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Sample GSM6735740 Query DataSets for GSM6735740
Status Public on Nov 17, 2022
Title M2 treated with Aza and TSA, biological rep 2
Sample type RNA
 
Source name M2 treated with Aza and TSA
Organism Mus musculus
Characteristics strain: Balb/c
genotype: WT
Sex: female
cell type: M2 macrophage
treatment: Aza and TSA
Treatment protocol Next, the cells were incubated with 20 ng/mL of recombinant mouse IL4 for 24–48 h to achieve M2 polarization.Then,macrophages were treated with 5-aza-dC for 24 h followed by treatment with 5-aza-dC and TSA for 48 h.
Growth protocol Bone marrow cells were isolated from tibias and femurs of Balb/c mice and cultured in DMEM supplemented with 10 ng/mL of colony-stimulating factor-1 (CSF-1; Gibco, Carlsbad, CA, USA) and 10% FBS for 7 d. The culture medium was changed every other day.
Extracted molecule total RNA
Extraction protocol RNAs for miRNA profiling were isolated using the miRNeasy® Mini Kit. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).
Label FlashTag Biotin HSR RNA label
Label protocol poly*(A) tailing and ligation were done using FlashTag Biotin HSR RNA labelling kit
 
Hybridization protocol Hybridization was done using GeneChip hybridization oven, followed by washing and staining using Genechip fluidics station.The labeled RNA was heated to 99°C for 5 minutes and then to 45°C for 5 minutes. RNA-array hybridization was performed with agitation at 60 rotations per minute for 16 hours at 48°C on an Affymetrix® 450 Fluidics Station. The chips were washed and stained using a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, California, United States).
Scan protocol The chips were then scanned with an Affymetrix GCS 3000 canner (Affymetrix, Santa Clara, California, United States).
Description miR expression in M2 macrophages after treatment with epigenetic modifiers
Data processing Signal values were computed using the Affymetrix® GeneChip™ Command Console software. Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Expression Console™ Software. Array data were filtered by probes annotated species. The comparative analysis between test sample and control sample was carried out using fold-change. For a significant DEmiRNA set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity. All Statistical test and visualization of differentially expressed genes was conducted using R statistical language v. 3.1.2
The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Expression Console™ Software. Array data were filtered by probes annotated species.The comparative analysis between test sample and control sample was carried out using fold-change. For a significant DEmiRNA set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity. All Statistical test and visualization of differentially expressed genes was conducted using R statistical language v. 3.1.2.
 
Submission date Nov 17, 2022
Last update date Nov 17, 2022
Contact name Byungheon Lee
E-mail(s) leebh@knu.ac.kr
Phone +82-10-5501-3457
Organization name Kyungpook National University
Department School of Medicine
Lab Department of Biochemistry and Cell Biology
Street address 680 Guckchaebosang-ro, Jung-gu
City Daegu
State/province Outside U.S. & Canada
ZIP/Postal code 41944
Country South Korea
 
Platform ID GPL19117
Series (1)
GSE218160 miR expression microarray analysis on M2 macrophages treated with epigenetic modifiers

Data table header descriptions
ID_REF
VALUE RMA signal
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
MIMAT0000001_st 12.7745 P
MIMAT0015091_st 1.286444 A
MIMAT0000002_st 0.6799455 A
MIMAT0015092_st 1.466494 A
MIMAT0020301_st 0.9578209 A
MIMAT0000003_st 0.8259446 A
MIMAT0020302_st 1.299201 P
MIMAT0000004_st 0.9578209 A
MIMAT0000005_st 2.639169 P
MIMAT0015093_st 1.681863 A
MIMAT0020303_st 0.9578209 A
MIMAT0000006_st 0.9578209 A
MIMAT0020304_st 0.6799455 A
MIMAT0000007_st 0.4345467 A
MIMAT0015094_st 1.681863 A
MIMAT0000008_st 0.6799455 A
MIMAT0020305_st 0.845649 A
MIMAT0000009_st 1.466494 P
MIMAT0020306_st 0.4874358 A
MIMAT0000010_st 0.9168785 A

Total number of rows: 36249

Table truncated, full table size 963 Kbytes.




Supplementary file Size Download File type/resource
GSM6735740_161012_5_M2AT_2_miRNA-4_0_.CEL.gz 733.6 Kb (ftp)(http) CEL
Processed data included within Sample table

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