|
| Status |
Public on May 05, 2021 |
| Title |
LPS Replicate Replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Murine bone marrow derived macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
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.
|
| 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 |
Gene expression analysis was conducted on 3 biological replicates using Affymetrix Mouse Genome 430 2.0 GeneChip® arrays (Affymetrix). Total RNA (50ng) was amplified as directed in the Nugen WT-Ovation Pico RNA Amplification System protocol and labeling with biotin following the Nugen Encore Biotin Module protocol.
|
| |
|
| Hybridization protocol |
Amplified biotin-cDNAs (5.5μg) were fragmented and hybridized for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification (GeneChip Hybridization, Wash and Stain Kit).
|
| Scan protocol |
Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using Transcriptome Analysis Console 4.0 Software.
|
| Description |
Gene expression data
|
| Data processing |
Array data were pre-processing and normalized by the affy package. The Robust Multichip Analysis (RMA) approach was applied for the normalization.
|
| |
|
| 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 |
GPL1261 |
| Series (2) |
| GSE155126 |
mRNA 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 |
|
