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Sample GSM1357329 Query DataSets for GSM1357329
Status Public on Mar 29, 2014
Title notochord_3 (mRNA)
Sample type RNA
 
Source name notochord,sample 3
Organism Homo sapiens
Characteristics gender: Male
age: 24 weeks
tissue: embryo intervertebral disc
Treatment protocol Paraffinsections from the fixed chordoma tissues were cut at 5 mm andstained with hematoxylin and eosin (H&E). All tissues were separated using laser capture microdissection(LCM)
Growth protocol All thesamples were stored at -80℃ until they were processed for RNA extraction in 1 batch
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from PFPE samples by usingRecoverAllTM Total Nucleic Acid Isolation Kit (Life Technologies, Carlsbad, CA, USA) for mRNA and miRNA microarrayanalysis, according to the manufacturer’s instructions.Sample purity and integrity was confirmed by A260/A280 spectrophotometry and capillary gel electrophoresis on a Bioanalyzer 2100 (Agilent)
Label biotin
Label protocol Total RNA per sample was amplified using a SensationPlus™ FFPE Amplification and WT Labeling Kit (Affymetrix). Samples were subjected to the first strand cDNA synthesis, promoter synthesis, subsequent in vitro transcription of senseRNA, double-stranded cDNA synthesis, and labeling of cDNA. Total RNA was reverse transcribed to form the cDNA, purified with Purification Beads subsequently. Total cDNA was poly (dA) tailed on the 3´ end. A T7 dT oligo with a 3´ blocking group is hybridized to the 3´ (dA) tail. klenow and dNTP mix generate a double stranded T7 promoter region on the single stranded cDNA. The promoter-modified cDNA was in vitro transcribed to form RNA. The senseRNA was purified with purification beads and reverse transcribed using random primer mix. second strand cDNA was made with klenow and RNase H. Finally, the double-stranded cDNA was purified, fragmented and end-labeled
 
Hybridization protocol Samples were prepared for hybridization using the GeneChip Hyb Wash and Stain Kit (Affymetrix); mixed with Control Oligonucleotide B2, Eukaryotic Hybridization Controls and Hybridization Mix from and loaded to Human Gene ST 1.0 Arrays (Affymetrix). Hybridization was done in a GeneChip Hybridization Oven 640 (Affymetrix) for 17 hours, at +45°C, 60 rpm. Arrays were washed and PE-labeled on a GeneChip Fluidics Station 450 (Affymetrix)
Scan protocol Arrays were scanned on a GeneChip Scanner 3000 7G with autoloader (Affymetrix). Raw data were generated with Affymetrix GeneChip Command Console
Description gene expression data from notochord IVD of sample 3
Data processing Raw data from the generated .CEL files were imported into Affymetrix Expression Console using the RMA method
 
Submission date Mar 25, 2014
Last update date Mar 29, 2014
Contact name zhongjun Liu
E-mail(s) starsky298@gmail.com
Phone 15281085496
Organization name Peking University Third Hospital
Department Department of Orthopedics
Lab Spine tumor center
Street address 49 North Garden Rd, Haidian, 100191, Beijing, China.
City Beijing, China
State/province Beijing
ZIP/Postal code 100191
Country China
 
Platform ID GPL10739
Series (1)
GSE56183 Integrated miRNA-mRNA analysis revealing the potential roles of miRNAs in chordomas

Data table header descriptions
ID_REF
VALUE Detected Above Background Confidence Score

Data table
ID_REF VALUE
7892501 0.53
7892502 0.07
7892503 0.02
7892504 0
7892505 0
7892506 0.72
7892507 0.27
7892508 0.32
7892509 0.58
7892510 0.4
7892511 0.06
7892512 0.34
7892513 0.73
7892514 0.69
7892515 0
7892516 0.69
7892517 0.86
7892518 0.53
7892519 0.78
7892520 0

Total number of rows: 257430

Table truncated, full table size 3223 Kbytes.




Supplementary file Size Download File type/resource
GSM1357329_N3.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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