NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM821606 Query DataSets for GSM821606
Status Public on Dec 31, 2011
Title Lepromatous Patient 4
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-lep4
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 0.438990103
aga-bantam_st2 2.47845491
aga-let-7_st1 7.000409359
aga-let-7_st2 6.226278781
aga-miR-10_st1 0.729855802
aga-miR-10_st2 1.901552563
aga-miR-124_st1 0.438990103
aga-miR-124_st2 -2.064549127
aga-miR-13b_st1 2.273196828
aga-miR-13b_st2 0.438990103
aga-miR-14_st1 2.47845491
aga-miR-14_st2 1.754824441
aga-miR-1_st1 0.438990103
aga-miR-1_st2 2.571416795
aga-miR-210_st1 1.413723004
aga-miR-210_st2 0.986504854
aga-miR-219_st1 0.986504854
aga-miR-219_st2 1.901552563
aga-miR-263_st1 0.438990103
aga-miR-263_st2 -1.579543603

Total number of rows: 28251

Table truncated, full table size 805 Kbytes.




Supplementary file Size Download File type/resource
GSM821606_Llep4.CEL.gz 217.8 Kb (ftp)(http) CEL
GSM821606_Llep4.txt.gz 119.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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