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Sample GSM1551895 Query DataSets for GSM1551895
Status Public on Jul 25, 2016
Title MEF_Lats2KO_#121_rep1_dyeswap
Sample type RNA
 
Channel 1
Source name Embryonic fibroblast cells derived from LAT2+/+ C57BL/6J mice
Organism Mus musculus
Characteristics strain: C57BL/6J
cell type: embryonic fibroblasts
genotype: Lats2+/+
clone name: #121-C
Treatment protocol no treatment
Growth protocol Mouse embyonic fibroblasts (MEFs) were cultured in DMEM + 10% inactivated fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.
Extracted molecule total RNA
Extraction protocol Cultured cells were lysed by QIAzol Lysis Reagent (Qiagen), then total RNA was extracted from aqueous phase of QIAzol homogenate with RNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).
Label cy5
Label protocol 500 ng of total RNA was labeled using Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).
 
Channel 2
Source name Embryonic fibroblast cells derived from LAT2-/- C57BL/6J mice
Organism Mus musculus
Characteristics strain: C57BL/6J
cell type: embryonic fibroblasts
genotype: Lats2-/-
clone name: #121-E
Treatment protocol no treatment
Growth protocol Mouse embyonic fibroblasts (MEFs) were cultured in DMEM + 10% inactivated fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.
Extracted molecule total RNA
Extraction protocol Cultured cells were lysed by QIAzol Lysis Reagent (Qiagen), then total RNA was extracted from aqueous phase of QIAzol homogenate with RNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).
Label cy3
Label protocol 500 ng of total RNA was labeled using Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).
 
 
Hybridization protocol Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).
Scan protocol The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Description MEF_Lats2KO_#121_rep1_dyeswap
Data processing Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .
 
Submission date Nov 21, 2014
Last update date Jul 25, 2016
Contact name Daisuke Okuzaki
E-mail(s) dokuzaki@biken.osaka-u.ac.jp
Phone +81-6-6879-4935
Organization name Osaka univ.
Department Immunology Frontier Research Center
Lab Human Immunology (Single Cell Genomics)
Street address Yamadaoka 3-1
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
 
Platform ID GPL4134
Series (2)
GSE63536 Transcriptome profiling of Lats2 deficient mouse embryonic fibroblasts
GSE63538 LATS2 regulates repressive epigenetic integrity via regulation of Polycomb repressive complex 2

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (KO/WT) representing test/reference

Data table
ID_REF VALUE
1 3.28E-02
2 1.40E-01
3 0.00E+00
4 7.74E-02
5 -1.04E-01
6 0.00E+00
7 0.00E+00
8 0.00E+00
9 0.00E+00
10 0.00E+00
11 0.00E+00
12 5.36E-01
13 -4.24E-01
14 3.37E-01
15 -1.83E-01
16 1.37E+00
18 0.00E+00
19 -4.23E-01
20 2.40E-01
21 2.44E-01

Total number of rows: 45018

Table truncated, full table size 667 Kbytes.




Supplementary file Size Download File type/resource
GSM1551895_Lats2_KO_121-E_Cy3_vs_Lats2_WT_121-C_Cy5.txt.gz 14.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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