|
| Status |
Public on Oct 12, 2023 |
| Title |
cs_RNAi4_rnaseq |
| Sample type |
SRA |
| |
|
| Source name |
spikelets at booting stage (Feeke 10)
|
| Organism |
Triticum aestivum |
| Characteristics |
cultivar: Fielder
tissue: spikelets at booting stage (Feeke 10)
genotype: RLG_7.3_enh_RNAi
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The spikelets at booting stage (Feeke 10) were harvested and frozen in liquid nitrogen for RNA isolation. More than 2 μg total RNA was used to prepare each sequencing sample.
Libraries were constructed and sequenced by Hanyubio Co. Ltd. (Shanghai, China) to produce 150-bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For RNA-sequencing data, The sequencing reads were trimmed with the Trim Galore(version 0.6.4) and cutadapt ,clean reads were aligned with HISAT2 program(version 2.1.0) . SortMeRNA was used to remove the reads originating from chloroplast, mitochondria and rRNA. The featureCount program of was used to determine the RNA-seq read density of the high-confidence genes in the IWGSC RefSeq genome assembly(version 1.1).
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each RNA-seq sample
|
| |
|
| Submission date |
Dec 14, 2022 |
| Last update date |
Oct 12, 2023 |
| Contact name |
yijing zhang |
| E-mail(s) |
zhangyijing@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Biochemistry
|
| Lab |
Functional Epigenomics Group
|
| Street address |
2005 Songhu Road
|
| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL25409 |
| Series (1) |
| GSE198284 |
Subgenome-specific usage of transposable element-derived promoters and enhancers in bread wheat development |
|
| Relations |
| BioSample |
SAMN32218672 |
| SRA |
SRX18690910 |
