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Sample GSM2528026 Query DataSets for GSM2528026
Status Public on Mar 16, 2017
Title SAM822650 Crushed.Cre+
Sample type RNA
 
Channel 1
Source name RNA from whole retinas 3 days after optic nerve crush
Organism Mus musculus
Characteristics tissue: retina
samid: SAM822650
treatment: Optic nerve crushed; Cre+
Treatment protocol To investigate the role of DLK after optic nerve crush, we generated mice with a tamoxifen-inducible Cre recombinase-estrogen receptor (Cre-ERT) transgene driven by the chicken beta-actin-CMV hybrid (CAG) promoter, resulting in high levels of Cre-ERT in many tissues, including retina. CAG Cre-ERT:DLKlox/lox (referred to as DLKlox:Crepos) mice survive to adulthood with no evidence of the developmental abnormalities seen in DLK-null animals (8, 18). Dosing of DLKlox:Crepos mice at 10-12 wk of age with tamoxifen (Fig. S2A) results in elimination of the majority of DLK expression in retina (Fig. 1 C and L), with the small amount of remaining DLK protein varying slightly from animal to animal (Fig. 1C and Fig. S2B). No differences in health or behavior were observed between tamoxifen-treated DLKlox:Crepos mice and their tamoxifen-treated DLKlox:Creneg control littermates.
Extracted molecule total RNA
Extraction protocol RNA was extracted from whole retina as described in Watkins et al. PNAS. (2013). 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 samid: NA
treatment: 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 SAM822650 Crushed.dlkMinus
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 Mar 17, 2017
Contact name Kevin Huang
E-mail(s) huang.kevin@gene.com
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 GPL11202
Series (1)
GSE96053 Dlk response to optic 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_55_P1989846 -0.1347 0.910873396614931
A_55_P1991598 0.0934 1.06688361056276
A_55_P2022211 2.4497 5.46309368711234
A_55_P1980764 0.2223 1.16661609175766
A_55_P1964375 1.1830 2.27045265464259
A_51_P128876 -3.0563 0.120217788762688
A_55_P2121042 0.1106 1.07968690275118
A_52_P219230 0.2731 1.20844209221024
A_51_P207591 -3.8499 0.0693521189795622
A_55_P2131920 -4.3283 0.0497808281852212
A_55_P2404223 -0.6477 0.63831306153976
A_55_P2101944 2.8439 7.17983096875008
A_52_P358860 -1.1191 0.460375635829914
A_51_P119031 0.2411 1.1818802402217
A_51_P309854 3.7906 13.8382726599975
A_51_P343900 -0.9257 0.526436520200242
A_51_P234359 2.9476 7.71481900608164
A_51_P487813 -4.4996 0.0442064056851432
A_52_P613977 -0.6084 0.655920370791241
A_55_P1957209 0.8991 1.86495209968152

Total number of rows: 39429

Table truncated, full table size 1481 Kbytes.




Supplementary file Size Download File type/resource
GSM2528026_Agilent_252665512760_S01_GE2_107_Sep09_1_4.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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