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Sample GSM2358766 Query DataSets for GSM2358766
Status Public on Nov 06, 2017
Title embryo, cellular, biological replicate 2 [cEMB_16C2]
Sample type RNA
 
Source name 16-cell_embryo_cellular
Organism Arabidopsis thaliana
Characteristics developmental stage: 16-cell
tissue: embryo
molecule subtype: total 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 cEMB_16C2
Gene expression data from whole 16-cell stage embryos
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

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AT1G01010_at 4.38179667928772
AT1G01020_at 6.26292383174109
AT1G01030_at 3.38135441873818
AT1G01040_at 13.4229456965443
AT1G01046_at 3.07436377074184
AT1G01050_at 33.5627098730959
AT1G01060_at 15.6409415529389
AT1G01070_at 3.09918785002864
AT1G01073_at 2.78460576721642
AT1G01080_at 6.02326967829867
AT1G01090_at 610.833960127214
AT1G01100_at 101.762227038075
AT1G01110_at 3.45243150355962
AT1G01115_at 4.12141551443393
AT1G01120_at 8.51644815767193
AT1G01130_at 4.16642410725189
AT1G01140_at 9.0852071807852
AT1G01150_at 3.06523468043176
AT1G01160_at 131.780533125273
AT1G01170_at 17.5156826723662

Total number of rows: 27826

Table truncated, full table size 812 Kbytes.




Supplementary file Size Download File type/resource
GSM2358766_cEMB_16C2.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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