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Sample GSM2528005 Query DataSets for GSM2528005
Status Public on Apr 26, 2017
Title SAM619451 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: SAM619451
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 SAM619451 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

Data table header descriptions
ID_REF ID in platform
VALUE log2 of PRE_VALUE
PRE_VALUE Expression Ratio (test/reference)

Data table
ID_REF VALUE PRE_VALUE
A_52_P616356 0.0135 1.00942396553207
A_52_P580582 0.2181 1.16317313837393
A_52_P403405 0.0730 1.05190158311127
A_52_P819156 0.0549 1.03879508953064
A_51_P331831 -2.3465 0.196616436653771
A_51_P430630 -0.0546 0.962840743612425
A_52_P502357 0.5739 1.48854539655388
A_52_P299964 0.0180 1.01256542707023
A_51_P356389 -0.0159 0.98902559929708
A_52_P684402 0.0899 1.06429840579184
A_51_P414208 -0.0173 0.988108858614914
A_51_P280918 2.5836 5.99451075766976
A_52_P613688 1.8917 3.71062285752997
A_52_P258194 4.6044 24.3250970745421
A_52_P229271 0.1143 1.08242251321139
A_52_P214630 -1.7389 0.299591263733646
A_52_P579519 -1.0076 0.49738582531685
A_52_P979997 0.1106 1.0796467653011
A_52_P453864 0.6132 1.52965858793743
A_52_P655842 1.7663 3.40183196120994

Total number of rows: 41174

Table truncated, full table size 1519 Kbytes.




Supplementary file Size Download File type/resource
GSM2528005_Agilent_251486826273_S01_GE2_105_Jan09_1_3.txt.gz 14.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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