|
| Status |
Public on Dec 31, 2013 |
| Title |
Col-0, root, control for nickel stress |
| Sample type |
SRA |
| |
|
| Source name |
Root, wild type, untreated
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
background: Col-0
genotype: wild type
tissue: root
treatment: none
|
| Treatment protocol |
For flowers, submergence stress was applied by submerging plants under sterile water for four hours prior to harvesting. For salt stress, 0.1 M NaCl or 0.3 M NaCl solutions were added to plants for 24 hours before harvesting. Cold stress was carried out by transferring plants to a 4°C cold room with continuous light for 24 hours. For seedlings, salt and submergence stresses were carried out by pouring 40 mL of sterile water with 0.3 M NaCl (salt) or without (submergence) eight hours before harvesting. Phosphate starvation stress was carried out by plating onto MS containing one tenth the normal amount of phosphate. For roots, 40 plants each of four-day-old Col-0 plants germinated on MS (with 3% sucrose) media were transferred to magenta boxes containing a mesh for separating roots and shoots with 100 mL each of MS liquid medium (with 1% sucrose). Further, the boxes were incubated on a rotary shaker set at 90 RPM illuminated with cool white fluorescent light at 25 ± 2 °C. The treatment flasks received 50 µM NiNO3 and control plants did not receive any NiNO3. Both the treatment and control flasks were incubated for 15 days, and the roots were harvested on the 15th day and the RNA was isolated for preparing the library.
|
| Growth protocol |
For flowers, seeds were sown directly onto soil and grown at 21°C in a growth chamber with 16 hours of light for six weeks. For seedlings, surface-sterilized seeds were plated onto Murashige and Skooge (MS) media and grown in a chamber at 21°C with 16 hours of light for two weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent.
Small RNA libraries were constructed as previously described (Lu et al. 2007 (PMID 17889797)) and sequenced on an llumina Genome Analyzer II. Sequencing was performed at Illumina or the Delaware Biotechnology Institute.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Small RNA
C0RC1
|
| Data processing |
The raw sequencing data was converted to SCARF format, trimmed of adapters, and matched to the Arabidopsis genome (TAIR9) by custom Perl scripts.
Genome_build: TAIR9
Supplementary_files_format_and_content: Text file containing distinct small RNAs with their raw abundance after removing the adapter sequences.
|
| |
|
| Submission date |
Feb 25, 2013 |
| Last update date |
Dec 31, 2013 |
| Contact name |
Dong-Hoon Jeong |
| E-mail(s) |
jeong@dbi.udel.edu
|
| Phone |
3027383769
|
| Organization name |
University of Delaware
|
| Street address |
15 Innovation Way
|
| City |
NEWARK |
| State/province |
DE |
| ZIP/Postal code |
19711 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE44622 |
Comprehensive investigation of miRNAs enhanced by analysis of sequence variants, expression patterns, AGO loading and target cleavage |
|
| Relations |
| BioSample |
SAMN02197156 |
