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Sample GSM2528033 Query DataSets for GSM2528033
Status Public on Mar 16, 2017
Title SAM822643 Uncrushed.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: SAM822643
treatment: Optic nerve uncrushed; 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 SAM822643 Crushed.dlkPlus
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
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
PRE_VALUE Expression Ratio (test/reference)

Data table
A_55_P1989846 -0.0793 0.946519990695804
A_55_P1991598 0.1845 1.136427423621
A_55_P2022211 2.3468 5.08706525983674
A_55_P1980764 0.0127 1.00884909057056
A_55_P1964375 1.0659 2.09353913232374
A_51_P128876 -2.8789 0.135947541788427
A_55_P2121042 0.2565 1.19454898616945
A_52_P219230 0.2333 1.17554701479654
A_51_P207591 -4.0792 0.0591617601147296
A_55_P2131920 -4.5531 0.0425975175808386
A_55_P2404223 -0.5488 0.683587339047642
A_55_P2101944 2.3045 4.94000312848642
A_52_P358860 -1.0961 0.467765405082672
A_51_P119031 0.6493 1.56838383994958
A_51_P309854 4.0972 17.115196724509
A_51_P343900 -0.5513 0.68242723456697
A_51_P234359 2.1239 4.35877790977718
A_51_P487813 -4.6090 0.0409770842093522
A_52_P613977 -0.1722 0.887484924728781
A_55_P1957209 0.9286 1.90344699974006

Total number of rows: 39429

Table truncated, full table size 1481 Kbytes.

Supplementary file Size Download File type/resource
GSM2528033_Agilent_252665512764_S01_GE2_107_Sep09_1_4.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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