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Sample GSM1005320 Query DataSets for GSM1005320
Status Public on Jul 31, 2013
Title 5-SD-L
Sample type RNA
 
Source name liver tissue
Organism Mus musculus
Characteristics tissue: Liver
age: one-year old
gender: male
strain: B6C57/J
diet: maintained on ad libitum AIN-93G SD until the end of their life
Treatment protocol Liver tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD until the end of their life.
Extracted molecule total RNA
Extraction protocol RNA was extracted from liver tissue using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.
Label Streptavidin-Cy3 bound to biotin-labeled cRNA.
Label protocol Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
 
Hybridization protocol Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description supplementary file:GEO_Supplementary_file_AS_Liver 9-14-12
Liver tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD until the end of their life.
Data processing Data was extracted using the Illumina GenomeStudio software(v1.6.0). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores will be included in the supplemental file.
 
Submission date Sep 17, 2012
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6885
Series (1)
GSE40936 Metformin mild supplementation improves health and survival of mice

Data table header descriptions
ID_REF
RAW_VALUE Raw intensity value from Illumina GenomeStudio software
VALUE Z transformation of the natural log of the raw intensity values

Data table
ID_REF RAW_VALUE VALUE
ILMN_1212607
ILMN_1212612 225 -0.280301092
ILMN_1212619
ILMN_1212628
ILMN_1212632 240.5 -0.223348712
ILMN_1212636 3220 1.994587223
ILMN_1212637 4711.8 2.320033427
ILMN_1212645 9998.1 2.963187209
ILMN_1212648 276.8 -0.103172697
ILMN_1212653 198.6 -0.386997672
ILMN_1212672 533.8 0.458254582
ILMN_1212682
ILMN_1212683
ILMN_1212685
ILMN_1212692
ILMN_1212693 428.5 0.270409585
ILMN_1212695
ILMN_1212698
ILMN_1212702 24486.7 3.728940469
ILMN_1212703 475.9 0.360101893

Total number of rows: 25694

Table truncated, full table size 592 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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