|
| Status |
Public on May 07, 2019 |
| Title |
cbfs treated with 0 h, rep 2 [cbf0_2] |
| Sample type |
SRA |
| |
|
| Source name |
cbfs treated with 0 h
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: cbfs-1 mutant
developmental stage: 14 d
tissue: seedling
treatment: under 4 degree for 0h
|
| Treatment protocol |
14-day-old plants were treated with 4 degree for indicated time: 0, 3 and 24 h
|
| Growth protocol |
The plants were grown on 1/2 MS mediam under long day condition at 22 degree for 14 d
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA extraction was performed following the protocol of Tiangen RNAprep pure Plant Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
cbf-0-2
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidopsis TAIR10 genome using TOPHAT v.2.1.0
CUFFLINKS v.2.2.1 was used to assemble the new transcripts
HTSEQ v.0.6.0 was used to calculate the raw read counts for each gene.
Gene expression normalization among samples was performed by using DESEQ2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
May 06, 2019 |
| Last update date |
May 07, 2019 |
| Contact name |
Yuxin Jia |
| Organization name |
China Agricultural University
|
| Department |
Biology
|
| Street address |
No. 2 Yuanmingyuan west road, Haidian district
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE130729 |
RNA-seq data for Arabidopsis cbfs-1 |
|
| Relations |
| BioSample |
SAMN11579856 |
| SRA |
SRX5794931 |
