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| Status |
Public on Jul 17, 2024 |
| Title |
PP_rep3_RNAseq |
| Sample type |
SRA |
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| Source name |
fruit
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| Organism |
Vaccinium corymbosum |
| Characteristics |
tissue: fruit
cell line: fruit
cell type: fruit
genotype: wild type
treatment: no
time: 56 days after anthesis
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The total RNA was isolated from the strain using the Trizol reagent according to manufacturer’s instructions (Invitrogen) and sent to Novogene (Tianjin, China) for library preparation and deep sequencing.
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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 |
For RNA-seq analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. The trimmed reads were aligned to the Vaccinium corymbosum cv ‘Draper’ genome using HISAT2 v2.2.1 under default settings. Since “Draper” is tetraploid, we selected largest scaffolds of each of the 12 homoeologous groups to represent the genome. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2 with default parameters.
Assembly: V_corymbosum_v1.0
Supplementary files format and content: The processed data is generated by HISAT2
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| Submission date |
Apr 06, 2023 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Zejia Wang |
| E-mail(s) |
wangzj@stu.pku.edu.cn
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| Organization name |
Peking University
|
| Street address |
Yanyuan Street
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL33280 |
| Series (2) |
| GSE229139 |
ROS1 regulates blueberry fruit ripening in a negatively ABA manner (RNA-Seq) |
| GSE229141 |
ROS1 regulates blueberry fruit ripening in a negatively ABA manner |
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| Relations |
| SRA |
SRX19806315 |
| BioSample |
SAMN33963427 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7153110_S21G0752_rep1_1_URNA_S111_L004.bw |
18.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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