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Sample GSM1645547 Query DataSets for GSM1645547
Status Public on Mar 27, 2016
Title hyb13811
Sample type RNA
 
Channel 1
Source name Liver_male_2month_E128_LKO
Organism Mus musculus
Characteristics strain: mixed strain
genotype/variation: conditional liver NIPP1 KO
gender: male
age: 2 months
tissue: liver
treatment: untreated
Extracted molecule total RNA
Extraction protocol Gen Elute Mammalian total RNA kit (Sigma)
Label Cy5
Label protocol RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
 
Channel 2
Source name Liver_male_2month_E116_CTR
Organism Mus musculus
Characteristics strain: mixed strain
genotype/variation: control
gender: male
age: 2 months
tissue: liver
treatment: untreated
Extracted molecule total RNA
Extraction protocol Gen Elute Mammalian total RNA kit (Sigma)
Label Cy3
Label protocol RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
 
 
Hybridization protocol A mixture of purified and labeled cRNA (Cy3 label: 825ng; Cy5 label: 825ng) was hybridised on Agilent's Whole Mouse Genome (4x44K v2) arrays followed by (manual) washing, according to the manufacturer’s procedures.
Scan protocol To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).
Description ---
Data processing Prior to normalization, data from control spots was removed. We used the processed signals obtained with the Agilent Feature extraction software (version 10.7.3.1). The presented values are log2-(Cy5/Cy3)-ratios.
 
Submission date Mar 27, 2015
Last update date Mar 27, 2016
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL10333
Series (1)
GSE67366 Conditional liver NIPP1 KO micro array on total liver RNA

Data table header descriptions
ID_REF
VALUE log2(Cy5/Cy3) ratio

Data table
ID_REF VALUE
12 -0.0204265078293844
13 -0.296635530413943
14 0.657519256765303
15 -0.0180276951849918
16 -0.122990591597731
17 -0.555782053899362
18 -0.30034506730384
19 -0.301002062740459
20 0.43902903199682
21 -0.30223600378464
22 0.0168857655096204
23 0.381959434699022
24 -0.453794448156776
25 0.0462563389422996
26 -0.117619955020599
27 -0.318079639000169
28 1.18664143305298
29 0.271452923727161
30 -0.144801790680878
31 -0.306713848146756

Total number of rows: 43020

Table truncated, full table size 1024 Kbytes.




Supplementary file Size Download File type/resource
GSM1645547_hyb13811.txt.gz 15.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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