 |
| Title |
dsGFP-3 |
| Sample type |
SRA |
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| Source name |
2 instar larvae of housefly
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| Organism |
Musca domestica |
| Characteristics |
tissue: whole body
developmental stage: 2 instar
treatment: RNAi with dsGFP
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| Extracted molecule |
total RNA |
| Extraction protocol |
The 2nd instar larvae were used for dsRNA injection (n = 3/group). The whole larval body was collected at 24 h post injection, then, immediately frozen in liquid nitrogen, and stored at -80 °C. The total RNA was extracted using Trizol reagent; 3 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Alignment： HISAT2 2.1.0， --dta –t –p 4， mapping reads to genome
Transcript Assembly: StringTie 1.3.2d, -G ref.gtf, sequence assembly
Gene Expression Quantity ：HTSeq 0.6.0 ，-i gene_id -f bam -s no -a 10 -q ，estimating gene expression level
Differential Expression ：DEGseq 1.18.0， method="MARS"
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Nov 24, 2021 |
| Last update date |
Nov 30, 2021 |
| Contact name |
Wen-Jing Zhao |
| E-mail(s) |
zhaowenjing@gmc.edu.cn
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| Organization name |
Guizhou Medical University
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| Department |
School of Basic Medical Sciences
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| Street address |
Dongqing Road
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| City |
Guiyang |
| State/province |
Guizhou |
| ZIP/Postal code |
550025 |
| Country |
China |
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| Platform ID |
GPL30537 |
| Series (1) |
| GSE189491 |
Function analysis and characterisation of a novel chitinase, MdCht9, in Musca domestica |
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| Relations |
| BioSample |
SAMN23424566 |
| SRA |
SRX13217311 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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