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Sample GSM821608 Query DataSets for GSM821608
Status Public on Dec 31, 2011
Title Lepromatous Patient 6
Sample type RNA
 
Source name leprosy skin lesion biopsy
Organism Homo sapiens
Characteristics leprosy type: lepromatous
Treatment protocol N/A
Growth protocol N/A, samples were skin biopsy specimens from leprosy patients.
Extracted molecule total RNA
Extraction protocol RNA was extracted from the OCT embedded and sections biopsies using guanidinium-isothiocyanate (CTC) buffer as previously described (Bleharski et al., 2003).
Label biotin
Label protocol Samples were processed by Ausragen through the Discovarray miRNA profiling service. Total RNA is dephosphorylated with calf intestinal phosphatase and the pCp-Biotin labeling molecule is ligated to the 3’ ends of the RNA molecules. Labeled RNA is purified using BioSpin6 (Bio-Rad, Hercules CA).
 
Hybridization protocol Samples were processed by Ausragen through the Discovarray miRNA profiling service. Hybridization, washing, staining, imaging, and signal extraction were performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.
Scan protocol Samples were processed by Ausragen through the Discovarray miRNA profiling service. The signal processing implemented for the Ambion miRCHIP is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes.
Description L-lep6
Data processing Samples were analyzed by Ausragen through the Discovarray miRNA profiling service, and normalized using Variation Stabilization Normalization (VSN).
 
Submission date Oct 24, 2011
Last update date Dec 31, 2011
Contact name Philip T. Liu
E-mail(s) ptliu@mednet.ucla.edu
Phone 310-206-8457
Organization name University of California at Los Angeles
Department Department of Orthopaedic Surgery
Lab Liu Lab
Street address 615 Charles E Young Drive South, 410 OHRC
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL14777
Series (1)
GSE33192 miRNA expression profile in leprosy skin biopsy specimens

Data table header descriptions
ID_REF
VALUE Normalized signal intensity.

Data table
ID_REF VALUE
aga-bantam_st1 3.729075634
aga-bantam_st2 1.617572417
aga-let-7_st1 8.534510735
aga-let-7_st2 8.641726445
aga-miR-10_st1 0.400621361
aga-miR-10_st2 -1.074769511
aga-miR-124_st1 0.710692322
aga-miR-124_st2 0.052242167
aga-miR-13b_st1 2.201023567
aga-miR-13b_st2 1.617572417
aga-miR-14_st1 2.201023567
aga-miR-14_st2 0.400621361
aga-miR-1_st1 2.201023567
aga-miR-1_st2 0.710692322
aga-miR-210_st1 2.874699269
aga-miR-210_st2 0.052242167
aga-miR-219_st1 0.052242167
aga-miR-219_st2 1.220851045
aga-miR-263_st1 0.710692322
aga-miR-263_st2 0.710692322

Total number of rows: 28251

Table truncated, full table size 804 Kbytes.




Supplementary file Size Download File type/resource
GSM821608_Llep6.CEL.gz 203.3 Kb (ftp)(http) CEL
GSM821608_Llep6.txt.gz 113.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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