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Sample GSM1528429 Query DataSets for GSM1528429
Status Public on Sep 08, 2015
Title MettL4 KO_vs_MettL4 KO 1
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 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 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 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 1.172597336
2 1.154423086
3 1.248589964
4 0.91793573
5 0.782355935
6 0.148219924
7 0.703144476
8 1.109868713
9 0.709114605
10 0.766558391
11 0.853848576
12 0.41632262
13 0.54865253
14 3.101398477
15 0.724023456
16 0.863456637
17 0.49525883
18 0.650073828
19 0.699154071
20 0.665511972

Total number of rows: 954073

Table truncated, full table size 17327 Kbytes.




Supplementary file Size Download File type/resource
GSM1528429_SG13145006_256415210007_S001_GE2_107_Sep09.txt.gz 257.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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