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| Status |
Public on Mar 10, 2017 |
| Title |
QLP |
| Sample type |
SRA |
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| Source name |
epidermis
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| Organism |
Bombyx mori |
| Characteristics |
genotype/variation: q-lp mutant
developmental stage: 4th instar
time: 6 hours after molting
tissue: epidermis
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| Treatment protocol |
The mutant purple quail-like (q-lp) is a new pigment mutant obtained from the plain silkworm strain 932VR. The characteristics of q-lp are inherited stably after more than 10 generations of inbreeding. Compared with individual exhibiting normal markings, the q-lp mutant has no obvious eye-spots but normal star-spots and semilunar marking. There are dots and lines with longitudinal wave markings on the dorsal sides of the 6th to 7th abdominal segments, which constitute quail markings, in between the star-spots and semilunar markings. The whole-body markings are very similar to those of the quail mutant (q). The larvae of q-lp show light purple skin, eat only small amounts of mulberry leaves, are weak, and develop slowly and unevenly; in addition their larval bodies and cocoons are small.
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| Growth protocol |
The silkworm strains 932VR and q-lp were provided by The Sericulture Research Institute, Chinese Academy of Agricultural Sciences (Zhenjiang, China). The silkworms were fed fresh mulberry leaves under standard conditions with alternating 12 hours of illumination and 12 hours of darkness at 25±2 °C. Epidermis samples were collected from every three silkworms after 6 hours of molting in the 4th instar. All samples were frozen and stored at -80 °C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAiso Plus (TaKaRa, China) and dissolved in RNase-free water. The concentration of total RNA was determined using a NANODROP1000 microspectrophotometer (Thermo, USA) after treatment with DNase.
Total mRNA was enriched using Oligo (dT) magnetic beads, after which the mRNAs were sheared into short fragments using hybridization-interruption reagents. These short RNA fragments were then synthesized into double-stranded cDNA using six-base random primers, and terminal modification was performed for the purified double-stranded cDNA; a base (A) tail was added, and the fragments were ligated. The quality of the cDNA library constructed was tested using an Agilent 2100 Bioanalyzer; after quality criteria were met, sequencing was executed using an Illumina HiSeqTM2500 system (Illumina, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
quail markings
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| Data processing |
Quality analysis was conducted for the original data obtained using the Illumina HiSeqTM2500 system
Clean reads were screened by filtering out low-quality reads
A second quality analysis for alignment, analysis of the distribution and coverage of the clean reads on the reference sequence was conducted
The sequences were aligned to the silkworm genome database SilkDB.
RPKM (Reads Per Kb per Million reads) was used to calculate the expression level of genes, with RPKM=mapped reads of gene/(the total mapped reads of all genes*the length of this gene)*10^9. The RPKM of a gene ranged up to 5, and difference in expression was considered at P < 0.05; the fold change of q-lp and 932VR RPKMs was greater than 2.
Genome_build: SilkDB (http://silkworm.swu.edu.cn/silkdb/)
Supplementary_files_format_and_content: All files are named with sample name followed by content name using files format of excel. The processed data include the RPKM of two samples wildtype 932VR and q-lp mutant, the differentially expressed genes between 932VR and q-lp with P≤0.05, SNP and Indel of 932VR and q-lp , alternative splicing of 932VR and q-lp respectively, extend gene and novel transcript of 932VR and q-lp.
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| Submission date |
Feb 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Pingyang Wang |
| E-mail(s) |
wangpingyang.yczg@163.com
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| Phone |
8618362890731
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| Organization name |
Jiangsu University of Science and Technology
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| Department |
School of Biotechnology
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| Street address |
Nanxu street
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| City |
Zhenjiang |
| State/province |
Jiangsu province |
| ZIP/Postal code |
212018 |
| Country |
China |
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| Platform ID |
GPL23127 |
| Series (1) |
| GSE95495 |
Transcriptome analysis of the epidermis of the purple quail-like (q-lp) mutant of silkworm, Bombyx mori |
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| Relations |
| BioSample |
SAMN06471061 |
| SRA |
SRX2598654 |
| 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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