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Sample GSM463359 Query DataSets for GSM463359
Status Public on Apr 09, 2010
Title Intervertebral disc-mutant-2
Sample type RNA
 
Source name IVD E13.5 days, mutant
Organism Mus musculus
Characteristics tissue: Intervertebral disc (IVD)
genotype: Cre+;Tgfbr2lox/lox
Treatment protocol Comparison of control and Col2aCre;Tgfbr2 deleted mice.
Growth protocol Mouse embryos, embryonic day E13.5 day.
Extracted molecule total RNA
Extraction protocol E13.5 day control and mutant mouse embryos were rinsed in DEPC treated PBS, embedded into OCT and frozen for sectioning. Using a cryostat, 8-12um sagittal cut frozen sections were collected and placed on PALM PEN-Membrane Slides (P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). The frozen sections were then quickly dehydrated (70 to 100% EtOH) and stored in Xylene prior to LCM. Laser Capture Microdissection (LCM) was carried out by using a Zeiss/ PALM Microbeam Instrument (Microdissection System; Carl Zeiss Microimaging GmbH, Munchen, Germany). The presumptive IVD from the lumbar region were collected into RNase/DNase free special PALM AdhesiveCaps (P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). After IVDs were collected, the adjacent presumptive vertebrae were collected into a separate adhesive cap. Collected sample tubes are stored at -80C until RNA was isolated. RNA was isolated using Ambion RNAqueous – Micro Kit (Austin, TX). The optional DNase treatment step was included.
Label biotin
Label protocol Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
 
Hybridization protocol Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day.
Scan protocol Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console).
Description Intervertebral disc-mutant-2
Data processing The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
 
Submission date Oct 20, 2009
Last update date Aug 28, 2018
Contact name Rosa Serra
E-mail(s) rserra@uab.edu
Phone 205-934-0842
Organization name University of Alabama at Birmingham
Department Cell Biology
Lab Serra
Street address 1918 University Blvd. 660 MCLM
City Birmingham
State/province AL
ZIP/Postal code 35294-0005
Country USA
 
Platform ID GPL1261
Series (2)
GSE18647 Gene expression in embryonic intervertebral disc and vertebrae.
GSE18649 Molecular Profiling of the Developing Axial Skeleton: A role for Tgfbr2 in the Development of the Intervertebral Disc.
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE log2 RMA summariztion value.

Data table
ID_REF VALUE
AFFX-BioB-5_at 0.7872753
AFFX-BioB-M_at 0.73580647
AFFX-BioB-3_at 0.86537457
AFFX-BioC-5_at 0.80454826
AFFX-BioC-3_at 0.74697113
AFFX-BioDn-5_at 0.605011
AFFX-BioDn-3_at 0.7275429
AFFX-CreX-5_at 0.26175404
AFFX-CreX-3_at 0.28635216
AFFX-DapX-5_at 0.14624858
AFFX-DapX-M_at 0.019005299
AFFX-DapX-3_at 0.17531753
AFFX-LysX-5_at 0.18367577
AFFX-LysX-M_at 0
AFFX-LysX-3_at 0.17408037
AFFX-PheX-5_at 0.09729648
AFFX-PheX-M_at 0.087343216
AFFX-PheX-3_at -0.028636456
AFFX-ThrX-5_at 0.03075695
AFFX-ThrX-M_at 0.19772434

Total number of rows: 45101

Table truncated, full table size 957 Kbytes.




Supplementary file Size Download File type/resource
GSM463359.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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