|
| Status |
Public on Mar 07, 2020 |
| Title |
fine_roots_senescence_first_stage_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
first stage of senescence: roots which had changed in colour from white to brown
|
| Organism |
Populus trichocarpa |
| Characteristics |
tissue: fine roots
|
| Treatment protocol |
Samples of fine roots and leaves were collected three times during a growing season. The first collection was considered as a control leaf (LC) and fine roots (RC) samples and was collected in early summer (July 7 - 15), when leaves and the root system were fully developed and functional. The second group of leaf and root samples were harvested in early autumn (October 1 - 7) when chlorophyll levels in leaves had decreased by approximately 40% (LS1) and when fine roots had changed in colour from white to brown (RS1). The third group of samples were harvested in the middle of autumn (November 2 - 9), when chlorophyll levels in leaves decreased by approximately 65% (LS2) and fine roots were dark brown or black colour (RS2). No special treatment was used in the experiment.
|
| Growth protocol |
All experiments were performed on seed-grown Populus trichocarpa (Torr. & Gray). Seeds were germinated on 0.8% agar medium in a growth chamber. After developing of first roots, seedlings were transfered into multi-pot trays filled with sterile garden substrate mixed with perlite and kept in phytotron chamber (16h/8h, 18℃/14℃). After 1.5 months of growth, plants were planted into rhizotrons filled with natural soil with shoots extending from the top into the air. Plants were grown in plastic tunel. Waterlogging was avoided by installing a drainage hole in the bottom of each rhizotron that permitted soil aeration and drainage of excess water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from three biological replicates of each stage of senescence of fine roots and leaves using an RNeasy Plant Mini kit (Qiagen, USA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix GeneChip Poplar Genome Array, A-AFFY-131).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized to an Affymetrix GeneChip Poplar Genome Array (A-AFFY-131) according to the provided Affymetrix protocol.
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000 7G (Thermo Fisher Scientific, USA)
|
| Description |
Gene expression data from Gene expression data from brown roots in the first stage of senescence.
|
| Data processing |
The raw image data from a total of three A-AFFY-131 arrays were normalized with Robust Multi-Array Average (RMA). The normalized data were statistically analyzed using GeneSpringGX7 13.1 (Agilent Technologies Inc., USA) software. Data were subjected to a one-way ANOVA with a Benjamini Hochberg corrected p-value cut-off = 0.05. The analysis was limited to genes with statistically significant differences in expression level and a fold difference equal to or larger than 2 between LC and LS1/LS2 in leaf samples and between RC and RS1/RS2 in fine root samples.
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| |
|
| Submission date |
Jan 13, 2020 |
| Last update date |
Mar 08, 2020 |
| Contact name |
Katarzyna Marzec-Schmidt |
| E-mail(s) |
katmar9@amu.edu.pl
|
| Organization name |
Adam Mickiewicz University
|
| Department |
General Botany
|
| Street address |
Umultowska 89
|
| City |
Poznan |
| ZIP/Postal code |
61-614 |
| Country |
Poland |
| |
|
| Platform ID |
GPL4359 |
| Series (1) |
| GSE143559 |
Transcriptomic changes during senescence of leaves and fine roots of Populus trichocarpa |
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