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Sample GSM111129 Query DataSets for GSM111129
Status Public on Mar 01, 2008
Title Pancreas_P1_HNF6-Tg_rep3
Sample type RNA
 
Source name pooled pancreata, post-natal day 1, HNF6 Transgenic
Organism Mus musculus
Characteristics Strain: B6D2
Developmental stage: post-natal day 1
Tissue: pooled pancreata
Genotype: HNF6 (hepatic nuclear factor 6) transgenic (overexpression)
Treatment protocol HNF6 expression was driven specifically to pancreatic endocrine cells beginning at embryonic day (e) 11.5 using a 1 kb enhancer from the 5’ pdx1 promoter region. This transgenic line, termed pdx1PBHnf6, was maintained on an inbred hybrid (B6D2) background. All mice were kept on a 12 hour light/dark cycle, fed Mouse diet 5015 (LabDiet), and given water ad lib. For embryonic analyses, the morning of the vaginal plug was considered e0.5. All mouse studies were performed in accordance with the Vanderbilt Institutional Animal Care and Use Committee guidelines under the supervision of the Division of Animal Care.
Extracted molecule total RNA
Extraction protocol Pancreata were dissected at e18.5 and postnatal day 1 in ice cold PBS and immediately placed into RNAlater (Ambion). Total pancreatic RNA was isolated using RNAqueous RNA Isolation Kit (Ambion) according to the manufacturer’s instructions. Agilent’s Bioanalyzer microfluidic assay (Agilent Technologies, Palo Alto CA) was used to assay RNA integrity. Spectrophotometric and fluorometric methods were combined to quantitate protein and nucleic acids present in the sample, and to ensure quality control of each sample. RNA samples were bioanalyzed individually and highly pure samples were pooled according to their genotype (3-5 animals per pool) in order to obtain an adequate quantity of RNA.
Label biotin
Label protocol Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
 
Hybridization protocol The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 Array containing 45,000 sets of 11 to 25-mer oligomers, representing 39,000 mouse transcripts (34,000 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.
Scan protocol GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.
Description No additional description necessary
Data processing CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis). The
 
Submission date May 25, 2006
Last update date Aug 28, 2018
Contact name Laura Crawford
Organization name Vanderbilt University
Department Diabetes, Endocrinology, & Metab Division
Lab Gannon Lab
Street address 715 PRB 2220 Pierce Ave
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL1261
Series (1)
GSE4926 Gene expression profiling of a mouse model of islet dysmorphogenesis
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMA-transformed signal intensity value

Data table
ID_REF VALUE
1415670_at 908.2352
1415671_at 1052.6881
1415672_at 1984.0511
1415673_at 250.31479
1415674_a_at 437.40005
1415675_at 560.62
1415676_a_at 2030.8715
1415677_at 478.2684
1415678_at 1188.197
1415679_at 2277.744
1415680_at 631.0867
1415681_at 626.3423
1415682_at 347.5429
1415683_at 1077.5803
1415684_at 290.1594
1415685_at 286.63242
1415686_at 453.8012
1415687_a_at 2401.5425
1415688_at 1503.0101
1415689_s_at 559.4338

Total number of rows: 45101

Table truncated, full table size 927 Kbytes.




Supplementary file Size Download File type/resource
GSM111129.CEL.gz 6.3 Mb (ftp)(http) CEL
GSM111129.CHP.gz 5.2 Mb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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