|
| Status |
Public on Apr 26, 2017 |
| Title |
SAM627975 Nerve control |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from L3/L4 DRGs 3 days after sciatic nerve transection in adult mice
|
| Organism |
Mus musculus |
| Characteristics |
sample_id: SAM627975
primary_tissue: Nerve (L3/L4 dorsal root ganglion)
cre: cre.neg
treatment: control
genotype: jun.wt
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DRGs were dissected and immediately transferred to RNAlater (Qiagen) and RNA isolated using RNeasy Plus Mini Kit (Qiagen). RNA sample quantity and quality were determined using an ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent Technologies), respectively.
|
| Label |
Cy5
|
| Label protocol |
The method for preparation of Cy-dye labeled cRNA and array hybridization was provided by Agilent. Briefly, 1 μg total RNA was converted to double-stranded cDNA and then to Cy5-labeled cRNA using Quick Amp Labeling Kit (Agilent). The labeled cRNA was purified using RNeasy mini kit (Qiagen). cRNA yield and Cy5 incorporation was determined using ND-1000 spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
universal mouse reference (Stratagene)
|
| Organism |
Mus musculus |
| Characteristics |
sample_id: NA
primary_tissue: NA
cre: NA
treatment: NA
genotype: NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
By vendor
|
| Label |
Cy3
|
| Label protocol |
Method for Cy-dye labeled cRNA preparation was provided by Agilent.
|
| |
|
| |
| Hybridization protocol |
750 ng of labeled cRNA was fragmented and hybridized to Agilent’s Whole Mouse Genome 4x44Kv2 arrays as described in manufacturer’s hybridization kit, against an equal amount of Cy3-labeled universal mouse reference (Stratagene).
|
| Scan protocol |
Following hybridization, microarrays were washed, dried, and scanned on Agilent’s G2505C scanner. Agilent’s Feature Extraction 11.5 software was used to analyze acquired array images.
|
| Description |
SAM627975 Nerve cre.neg control jun.wt
|
| Data processing |
Data were analyzed using the limma package from Bioconductor. ControlType weights were set to 0, spots with background signal more than 50 above the foreground signal were set to the median background intensity, background correction was performed with limma::backgroundCorrect() using the "normexp" method and an offset of 50, limma::normalizeWithinArrays() with the "loess" method, and finally limma::normalizeBetweenArrays() with the "Aquantile" method. This gives the "test" and "reference" normalized probe intensities. Finally, for each probe an "expression ratio" was calculated, the ratio of the normalized signals in the test and reference channels.
|
| |
|
| Submission date |
Mar 09, 2017 |
| Last update date |
Apr 26, 2017 |
| Contact name |
Kevin Huang |
| E-mail(s) |
[email protected]
|
| Organization name |
Genentech
|
| Department |
Bioinformatics
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE96051 |
Expression changes in L4 DRG initiated by sciatic nerve injury |
|
