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Sample GSM1146031 Query DataSets for GSM1146031
Status Public on Aug 20, 2013
Title neonatal rat beta cells: endocrine cells from postnatal day 2-3 pancreas of male and female rats, bio rep 1
Sample type RNA
 
Source name neonatal rat beta cells: endocrine cells, FACS-sorted for their high side scatter (HSSC), from postnatal day 2-3 pancreas of male and female Wistar rats, and containing approximately 65-70% insulin+ cells
Organism Rattus norvegicus
Characteristics cell type: neonatal rat beta cells
gender: male and female
strain: Wistar
age: 2-3 d
Treatment protocol None, freshly isolated beta cells snap frozen in liquid nitrogen immediately after isolation
Growth protocol Pancreatic beta cells were FACS-purified from neonatal (postnatal day 2-3)and 10-weeks old Wistar rat pancreas, and immediately snap frozen in liquid nitrogen, prior to total RNA extraction in batch, from all biological replicates.
Extracted molecule total RNA
Extraction protocol RNEasy extraction of total RNA was performed according to the manufacturer's instructions. RNA integrity verified on Bioanalyzer with minimal RIN cutoff = 8.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol After fragmentation at 94°C for 35 min in fragmentation buffer (40mM Tris, 30mM magnesium acetate, 10mM potassium acetate), the labelled cRNA was hybridized for 16h to the Affymetrix HG133A
Scan protocol Arrays were stained with phycoerythrin-streptavidin with the Affymetrix Fluidics Station 400, and scanned in the Affymetrix GeneArray2500scanner.
Description neonatal rat beta cells: endocrine cells, FACS-sorted for their high side scatter (HSSC), from postnatal day 2-3 pancreas of male and female Wistar rats, and containing approximately 65-70% insulin+ cells, biological replicate 1, pool of 30 animals
Data processing Scanned arrays were analyzed with dChip model-based expression analysis to the array with the median intensity and correction for mismatch hybridization using the perfect match-mismatch correction option.
 
Submission date May 22, 2013
Last update date Aug 20, 2013
Contact name Geert A. Martens
E-mail(s) geert.martens@vub.ac.be
Organization name Vrije Universiteit Brussel
Department Diabetes Research Center
Street address Laarbeeklaan 103
City Brussels
ZIP/Postal code 1090
Country Belgium
 
Platform ID GPL1355
Series (1)
GSE47174 Genome-wide mRNA expression profiles of FACS-enriched rat beta cells freshly isolated from neonatal (postnatal day 2-3) and adult (10 weeks-old) Wistar rats

Data table header descriptions
ID_REF
VALUE dChip intensity, using perfect match-mismatch correction model (PM-MM).
ABS_CALL
HSSC1 SE

Data table
ID_REF VALUE ABS_CALL HSSC1 SE
AFFX-BioB-5_at 333.52 P 14.03
AFFX-BioB-M_at 463.07 P 23.62
AFFX-BioB-3_at 407.67 P 23.11
AFFX-BioC-5_at 933.69 P 39.97
AFFX-BioC-3_at 1050.59 P 59.52
AFFX-BioDn-5_at 2920.8 P 109.56
AFFX-BioDn-3_at 3758.66 P 168.78
AFFX-CreX-5_at 13333.27 P 329.11
AFFX-CreX-3_at 13056.77 P 450.06
AFFX-DapX-5_at 243.94 P 8.61
AFFX-DapX-M_at 402.19 P 13.05
AFFX-DapX-3_at 388.37 P 14.69
AFFX-LysX-5_at 24.46 P 2.56
AFFX-LysX-M_at 40.26 P 3.93
AFFX-LysX-3_at 85.39 P 5.18
AFFX-PheX-5_at 38.93 P 3.82
AFFX-PheX-M_at 39.72 P 4.83
AFFX-PheX-3_at 40.55 P 6.11
AFFX-ThrX-5_at 77.83 P 5.09
AFFX-ThrX-M_at 58.47 P 5.35

Total number of rows: 31099

Table truncated, full table size 744 Kbytes.




Supplementary file Size Download File type/resource
GSM1146031_HSSC1.CEL.gz 2.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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