|
| Status |
Public on Apr 01, 2015 |
| Title |
WT-0 rep1 and rep2 |
| Sample type |
SRA |
| |
|
| Source name |
plant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: plant
age: 11-day-old
genotype: wild type
treatment: MS liquid medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 11-d-old seedlings treated with MS liquid medium or MS liquid medium containing 200 mM NaCl for 4 h with Trizol reagent (Invitrogen) as recommended by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Tair10 whole genome using tophat with parameters -p -r -G -o genome C1_R1_1.fq C1_R1_2.fq
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Mar 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xu Zhao Gao |
| E-mail(s) |
gaozx@pku.edu.cn
|
| Organization name |
Peking University
|
| Department |
College of Biological Sciences
|
| Lab |
Plant molecular genetics and agricultural biotechnology research laboratory
|
| Street address |
The Summer Palace Road No. 5
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE55632 |
SKIP Confers Salt Tolerance through Controlling Gene Alternative Splicing in Arabidopsis |
|
| Relations |
| BioSample |
SAMN02673525 |
| SRA |
SRX481644 |
