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| Status |
Public on Oct 01, 2024 |
| Title |
brobcKO_rep1 |
| Sample type |
SRA |
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| Source name |
BmN cells
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| Organism |
Bombyx mori |
| Characteristics |
cell line: BmN cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
BmN cells (1e6) with indicated treatments were harvested and total RNA of the cells was extracted using Trizol.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the instructions.
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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 |
Raw data was cleaned by Trim Galore (Version 0.6.6) with the parameters "-q 25 --phred33 --length 36 -e 0.1 --stringency 5", and maped to silkworm genome using HISAT2 (Version 2.2.1). The resulted SAM file was transformed to BAM file and sorted by SAMtools (Version 1.12). Mapped reads at the exons of each gene were counted via featureCounts, which is a part of the Subread (Version 2.0.1).
Assembly: SilkBase November 2016
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
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| Submission date |
Sep 26, 2024 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Shudi Zhao |
| E-mail(s) |
shudi.zhao@zju.edu.cn
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| Organization name |
Zhejiang University
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| Street address |
Yuhangtang Road No.866
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL29210 |
| Series (1) |
| GSE278147 |
Functional analysis of BmNPV cis-interacting sites |
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| Relations |
| BioSample |
SAMN43826088 |
| SRA |
SRX26124722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8540790_brobcKO_rep1.txt.gz |
937.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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