|
| Status |
Public on Jun 30, 2016 |
| Title |
4_4340_Ctrl |
| Sample type |
RNA |
| |
|
| Source name |
Normal control_Putamen tissue
|
| Organism |
Homo sapiens |
| Characteristics |
raw data id: 4
neuropathology: Normal control
gender: M
additional neurological diagnosis: none
age at death: 47
postmortem interval (h): 12.5
tissue: postmortem putamen tissue
rin: 4.6
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human postmortem putamen tissues from Parkinson's disease patients and the neurologically normal controls were obrtained from the Human Brain and Spinal Fluid Resource Center, Los Angeles, CA through NIH NeuroBioBank, and stored at -80°C until RNA isolation. Total RNA was extracted using the miRvana RNA isolation kit, following the manufacturer’s instructions (Ambion).
|
| Label |
Biotin & color-coded tag
|
| Label protocol |
Using 225 ng total RNA, 134 gene transcrpts levels were assayed using Nanostring nCounter assay kits by direct digital detection following the manufacturer’s guidelines (NanoString Technologies, Seattle, WA).
|
| |
|
| Hybridization protocol |
Reporter and Capture probes against genes of interest were prepared as previously described by Geiss et al. (2008; PMID: 18278033). Data were collected and analyzed using the nCounter Digital Analyzer.
|
| Scan protocol |
according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)
|
| Description |
13
|
| Data processing |
The nSolver Analysis Software (NanoString Technologies) was used for the extraction of raw miRNA data and for checking the quality of the data. Using the positive control data, a generalized linear model was fitted with 8 negative and 6 positive controls, where the counts for each positive control follow a Poisson’s distribution with the mean modeled as a linear function of concentration. Each sample was then normalized to the median slope and intercept of all samples and log2 transformed. Using the transformed data of all genes, a Bland-Altman plot was generated for each sample to compare the sample to the average of all samples. A loess curve was fitted for each Bland-Altman plot to globally normalize the transformed data as described in our recent publication. A two sample t-statistical was performed on each miRNA, and the miRNA was filtered based on the following three criteria: (a) p-value ≤ 0.08; (b) the log2 fold change between PD and control is greater than 0.263 in absolute value, equivalent to 20% change; and (c) the mean of the log2 transformed gene expression for one of the two groups is at least 5.
Please note that *RCC files are raw data collected using the Nanostring digital analyzer, whereas, *csv files are raw data extracted from the RCC files using the Nanostring nSolver software.
|
| |
|
| Submission date |
Feb 08, 2016 |
| Last update date |
Jul 02, 2016 |
| Contact name |
Venugopalan Nair |
| E-mail(s) |
venugopalan.nair@mssm.edu
|
| Phone |
212-241-5809
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neurology
|
| Street address |
1468 Madison Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL21436 |
| Series (2) |
| GSE77666 |
Expression mRNA data from human postmortem putamen samples measured using the NanoString nCounter platform |
| GSE77668 |
Expression mRNA and miRNA data from human postmortem putamen samples measured using the NanoString nCounter platform |
|
