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Sample GSM1899427 Query DataSets for GSM1899427
Status Public on May 16, 2016
Title MEFs_KO_rep1
Sample type RNA
Source name Ip6k1-/- MEFs biological replicate 1
Organism Mus musculus
Characteristics cell type: Mouse embryonic fibroblasts
developmental stage: E14
genotype: Ip6k1-/-
Treatment protocol MEFs were isolated from E14 embryos from a single heterozygous female mouse that had been paired with a heterozygous male, and were genotyped to select two Ip6k1+/+ and Ip6k1-/- embryos each (Ref: Bhandari et al., Proc. Natl. Acad. Sci. USA, 2008, 105, 2349-53). These MEFs were immortalised by the expression of SV40 large T antigen and frozen in liquid nitrogen. Thawed cells were grown at 37°C in a humidified incubator with 5% CO2, passaged twice, harvested by trypsinization, and their genotype was re-confirmed. 10^7 cells were resuspended in 100 µl phosphate buffered saline and 5 volumes of RNAlater (Sigma-Aldrich).
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy minikit (Qiagen)
Label Cy3
Label protocol The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.
Hybridization protocol 600ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)
Scan protocol Scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution.
Description Gene expression in exponentially growing Ip6k1-/- MEFs
Treated A
Data processing Data extraction from Images was done using Feature Extraction software and Normalization of the data was done in GeneSpring GX : 75th percentile shift method
Submission date Sep 30, 2015
Last update date May 16, 2016
Contact name Rashna Bhandari
Phone +91-40-24749430
Organization name Centre for DNA Fingerprinting and Diagnostics
Lab Laboratory of Cell Signalling
Street address Bldg 7, Gruhakalpa, 5-4-399/B Nampally
City Hyderabad
State/province Telangana
ZIP/Postal code 500001
Country India
Platform ID GPL7202
Series (1)
GSE73612 Gene expression analysis of inositol hexakisphosphate kinase 1 (IP6K1) knockout mouse embryonic fibroblasts

Data table header descriptions
VALUE Log base 2 normalized signal

Data table
A_51_P100021 -6.53
A_51_P100034 2.97
A_51_P100052 -6.38
A_51_P100063 -3.77
A_51_P100084 -4.65
A_51_P100099 -0.47
A_51_P100155 2.9
A_51_P100174 2.86
A_51_P100181 0.28
A_51_P100218 -6.96
A_51_P100227 3.04
A_51_P100238 -6.92
A_51_P100246 2.54
A_51_P100289 3.45
A_51_P100298 -1.63
A_51_P100309 -6.51
A_51_P100327 0.19
A_51_P100347 -5.15
A_51_P100379 -4.1
A_51_P100428 -6.7

Total number of rows: 41174

Table truncated, full table size 748 Kbytes.

Supplementary file Size Download File type/resource
GSM1899427_US83000164_251486817293_S01_GE1_105_Dec08_1_3.txt.gz 9.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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