|
| Status |
Public on Dec 30, 2015 |
| Title |
IT 1-week-cold rep2 |
| Sample type |
SRA |
| |
|
| Source name |
aerial part
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: entire aerial part
age: 18 days after germination, 1 week at cold
ecotype: Italian
|
| Treatment protocol |
Cold treatment was for 1 or 2 weeks at 4⁰C under a 12 h photoperiod of ~35 µmol m-2 sec-1
|
| Growth protocol |
Plants were grown on soil at 22⁰C under a 12 h photoperiod with 100-120 μmol m-2 s-1 light intensity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cold treated and control samples (all samples) were collected at ZT4
RNA was extracted using the RNeasy plant mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
IT grown at 22°C on soil under a photoperiod of 12 h for 18 days, one week at 4C, sampled at ZT4
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were mapped to the Arabidopsis reference genome (TAIR10) using Tophat version 1.4.1 in default mode with minimum and maxmum intron lengths being set to 10 and 15,000 bp, respectively. The transcript abundance (FPKM) was estimated using Cufflinks (version 2.1.1). Cuffdiff was run using default parameters with inputs of the TAIR10 genome and transcript annotations.
Genome_build: TAIR v10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sunchung Park |
| E-mail(s) |
Sunchung.park@usda.gov
|
| Organization name |
USDA -ARS
|
| Department |
ARS-NEA
|
| Lab |
SPCL
|
| Street address |
10300 Baltimore ave, Bldg001
|
| City |
Beltsville |
| State/province |
MD |
| ZIP/Postal code |
20705 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE67332 |
Potential role of natural variation in the Arabidopsis CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden |
|
| Relations |
| BioSample |
SAMN03448740 |
| SRA |
SRX970687 |
