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| Status |
Public on May 20, 2024 |
| Title |
sharpblue_rep2_RNAseq |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Vaccinium corymbosum |
| Characteristics |
tissue: leaf
genotype: wild type
time: after flowering
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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.
V_corymbosum_v1.0
The processed data is generated by HISAT2
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.
V_corymbosum_v1.0
The processed data is generated by HISAT2
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| Submission date |
Sep 15, 2023 |
| Last update date |
May 20, 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 (1) |
| GSE228041 |
RNAseq and WGBS of Vaccinium corymbosum |
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| Relations |
| BioSample |
SAMN37414858 |
| SRA |
SRX21788965 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7784227_sharp_2.bw |
23.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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