|
| Status |
Public on Nov 06, 2017 |
| Title |
embryo, nuclei, biological replicate 1 [nEMB_16C1] |
| Sample type |
RNA |
| |
|
| Source name |
16-cell_embryo_nuclei
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 16-cell
tissue: embryo
molecule subtype: nuclear RNA
|
| Treatment protocol |
Embryos of the approriate stage where either 1) manually isolated using a inverted microscope together with an micromanipulator or 2) 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 |
Biotinylated cDNA (4.25 ug) were prepared from RNA using the Ovation Pico WTA System V2 (NuGEN, P/N 3302-60) and the ENCORE Biotin Module (NuGEN, P/N 4200-60) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Hybridization of labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual.
|
| Scan protocol |
Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
|
| Description |
nEMB_16C1
Gene expression data from 16-cell stage embryos nuclei
|
| Data processing |
The data were analyzed using the MadMax pipeline (https://madmax.bioinformatics.nl/) and a custom CDF file (aragene10st_At_TAIRG_19.0.0, http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp), and normalized using RMA.
|
| |
|
| 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 |
GPL22603 |
| Series (2) |
| GSE89098 |
Nuclear and cellular expression data from the whole 16-cell stage 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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