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Sample GSM742090 Query DataSets for GSM742090
Status Public on Aug 04, 2011
Title YI-KO-10
Sample type RNA
 
Source name Mus musculus liver tissue
Organism Mus musculus
Characteristics tissue: Liver
age: 3 month old
strain: C57B/6J
genotype/variation: mINDY(-/-) knockout
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 Liver tissue, C57B/6J mINDY(-/-) knockout
Data processing Data was extracted using the Illumina BeadStudio software(v3.4.0). 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 Jun 15, 2011
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)
GSE29984 Deletion of the Mammalian INDY Homologue in Mice Mimics Aspects of Dietary Restriction and Protects Against Diet and Age-Induced Adiposity and Insulin Resistance

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 105.6934 -0.46595095
ILMN_1212619
ILMN_1212628
ILMN_1212632 136.9785 -0.210856388
ILMN_1212636 1523.744 2.159342372
ILMN_1212637 1070.671 1.81215597
ILMN_1212645 2773.418 2.748580998
ILMN_1212648 147.1249 -0.140552408
ILMN_1212653 123.7123 -0.311076703
ILMN_1212672 266.6736 0.444587021
ILMN_1212682 102.7294 -0.493935728
ILMN_1212683
ILMN_1212685
ILMN_1212692 98.63118 -0.533989222
ILMN_1212693 201.1938 0.167380111
ILMN_1212695 99.74744 -0.522917003
ILMN_1212698
ILMN_1212702 13959.64 4.338573638
ILMN_1212703 296.9152 0.550273485

Total number of rows: 25697

Table truncated, full table size 625 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table
Raw data included within Sample table

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