|
| Status |
Public on Oct 23, 2023 |
| Title |
Pollen_ATG5_1 |
| Sample type |
SRA |
| |
|
| Source name |
Pollen
|
| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: Pollen
developmental stage: Bicellular pollen
genotype: ATG5 RNAi plants
|
| Growth protocol |
All plants were grown under 12 h of daylight at 25 ± 2 °C in a glasshouse
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using MiniBEST Plant RNA Extration Kit (TaKaRa).
Sequencing libraries were then generated using MGIEasy RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Extracted by MiniBEST Plant RNA Extration Kit (TaKaRa)
|
| Data processing |
Base-calling was performed using a propriety Sub-pixel Registration algorithm.
Reads contained adaptors and low quality reads were removed by SOAPnuke.
Clean reads were then mapped to the tobacco genome and reference transcript sequences using the HISAT2 and Bowtie 2.
The expression level of each gene in the transcriptome as quantified as fragments per kilobase of transcript per million mapped reads using RSEM.
Differentially expressed genes were identified using DESeq2.
Genome_build: Ntab-TN90 reference Annotation Release 100
Supplementary_files_format_and_content: Excel file includes FPKM vaule of each gene
|
| |
|
| Submission date |
Oct 02, 2020 |
| Last update date |
Oct 23, 2023 |
| Contact name |
Xuemei Zhou |
| E-mail(s) |
xmzhou@whu.edu.cn
|
| Phone |
0086-027-68752378
|
| Organization name |
South-Central University for Nationalities
|
| Street address |
182 Minyuan Road, Hongshan district
|
| City |
Wuhan |
| ZIP/Postal code |
430074 |
| Country |
China |
| |
|
| Platform ID |
GPL29212 |
| Series (1) |
| GSE158922 |
Transcriptome analysis of ATG-silenced pollen |
|
| Relations |
| BioSample |
SAMN16351311 |
| SRA |
SRX9235223 |
