 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 14, 2012 |
| Title |
High Mg2+ 7 days treatment |
| Sample type |
SRA |
| |
|
| Source name |
Col-1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: High_Mg2+
tissue: Root
cultivar: Col-1
|
| Treatment protocol |
Roots were sampled from five-week-cultivated Arabidopsis after 7 d treatment of low Mg (supplied with 0.5 μM Mg2+) and high Mg (supplied with 10 mM Mg2+).
|
| Growth protocol |
All plants were grown in the controlled-environment growth chambers (Conviron E7/2, Winnipeg, Manitoba, Canada) with a humidity of 80%, a daily cycle of 24 °C, 10-h day and 20 °C, 14-h night. The daytime light intensity was 120 µmol photons m−2 s−1. The wild ecotype line was from the Nottingham Arabidopsis Stock Centre (http://nasc.nott.ac.uk).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The roots were ground in liquid nitrogen and total RNA was subsequently extracted with RNAisoPlus reagent from 70 mg of tissue powder according to the manufacturer’s instructions (Takara, Otsu, Shiga, Japan). All RNA samples were checked for DNA contamination.
Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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 TAIR10 whole genome using CLC Genomics Workbench 5.1.5 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench 5.1.5
Genome_build: TAIR v10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Dec 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gulei Jin |
| E-mail(s) |
guleijin@zju.edu.cn
|
| Organization name |
Zhejiang University
|
| Street address |
Yuhangtang Road 388#
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310059 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE42899 |
Magnesium Availability Regulates Development of Root Hairs in Arabidopsis thaliana |
|
| Relations |
| SRA |
SRX209793 |
| BioSample |
SAMN01831119 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1053066_high_mg.txt.gz |
180.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
