|
| Status |
Public on Apr 28, 2024 |
| Title |
Rapeseed_young_leaves_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
young leaves
|
| Organism |
Brassica napus |
| Characteristics |
tissue: young leaves
cell line: Zhongshuang 11
cell type: young leaves cells
|
| Growth protocol |
For the collection of economically important plant organs, the plants were planted and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. For the collection of vegetativetissues, the plants were planted in greenhouses.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 74904).
The RNA was used for library construction using the Illumina TruSeq RNA kit, according to the manufacturer’s recommendations. The libraries were sequenced using an Illumina Novaseq 6000 system (paired-end 150 bp reads, Annoroad Gene Technology).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The quality of the sequencing datasets was evaluated using FastQC
Fastp was used with “-l 15 -f 0 -t 0” parameters to filter out adapters and low-quality reads.
The filtered reads were aligned to the corresponding reference genome using Hisat2 with default parameters.
SAMtools with the parameter “-q 30” was used to remove low-quality mapped reads.
The normalization method employed in gene expression was EdgeR’s TMM (Trimmed Mean of M-values).
Assembly: GWHANRE00000000
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include TMM values for each Sample
|
| |
|
| Submission date |
Sep 22, 2023 |
| Last update date |
Apr 28, 2024 |
| Contact name |
Wenying Zhong |
| E-mail(s) |
wenyingzhong@webmail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Lion Rock Street
|
| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL29911 |
| Series (2) |
| GSE243805 |
aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [RNA-Seq] |
| GSE243806 |
aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs |
|
| Relations |
| BioSample |
SAMN37513972 |
| SRA |
SRX21859073 |
