|
| Status |
Public on Dec 20, 2016 |
| Title |
wt_repl2 |
| Sample type |
RNA |
| |
|
| Source name |
3-week old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: aerial parts of soil-grown plants
genotype: WT
ecotype: Col-0
age: 3-weeks old
|
| Treatment protocol |
Plant material was harvested, frozen in liquid nitrogen and ground into powder
|
| Growth protocol |
RNA was isolated from 3-week-old seedlings of wild-type Arabidopsis (Col-0 ecotype) grown in soil under long-day conditions. Aerial parts of plants were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol, followed by treatment with TURBO DNase (Ambion) and RiboMinus™ Plant Kit (Invitrogen) to reduce the rRNA fraction.
|
| Label |
biotin
|
| Label protocol |
100 ng of RNA was used for cDNA synthesis with an Ambion WT Expression Kit. Fragmentation and labeling was done using a GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer`s protocol.
|
| |
|
| Hybridization protocol |
5.5 μg of cRNA was hybridized with an Agronomics array (Rehrauer et al., 2010) using a GeneChip Hybridization Wash and Stain Kit, according to the manufacturer’s recommendations (Affymetrix).
|
| Scan protocol |
Microarrays were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
gene expression data from Arabidopsis plants grown under long-days conditions
|
| Data processing |
Probe intensities for strand-specific signals were extracted using Affymetrix apt-cel software. Probe positions were transformed to the TAIR10 genome assembly. The signal was normalized separately for each of the three biological replicates and the average of the replicates for each probe was used for gene expression measurements. The .sgr files contain normalized signals for each probe.
|
| |
|
| Submission date |
Aug 03, 2015 |
| Last update date |
Dec 20, 2016 |
| Contact name |
Rafal Archacki |
| E-mail(s) |
rafa@ibb.waw.pl
|
| Organization name |
University of Warsaw
|
| Lab |
Laboratory of Systems Biology
|
| Street address |
Pawinskiego 5A
|
| City |
Warsaw |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
| |
|
| Platform ID |
GPL20763 |
| Series (2) |
| GSE71655 |
Expression data from 3-week old Arabidopsis seedlings of WT and brm-1 mutant |
| GSE71657 |
ChIP-chip and transcriptomic analysis of Arabidopsis BRM chromatin remodeler |
|
