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Status |
Public on May 05, 2021 |
Title |
miRNA_LPS Replicate Replicate 3 |
Sample type |
RNA |
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|
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 (1.25M), TET Br (10M), or sterile saline for 6 hours.
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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 2.5L DNase I and 10L 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.
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|
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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.
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Description |
miRNA Expression Profile
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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.
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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 |
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