|
| Status |
Public on Nov 06, 2017 |
| Title |
16-cell_embryo, nuclei biological replicate 2 [nEMB_16C2] |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis embryo_16-cell_embryo
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: embryo
developmental stage: 16-cell (16C)
molecule subtype: nuclear RNA
|
| Treatment protocol |
Embryos of the approriate stage where used for isolating nuclei using a two-compoenent labelling system called INTACT for immediate RNA extraction.
|
| Growth protocol |
Seedlings were grown on soil at a constant temperature of 22°C under long-day conditions (16 hours light/8 hours dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted according to the TRIzol reagent protocol for small sample quantaties (ThermoFisher, P/N 15596026) with some modifications.
|
| Label |
biotin
|
| Label protocol |
RNA was amplified using the Ovation PicoSL WTA System V2 (NuGEN, P/N 3302-60) according to the manufacturer's instructions. For fragmentation and labelling, 3 ug of biotinylated cDNA was used in a half-volume reaction using the ENCORE Biotin Module kit (NuGEN, P/N 4200-60).
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| |
|
| Hybridization protocol |
The Affymetrix Gene 1.1 ST 24-Array Plate was processed on the Affymetrix GeneTitan System and was performed according to the NuGEN Ovation PicoSL WTA System V2 user guide (Appendix C, page 28) using GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates (Affymetrix, P/N 901622) and GeneChip Hybridization Control Kit (Affymetrix, P/N 90457).
|
| Scan protocol |
Hybridization, washing, staining and scanning of the arrays were done on the Affymetrix GeneTitan System using the hyp-wash-scan protocol.
|
| Description |
Map2_nEMB_16C2
Gene expression data from nuclei isolated from 16-cell stage Arabidopsis embryo
|
| Data processing |
The data were analyzed using the MadMax pipeline (https://madmax.bioinformatics.nl/) and a custom CDF file (aragene11st_At_TAIRG_19.0.0, http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp), and normalized using RMA.
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| |
|
| Submission date |
Oct 24, 2016 |
| Last update date |
Nov 06, 2017 |
| Contact name |
Joakim Palovaara |
| E-mail(s) |
joakim@uni-bremen.de
|
| Organization name |
Wageningen Univeristy
|
| Department |
Biochemistry
|
| Lab |
Dolf Weijers Lab
|
| Street address |
Stippeneng 4
|
| City |
Wageningen |
| State/province |
Gelderland |
| ZIP/Postal code |
6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL22599 |
| Series (2) |
| GSE89100 |
Cell type-specific expression atlas of the early Arabidopsis thaliana embryo |
| GSE89101 |
Nuclear and cellular expression data from the whole 16-cell stage Arabidopsis thaliana embryo and a cell type-specific expression atlas of the early Arabidopsis embryo |
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