|
| Status |
Public on Nov 06, 2022 |
| Title |
Pi_sufficient_phl4_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root
genotype: phl4
treatment: +Pi
|
| Treatment protocol |
various mutants grown under Pi sufficiency and deficiency conditions for 8days
|
| Growth protocol |
Surface-sterilized seeds were sown on agar or agarose plates containing the +Pi or -Pi medium, 1.0% (w/v) sucrose, 0.5% MES, and 1.2% (w/v) agar or 0.8% (w/v) agarose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from roots of 8-day-old seedlings of the WT and various mutants grown under Pi sufficiency and deficiency using the RNeasy plant mini kit (Qiagen, catalog: 74904).
mRNAs were purified from total RNAs using Oligo d(T) beads and were reversely transcribed into cDNAs. The cDNAs were fragmented, and sequencing libraries were prepared by end repairing, “A” tail addition, and adaptor ligation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The libraries that passed the quality control were sequenced using the Illumina platform by BIONOVA Co. (Beijing).
The clean sequencing data were aligned into the Arabidopsis TAIR 10 genome by Tophat software.
The Q30 values of all RNA-seq samples were greater than 90%, and the ratios of mapped rates to clean reads were above 90%.
Quantification of transcripts and comparative analyses among the mutants were performed with EdgeR software using TPM
Differentially expressed genes were selected using EdgeR software. GO analysis was performed with two online softwares, agrigo v2 and metascape. The Venn diagrams were drawn by Venny 2.1.0.
Assembly: TAIR 10
|
| |
|
| Submission date |
Nov 03, 2022 |
| Last update date |
Nov 06, 2022 |
| Contact name |
Dong Liu |
| E-mail(s) |
liu-d@mail.tsinghua.edu.cn
|
| Phone |
+861062783603
|
| Organization name |
Tsinghua University
|
| Street address |
School Of Life Sciences
|
| City |
Beijing |
| State/province |
Select Region |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE217158 |
Functions of four members of PHR1 family in plant responses to phosphate starvation |
|
| Relations |
| BioSample |
SAMN31580634 |
| SRA |
SRX18143535 |
