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Sample GSM1528425 Query DataSets for GSM1528425
Status Public on Sep 08, 2015
Title MettL4 KO_vs_SCR Ctl 3
Sample type RNA
 
Channel 1
Source name mESC transfected with siRNA for Mett14
Organism Mus musculus
Characteristics genotype/variation: Mettl14 knockout (M14)
strain: J1
Treatment protocol ES cells J1 were seeded 2×105 per well in 6-well plate and transfected with siRNAs by lipofectamine RNAiMAX (Invitrogen) following manufacturer’s protocol. After 48 hours cells were reseeded and transfected with siRNA again. After another 48 hours cells were collected for analysis. Target sequences of siRNA: Mettl14, CCGGATGTACAGAGGAAAT, GGGAACTCATCAGACTAAA, GCACCTCGGTCATTTATAT Scramble
Growth protocol Mouse ES cells were maintained on feeder layers of irradiated mouse embryonic fibroblasts (MEFs) in DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM L-glutamine, 0.1 mM non-essential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma) and 500 units/ml leukemia inhibiting factor (LIF, Chemicon). Lentiviral constructs including shRNA were purchased from Sigma. To produce lentivirus, lentiviral constructs and packaging constructs were transfected into 293ft cells by calcium phosphate reagent (Clontech). About 36 hours after transfection, viral supernatants were collected and supplemented with 6 μg/μl polybrene (Millipore). ES cells were incubated with virus-containing medium for 12 h. 3 days after infection, 2 μg/ml puromycin (Sigma) were added to medium for stable cell lines selection.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen). RNA was treated with RNAse free DNAse I (Roche) to deplete DNA contamination. PolyA RNA was purified using GenElute™ mRNA Miniprep Kit (Sigma Aldrich) per manufacturer’s instruction.
Label Cy5
Label protocol RNA was labeled using Cy5 or Cy3 subject to two-channel Agilent microarray protocol
 
Channel 2
Source name mESC treated with scrambled control
Organism Mus musculus
Characteristics genotype/variation: Wild type
strain: J1
Treatment protocol ES cells J1 were seeded 2×105 per well in 6-well plate and transfected with siRNAs by lipofectamine RNAiMAX (Invitrogen) following manufacturer’s protocol. After 48 hours cells were reseeded and transfected with siRNA again. After another 48 hours cells were collected for analysis. Target sequences of siRNA: Mettl14, CCGGATGTACAGAGGAAAT, GGGAACTCATCAGACTAAA, GCACCTCGGTCATTTATAT Scramble
Growth protocol Mouse ES cells were maintained on feeder layers of irradiated mouse embryonic fibroblasts (MEFs) in DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM L-glutamine, 0.1 mM non-essential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma) and 500 units/ml leukemia inhibiting factor (LIF, Chemicon). Lentiviral constructs including shRNA were purchased from Sigma. To produce lentivirus, lentiviral constructs and packaging constructs were transfected into 293ft cells by calcium phosphate reagent (Clontech). About 36 hours after transfection, viral supernatants were collected and supplemented with 6 μg/μl polybrene (Millipore). ES cells were incubated with virus-containing medium for 12 h. 3 days after infection, 2 μg/ml puromycin (Sigma) were added to medium for stable cell lines selection.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen). RNA was treated with RNAse free DNAse I (Roche) to deplete DNA contamination. PolyA RNA was purified using GenElute™ mRNA Miniprep Kit (Sigma Aldrich) per manufacturer’s instruction.
Label Cy3
Label protocol RNA was labeled using Cy5 or Cy3 subject to two-channel Agilent microarray protocol
 
 
Hybridization protocol RNA was hybridized to Agilent arrays following manufacturers instructions
Scan protocol Arrays were scanned following manufacturers instructions
Description RNA m6a methylation data from mouse embryos stem cell treated with scrambled control or siRNA for Mettl14
Data processing Microarray files were imported and normalized using Bioconductor package limma.
 
Submission date Oct 20, 2014
Last update date Sep 08, 2015
Contact name Yue Li
E-mail(s) gorillayue@gmail.com
Organization name Massachusetts Institute of Technology
Street address 32 Vassar Street, 32-D528
City Cambridge
State/province Massachusetts
ZIP/Postal code 02139
Country USA
 
Platform ID GPL19318
Series (1)
GSE62530 Genome-wide identification of N6-methyladenosine by microarray

Data table header descriptions
ID_REF
VALUE log2 Cy5/Cy3 signal

Data table
ID_REF VALUE
1 0.231547913
2
3 1.122293418
4 -1.183757216
5 -0.220540873
6 0.496651862
7 -0.530094705
8 -0.236925324
9 -0.377932458
10 -0.366946183
11 0.74720391
12 -0.539903479
13 -0.43384872
14 0.61375523
15 -0.449528579
16 -0.696200178
17 -0.546085835
18 0.186132754
19 -0.383681208
20 -0.592705316

Total number of rows: 954073

Table truncated, full table size 16692 Kbytes.




Supplementary file Size Download File type/resource
GSM1528425_SG13145006_256415210003_S001_GE2_107_Sep09.txt.gz 256.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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