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Sample GSM1337793 Query DataSets for GSM1337793
Status Public on Jun 04, 2015
Title Cerebellum_WT_NR-Replicate-2
Sample type RNA
 
Source name Cerebellum_WT_Nicotinamide riboside
Organism Mus musculus
Characteristics strain: C57BL/6 WT 3 months old
treatment: WT mice, 3 months old were given subcutaneous interscapular injections of Nicotinamide riboside, 500 mg /kg body weight/day for 14 consecutive days at 4:00 pm.
gender: male
tissue collection: On day 15, the mice were sacrificed and half of the cerebellum was harvested for purification of mitochondria, with the left half snap-frozen, homogenized, and aliquoted for western blotting, microarray, and detection of ATP and NAD+.
Treatment protocol CX and WT (C57BL/6) mice of 3 months of age were given subcutaneous interscapular injections of 500 mg NR/kg body weight/day or the equivalent volume of saline for a consecutive of 14 days at 4:00 pm
Growth protocol Mice carrying WT, or CX (Csa-/-/Xpa-/-) alleles in a C57BL/6 background were maintained under standard laboratory conditions at Harvard School of Public Health and allowed free access to water and control casein pelleted diet (Research Diets D12450B).
Extracted molecule total RNA
Extraction protocol On day 15, mice were sacrificed and half of a cerebellum was harvested for purification of mitochondria, with the left half snap-frozen, homogenized, and aliquoted for RNA isolation. Total RNA extraction was done using a TRIzol Plus RNA purification kit as per manufacturer’s protocol. Quality and quantity of the total RNA was tested using the Agilent 2100 Bio-Analyzer and RNA 6000 nano kits.
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, 0.5ug 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 Cerebellum_WT_NR-Replicate-2
Data processing Data was extracted using the Illumina BeadStudio software(v1.9.0). 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 Mar 01, 2014
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 (2)
GSE55485 Defective Mitophagy in XPA via PARP1 activation and NAD+/SIRT1-depletion: Implications for neurodegeneration (mouse)
GSE55486 Defective Mitophagy in XPA via PARP1 activation and NAD+/SIRT1-depletion: Implications for neurodegeneration

Data table header descriptions
ID_REF
VALUE Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection Pval Detection Pvalue from Illumina GenomeStudio software, ver 1.9.0.

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 -0.865439933 0.72431
ILMN_1212612 1.804998677 0
ILMN_1212619 0.013411246 0
ILMN_1212628 -0.785135358 0.37469
ILMN_1212632 0.182972397 0
ILMN_1212636 2.093948001 0
ILMN_1212637 0.599830994 0
ILMN_1212645 0.698011745 0
ILMN_1212648 0.552285292 0
ILMN_1212653 1.250609636 0
ILMN_1212672 0.362628008 0
ILMN_1212682 -0.655092322 0.10652
ILMN_1212683 -0.796750405 0.42231
ILMN_1212685 -0.945884805 0.94486
ILMN_1212692 -0.519212141 0.02005
ILMN_1212693 -0.063192865 0
ILMN_1212695 -0.748514463 0.25689
ILMN_1212698 -0.876677742 0.76692
ILMN_1212702 3.793825596 0
ILMN_1212703 0.035850663 0

Total number of rows: 25697

Table truncated, full table size 770 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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