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Sample GSM4695878 Query DataSets for GSM4695878
Status Public on May 05, 2021
Title miRNA_LPS Replicate Replicate 3
Sample type RNA
 
Source name Murine bone marrow derived macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: bone marrow derived macrophages
treatment: LPS prime
Treatment protocol On DIV6, cells were treated with 33 ng/mL ultrapure LPS for 3 hours prior to the addition of either TMT OH (1.25M), TET Br (10M), or sterile saline for 6 hours.
Growth protocol C57BL6 mice (6-12-weeks-old) were euthanized under CO2, the femur excised, bone marrow extruded, and primary BMDMs cultured. Isolated cells were plated 1,000,000 cells/well/12-well plate in 3 mL DMEM supplemented with 10% FBS, 100 U/mL penicillin/streptomycin, and 10% L929 conditioned-media. On days-in-vitro (DIV)4, cells underwent a half-media change. On DIV5, media was changed to DMEM without L929 conditioned medium. Cells were used in experiments on DIV6.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from BMDMs using TRIzol® (Invitrogen). Resuspended pellets were treated with 2.5L DNase I and 10L Buffer RDD for 10 min at RT followed by column separation (RNeasy mini prep, Qiagen).
Label biotin
Label protocol miRNA analysis was conducted on 3 biological replicates using Affymetrix GeneChipTM Version 4 miRNA arrays (Affymerix, Santa Clara, CA) following the Affymetrix hybridization protocols. Affymetrix FlashTagTMBiotin HSR labeling was used to label 110 ng of total RNA according to the manufacturer’s protocol.
 
Hybridization protocol Each labeled sample was hybridized for 16 hours at 48°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol (Affymetrix, Santa Clara, CA).
Scan protocol Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using Transcriptome Analysis Console 4.0 Software.
Description miRNA Expression Profile
Data processing The raw microRNA data were pre-processing and normalized using Affymetrix Expression Console (Build 1.4.1.46, Thermo Fisher Affymetrix, Santa Clara, CA). Only mouse microRNAs were retained for the downstream analysis.
 
Submission date Jul 26, 2020
Last update date May 05, 2021
Contact name Jian-Liang Li
Organization name NIEHS
Street address 111 TW Alexander Dr
City Durham
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL19117
Series (2)
GSE155127 microRNA Expression Changes in Organotin-Driven NLRP3 Inflammasome Activation in Murine Bone Marrow Derived Macrophages
GSE155128 mRNA Expression and microRNA Expression Changes in Organotin-Driven NLRP3 Inflammasome Activation in Murine Bone Marrow Derived Macrophages

Data table header descriptions
ID_REF
VALUE Log2 normalized expression signal

Data table
ID_REF VALUE
MIMAT0000121_st 1.646362
MIMAT0004519_st 1.166118
MIMAT0000122_st 5.617889
MIMAT0004520_st 0.9553322
MIMAT0016979_st 1.28327
MIMAT0000123_st 0.9106787
MIMAT0000124_st 6.198108
MIMAT0004521_st 1.072649
MIMAT0016980_st 1.919809
MIMAT0000125_st 9.924537
MIMAT0004522_st 1.060624
MIMAT0000126_st 3.440691
MIMAT0004523_st 1.164622
MIMAT0000127_st 1.047789
MIMAT0000128_st 1.029168
MIMAT0000129_st 0.8374985
MIMAT0000130_st 1.579821
MIMAT0004524_st 0.8878545
MIMAT0000131_st 1.868929
MIMAT0016981_st 0.7223907

Total number of rows: 3163

Table truncated, full table size 74 Kbytes.




Supplementary file Size Download File type/resource
GSM4695878_P1143_LPS_3.CEL.gz 698.8 Kb (ftp)(http) CEL
Processed data included within Sample table

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