|
| Status |
Public on Jul 18, 2023 |
| Title |
HZ62_seedling_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Brassica napus |
| Characteristics |
tissue: seedling
cell type: 2 weeks
genotype: WT
treatment: a day/night cycle of 16h/8h and a temperature of 22/18℃
|
| Treatment protocol |
a day/night cycle of 16h/8h and a temperature of 22/18℃
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from the tissues (seedling, flower bud, silique) using the RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions. About 2ug RNA was used for library construction using Illumina TruSeq RNA Kit according to the manufacturer’s instruction.
About 2ug RNA was used for library construction using Illumina TruSeq RNA Kit according to the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Adaptors and low-quality reads were first trimmed using Fastp with default parameters
Clean reads were mapped to the Brassica napus ZS11 genome（Chen et al., 2021）using Hisat2 with default parameters
SAMtools with parameters “-q 30 -f 2” was used to remove the low mapping quality reads，then GATK MarkDuplicates was used to rm duplicated reads
Reads numbers per gene were counted using FeatureCounts
The trimmed mean of M-values (TMM) method of EdgeR was used to normalization reads counts per gene
Assembly: Brassica napus ZS11 （Chen et al., 2021）
Supplementary files format and content: tab-delimited text files include TMM values for each sample
Supplementary files format and content: tab-delimited text files include reads numbers per gene for each sample
|
| |
|
| Submission date |
Nov 22, 2022 |
| Last update date |
Jul 18, 2023 |
| Contact name |
Wenying Zhong |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Lion Rock Street
|
| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL26378 |
| Series (2) |
| GSE218591 |
Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids [RNA-seq] |
| GSE218592 |
Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids |
|
| Relations |
| BioSample |
SAMN31840981 |
| SRA |
SRX18353228 |
