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| Status |
Public on Dec 17, 2021 |
| Title |
Testis GMS rep3 |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Bombyx mori |
| Characteristics |
strain: GMS
tissue: testis
age: day 5 of fifth-instar larvae
genotype: mutant type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from testes using TRIzol reagent according to the manufacturer’s protocol (Invitrogen, USA).The sequencing libraries were generated using the TruSeq RNA Sample Prep Kit v2 (Illumina, USA) following manufacturer’s recommendations.
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 |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
The quality of the raw data was controlled by the FasQC. At the initial filtering step, we discarded poor quality reads using SOAPnuke , including reads that have adaptors, reads with more than 10% unknown bases, and reads that have more than 50% bases with quality value less than 5. The clean reads were mapped onto reference genome of silkworm independently by HISAT2 version 2.1.0 . The parameters were set to default values. And we used RSeQC packages (version 2.6.4) to process a comprehensively evaluation on RNA-Seq data after alignment.
Based on the HISAT2 alignment BAM file, featureCounts v1.6.2 was used to estimate and quantify gene expression with default parameters, yielding raw read counts for each gene. Gene expression was normalized by reads per kilobase of exon per million reads mapped (RPKM).
Genome_build: ASM15162v1 reference Annotation Release 102
Supplementary_files_format_and_content: Text files include RPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Dec 16, 2021 |
| Last update date |
Dec 17, 2021 |
| Contact name |
Xinglin Mei |
| E-mail(s) |
mxlever@126.com
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| Organization name |
Jiangsu University of Science and Technology
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| Street address |
No.666, Changhui Road, Dantu New District, Zhenjiang city, Jiangsu Province
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| City |
Zhenjiang |
| State/province |
Jiangsu |
| ZIP/Postal code |
212018 |
| Country |
China |
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| Platform ID |
GPL30062 |
| Series (1) |
| GSE191033 |
Comparative analysis of testis transcriptome between a genetic male sterile line (GMS) and its wild-type 898WB in silkworm, Bombyx mori |
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| Relations |
| BioSample |
SAMN24115431 |
| SRA |
SRX13426367 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5737755_TT-3.txt.gz |
122.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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