NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1310353 Query DataSets for GSM1310353
Status Public on Aug 16, 2014
Title superficial zone rep 2
Sample type RNA
 
Source name articular cartilage superficial zone of 10-day-old rat proximal tibia
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
tissue: proximal tibial epiphysis
number of tissues: 2 from animal 6
age: 10 days postnatal
zone: superficial zone
Treatment protocol Proximal tibial epiphyses of 10-day-old Sprague-Dawley rats (n=8) were rapidly excised, trimmed of any soft connective tissues, embedded in Tissue-Tek O.C.T. Compound, sectioned (60 μm thick), mounted on Superfrost Plus slides, and stored at -80°C for subsequent processing. Slides were thawed for 15 s and then placed in 70% ethanol, fixed in 100% methanol, washed in 95% ethanol, stained in eosin (0.2% eosin, 0.5% acetic acid, 75% ethanol), washed in 70% ethanol, dehydrated in 100% ethanol, and placed in xylene (each step for 1 min, at room temperature). Microdissection was performed using an inverted microscope, razor blades, and hypodermic needles. Tissues were microdissected in a xylene droplet and collected in 10 μl of 4M guanidine thiocyanate, 25mM sodium citrate pH7, and 0.1M β-mercaptoethanol on ice. Enzymatic digestion of microdissected tissues was performed using buffered proteinase K solution (1,500 μl DEPC-treated water, 30 μl 1M Tris-HCl pH7, and 57.5 μl proteinase K (20 mg/ml in glycerol)).
Growth protocol Animals were maintained under standardized conditions and handled in accordance with the Animal Ethics Committee of Northern Stockholm.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using phenol:chloroform:isozmyl alcohol (25:24:1), precipitated in 3M NaOAc and then 8M LiCl, and washed with 75% ethanol. For the complete protocol please refer to Nilsson et al. J Endocrinol April 1, 2007 193 75-84 (doi: 10.1677/joe.1.07099).
Label biotin
Label protocol ss cDNA was prepared with the Ambion WT Expression kit from 100ng of total RNA
 
Hybridization protocol Following fragmentation and biotinylation (Affymetrix Gene Chip WT Labeling Kit), 5 ug of ss cDNA were hybridized for 16 hr at 45C on GeneChipRat 1.0 STArray. They were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Description SZ #2
Data processing The data were analyzed with Partek Genomics Suite 6.6 using robust multi-array average (RMA) analysis, which adjusts for background noise on each array using only the PM probe intensitites and subsequently normalizes data across all arrays using quantile normalization followed by median polish summarization to generate a single measure of expression. These expression measures were then log transformed (base 2) and lists of spatially regulated genes were generated.
 
Submission date Jan 20, 2014
Last update date Aug 16, 2014
Contact name Michael Chau
E-mail(s) [email protected]
Organization name Karolinska Institutet
Department Department of Women's and Children's Health
Street address Astrid Lindgren Children's Hospital, Q2:08
City Stockholm
ZIP/Postal code 17176
Country Sweden
 
Platform ID GPL6247
Series (1)
GSE54216 Expression data of articular and growth plate cartilage zones in 10-day-old rat proximal tibial epiphysis

Data table header descriptions
ID_REF
VALUE log2 RMA signal intensity

Data table
ID_REF VALUE
10700001 11.4884
10700002 6.99554
10700003 9.92333
10700004 5.3258
10700005 8.62524
10700006 2.98747
10700007 3.25078
10700008 2.85596
10700009 8.9994
10700010 3.59941
10700011 5.02319
10700012 4.39348
10700013 10.7845
10700014 9.91049
10700015 9.01037
10700016 3.03496
10700017 6.40035
10700018 2.81884
10700019 3.15252
10700020 11.5388

Total number of rows: 27342

Table truncated, full table size 450 Kbytes.




Supplementary file Size Download File type/resource
GSM1310353_SZ_2_6.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap