NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM399629 Query DataSets for GSM399629
Status Public on Jul 01, 2009
Title NKT 3
Sample type RNA
 
Channel 1
Source name NKT 3
Organism Mus musculus
Characteristics cell type: NKT cell
strain: C57BL/6
age: 4 weeks
tissue: 18 pooled thymi
Treatment protocol Enrichment of HSA low mature thymocytes by anti-HSA mAb and rabbit complement; sorting of mature NKT and T cells
Extracted molecule total RNA
Extraction protocol miRVana kit (Ambion)
Label Hy3
Label protocol miRCURY LNA Array power labeling kit (Exiqon, Denmark)
 
Channel 2
Source name Total thymocytes
Organism Mus musculus
Characteristics strain: C57BL/6
age: 4 weeks
tissue: 18 pooled thymi X 3 replicates; pool of all the thymi used in the sortings; used as a common reference
Extracted molecule total RNA
Extraction protocol miRVana kit (Ambion)
Label Hy5
Label protocol miRCURY LNA Array power labeling kit (Exiqon, Denmark)
 
 
Hybridization protocol The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 12.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
Scan protocol Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).
Description microRNA expression
Data processing The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
 
Submission date May 01, 2009
Last update date Nov 19, 2010
Contact name Maya Fedeli
E-mail(s) fedeli.maya@hsr.it
Phone 00390226434735
Organization name San Raffaele Scientific Institute
Department DIBIT
Lab Experimental Immunology Unit
Street address via Olgettina 58
City Milan
State/province MI
ZIP/Postal code 20132
Country Italy
 
Platform ID GPL7723
Series (1)
GSE15925 Mature thymic NKT and T cells

Data table header descriptions
ID_REF
RATIO normalized ratio (test/reference)
VALUE normalized log2 ratio (test/reference)

Data table
ID_REF RATIO VALUE
13138 null null
4610 0.887450302 -0.172261766
11013 0.83694415 -0.256796742
11102 0.92621987 -0.110573387
19604 1.395940439 0.481237387
17306 1.170678409 0.227344815
17529 1.281392764 0.357712748
17660 0.856163806 -0.224041247
17940 1.258484978 0.331687996
5740 7.607496826 2.927421827
11020 1.004212807 0.00606503
11111 1.005751333 0.00827365
11222 1.245940712 0.317235419
17327 0.984520457 -0.022506911
17536 1.292354938 0.370002352
14257 0.337137033 -1.568592984
17732 1.099481514 0.136823348
17953 0.756367091 -0.402841501
10306 1.468214456 0.554062712
11024 1.338129767 0.42021803

Total number of rows: 1997

Table truncated, full table size 58 Kbytes.




Supplementary file Size Download File type/resource
GSM399629_0_Exiqon_13973758_S01_Cropped.txt.gz 679.3 Kb (ftp)(http) TXT
GSM399629_1_Exiqon_13973758_S01_Cropped.txt.gz 787.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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