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Sample GSM952948 Query DataSets for GSM952948
Status Public on Jun 28, 2012
Title HSALR-ASO190401 5543266022_B
Sample type RNA
 
Source name quadriceps muscle
Organism Mus musculus
Characteristics treatment: ASO 190401
genotype: HSALR transgenic
genetic background: FVB/n
tissue: quadriceps muscle
Treatment protocol Subcutaneous saline or oligo injections were administered to adult mice biweekly for 4 weeks.
Extracted molecule total RNA
Extraction protocol Quadriceps muscles were homogenized with a Polytron homogenizer in Trizol reagent according to the manufacturer's recommendations.
Label biotin
Label protocol Samples for mRNA profiling studies were processed by Asuragen, Inc., according to the company’s standard operating procedures. The purity and quantity of total RNA samples were determined by absorbance readings at 260 and 280 nm using a NanoDrop ND-1000 UV spectrophotometer. The integrity of total RNA was qualified by Agilent Bioanalyzer 2100 capillary electrophoresis. Total RNA (100 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using Illumina’s TotalPrep Kit (Ambion Inc., Austin, TX) and one round of amplification. The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.
 
Hybridization protocol Labeled cRNA was used to probe MouseRef-8 Expression BeadChips. Hybridization, washing, and scanning of the Illumina arrays were carried out according to the manufacturer’s instructions. Briefly, cRNA/hybridization buffer mixtures were incubated at 65°C for 5 minutes, followed by brief centrifugation to collect. The mixtures were added to BeadChips and then BeadChips inserted into hybridization chambers, and hybridization was carried out at 58°C for 16-18 hours at rocking speed set to 5.
Scan protocol BeadChips were washed and stained in the following steps: 1) 55°C for 10 minutes static in HighTemp Wash Buffer in a Hybex waterbath, 2) ambient temperature shaking for 5 minutes in E1BC wash buffer, 3) ambient temperature shaking for 10 minutes in ethanol, 4) ambient temperature shaking for 2 minutes in E1BC buffer, 5) ambient temperature for 10 minutes rocking in Block E1 buffer, 6) ambient temperature for 10 minutes rocking in Block E1 buffer containing 1ug/ml Cy3-streptavidin, and 7) ambient temperature shaking for 5 minutes in E1BC buffer. BeadArrays were dried in a centrifuge for 4 minutes and scanned using an Illumina BeadArray Reader. Illumina BeadScan software was used to produce .idat, .xml, and .tif files for each array on a slide and .sdf files for each barcode on a slide of 8 arrays. Raw data were extracted using Illumina BeadStudio software v3. Following quality assessment, data from the replicate beads on each array were summarized into raw intensity values with and without background subtraction in an Excel report.
Description 5543266022_B
Data processing Background subtracted data were quantile normalized with the bioconductor affy package. If the minimum value in a row was less than 2, a constant was added to all values in that row such that the minimum was increased to 2.
 
Submission date Jun 27, 2012
Last update date Jun 28, 2012
Contact name Stephen Welle
E-mail(s) swelle@rochester.rr.com
Organization name University of Rochester
Street address 601 Elmwood Avenue
City Rochester
State/province NY
ZIP/Postal code 14642
Country USA
 
Platform ID GPL6885
Series (1)
GSE38962 Antisense oligonucleotides targeting nuclear RNA for in vivo correction of myotonic dystrophy

Data table header descriptions
ID_REF
VALUE quantile normalized signals
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 6865.2 0
ILMN_2721178 1309.5 0
ILMN_3033922 901.5 0
ILMN_3092673 4715.6 0
ILMN_2816356 46.6 0.00877
ILMN_2808939 25.8 0.05263
ILMN_2634564 577.7 0
ILMN_2737647 22.3 0.14536
ILMN_2734484 867.4 0
ILMN_2952292 50.5 0.00376
ILMN_2699078 19.1 0.59399
ILMN_1213681 951.7 0
ILMN_2735413 19.8 0.46617
ILMN_2735415 33.9 0.0589
ILMN_2891688 1078.3 0
ILMN_2637698 763.2 0
ILMN_2674228 220.7 0
ILMN_2601546 41.5 0.02632
ILMN_1230831 21.0 0.27068
ILMN_2848071 36.6 0.10526

Total number of rows: 25697

Table truncated, full table size 621 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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