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| Status |
Public on Feb 29, 2024 |
| Title |
stem, height 40 cm, 17-20 cm, rep1 |
| Sample type |
SRA |
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| Source name |
stem
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| Organism |
Asparagus officinalis |
| Characteristics |
tissue: stem
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Tiangen polysaccharide polyphenol kit (QIAGENļ¼Germany) following manufacture's protocols
strand-specific RNA-Seq library construction and sequencing were performed according to Illumina standard 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 |
Quality control: At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome using Hisat2
Novel transcripts prediction using StringTie
Quantification of gene expression level. FeatureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis using the DESeq2 R package
Assembly: GCF_001876935.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jan 04, 2024 |
| Last update date |
Feb 29, 2024 |
| Contact name |
lin mao he |
| E-mail(s) |
hemaolin111@yeah.net
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| Organization name |
sichuan agricultural university
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| Street address |
wenjiang
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| City |
chengdu |
| State/province |
sichuan |
| ZIP/Postal code |
611100 |
| Country |
China |
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| Platform ID |
GPL34062 |
| Series (1) |
| GSE252560 |
Transcriptome analysis during the growth and development of asparagus stems |
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| Relations |
| BioSample |
SAMN39263345 |
| SRA |
SRX23103674 |
| 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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