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Sample GSM399628 Query DataSets for GSM399628
Status Public on Jul 01, 2009
Title NKT 2
Sample type RNA
 
Channel 1
Source name NKT 2
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 1.098930159 0.136099701
11013 0.846649384 -0.240163453
11102 0.8482461 -0.237445203
19604 1.238280419 0.308338062
17306 1.308281142 0.387672601
17529 1.041179857 0.058219307
17660 0.712492956 -0.489052343
17940 1.327979259 0.409232614
5740 8.750328627 3.1293372
11020 1.039458552 0.055832232
11111 1.100802217 0.13855528
11222 1.405426518 0.491008025
17327 1.219044183 0.285750416
17536 1.15645781 0.209712634
14257 0.290931645 -1.781247865
17732 0.938391288 -0.091738475
17953 0.73267457 -0.448755552
10306 1.701369667 0.766696638
11024 1.266004401 0.34028242

Total number of rows: 1997

Table truncated, full table size 59 Kbytes.




Supplementary file Size Download File type/resource
GSM399628_0_Exiqon_13973757_S01_Cropped.txt.gz 720.7 Kb (ftp)(http) TXT
GSM399628_1_Exiqon_13973757_S01_Cropped.txt.gz 874.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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