|
| Status |
Public on Mar 23, 2016 |
| Title |
Patient 15 P3655_L7 |
| Sample type |
RNA |
| |
|
| Source name |
Bladder cancer
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: Patient 15
age: 37
Sex: Female
race: Caucasian
Stage: Ta
grade: G2
surgery type: Transurethral Resection
patient status: Alive
tissue: Bladder cancer
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.
|
| Label |
Biotin
|
| Label protocol |
Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.
|
| |
|
| Hybridization protocol |
Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.
|
| Scan protocol |
Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.
|
| Description |
Tissues were defined as bladder cancer
|
| Data processing |
The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 4.0). Intensities of each spot were the median intensities of foreground. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. MicroRNA oligos are represented as duplicate, quadruplicate, or sextuplet spots. Duplicate and sextuplet spots were averaged while quadruplicate spots, represented by quadruplicate spots as two distant pairs of two adjacent spots, may have been flagged according to the following. If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package and all replicate spots were averaged.
|
| |
|
| Submission date |
May 06, 2015 |
| Last update date |
Mar 23, 2016 |
| Contact name |
Amelia Cimmino |
| E-mail(s) |
[email protected]
|
| Organization name |
CNR
|
| Department |
IGB
|
| Lab |
Cimmino
|
| Street address |
via pietro Castellino 111
|
| City |
Naples |
| ZIP/Postal code |
80131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL20120 |
| Series (1) |
| GSE68594 |
Hyperexpression of transcribed noncoding RNA containing ultraconserved genomic regions 8 promotes bladder tumorigenesis |
|
