|
| Status |
Public on Jan 03, 2016 |
| Title |
phl2 P-_5 |
| Sample type |
SRA |
| |
|
| Source name |
phl2 P-
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: seedling
tissue: root
age: 8 days
ecotype: Col-0
genotype/variation: phl2
treatment: Phosphate deficiency
|
| Treatment protocol |
Phosphate starvation
|
| Growth protocol |
Total RNAs were extracted from the roots of P+ and P- WT seedlings (i.e., seedling grown on P-sufficient and P-deficient media) and of P- phl2 seedlings.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The total RNAs were extracted using the RNeasy plant mini kit (Qiagen).
dUTP based strand-specific library construction protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
LD_5
|
| Data processing |
Remove reads contain N and adapter sequence
Remove first 12 nt of reads
Remove duplicated reads
Remove reads mapped to rRNA
Map to Arabidopsis genome using Tophat2
Calculate RPKM using DEGseq
Do the differential expression using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Expression_level_rpkm.txt contains rpkm of genes annotated in TAIR10 among 6 samples
|
| |
|
| Submission date |
Nov 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lichao Sun |
| E-mail(s) |
sun2004go@163.com
|
| Organization name |
Tsinghua university
|
| Department |
Life of Science
|
| Lab |
Dong Liu
|
| Street address |
Tsinghua University
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE74972 |
Arabidopsis PHL2 act as the key component of the central regulatory system controlling transcriptional responses to phosphate starvation |
|
| Relations |
| BioSample |
SAMN04266509 |
| SRA |
SRX1430643 |
