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Sample GSM2358812 Query DataSets for GSM2358812
Status Public on Nov 06, 2017
Title Late globular (LG)_vascular, nuclei, biological replicate 4 [nVSC_LG4]
Sample type RNA
 
Source name Arabidopsis embryo_Late globular (LG)_vascular
Organism Arabidopsis thaliana
Characteristics tissue: vascular
developmental stage: Late globular (LG)
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).
 
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_nVSC_LG4
Gene expression data from vascular nuclei isolated from LG 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.
 
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

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AT1G01010_at 5.06268
AT1G01020_at 8.18134
AT1G01030_at 3.31483
AT1G01040_at 10.86212
AT1G01046_at 6.24679
AT1G01050_at 13.09097
AT1G01060_at 4.70597
AT1G01070_at 3.11540
AT1G01073_at 3.37108
AT1G01080_at 5.04225
AT1G01090_at 83.33416
AT1G01100_at 47.16183
AT1G01110_at 13.71853
AT1G01115_at 10.30539
AT1G01120_at 6.69519
AT1G01130_at 6.80826
AT1G01140_at 28.11568
AT1G01150_at 5.47151
AT1G01160_at 34.31295
AT1G01170_at 11.15634

Total number of rows: 27826

Table truncated, full table size 578 Kbytes.




Supplementary file Size Download File type/resource
GSM2358812_nVSC_LG4.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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