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Sample GSM4695870 Query DataSets for GSM4695870
Status Public on May 05, 2021
Title LPS+TMT 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+TMT
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 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

Data table header descriptions
ID_REF
VALUE Log2 normalized RMA expression signal

Data table
ID_REF VALUE
1415670_at 10.95055855
1415671_at 11.3126078
1415672_at 11.67091754
1415673_at 7.882273707
1415674_a_at 10.5030675
1415675_at 9.915652622
1415676_a_at 11.67229838
1415677_at 9.173301809
1415678_at 10.78527258
1415679_at 10.66908835
1415680_at 9.71651087
1415681_at 10.68261854
1415682_at 7.920403245
1415683_at 12.4920377
1415684_at 7.871371666
1415685_at 9.026812158
1415686_at 10.92489388
1415687_a_at 11.73706579
1415688_at 10.19187679
1415689_s_at 8.380770193

Total number of rows: 45037

Table truncated, full table size 1024 Kbytes.




Supplementary file Size Download File type/resource
GSM4695870_P1179_LPS-TMT_1.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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