NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5392346 Query DataSets for GSM5392346
Status Public on Dec 29, 2021
Title BMDM_HMB+LPS_3
Sample type RNA
 
Source name BMDM
Organism Mus musculus
Characteristics cell type: macrophage
treatment: HMB+LPS
Treatment protocol To induce M1-like polarization, BMDM were treated with 10ng/ml LPS for 48 h in the presence or absence of HMB (1mM)
Growth protocol bone marrow cells were isolated from C57/bl6 mice, cells were differentiated using L929 cell conditioned media as published http://abc.org.br/IMG/pdf/doc-4272.pdf
Extracted molecule total RNA
Extraction protocol RNA was extracted using qiagen RNeasy Micro Kit, RNA quality was checked using an Agilent bioanalyzer.
Label biotin
Label protocol GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate sense-strand cDNA from total RNA. Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the kit. Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays
 
Hybridization protocol Hybridization, washing, staining and scanning of the Affymtrix peg plate was carried out using the Affymetrin GeneTitan MC Instrument.
Scan protocol Hybridization, washing, staining and scanning of the Affymtrix peg plate was carried out using the Affymetrin GeneTitan MC Instrument.
Data processing data were normalized and batch corrected using TAC4 software
 
Submission date Jun 18, 2021
Last update date Dec 29, 2021
Contact name michael francis coleman
E-mail(s) mcoleman@unc.edu
Phone 9199850347
Organization name UNC
Street address 235 dauer drive
City chapel hill
State/province North Carolina
ZIP/Postal code 27516
Country USA
 
Platform ID GPL24242
Series (2)
GSE178475 Modulation of macrophage polarization by HMB [macrophage]
GSE178478 Modulation of macrophage polarization by HMB

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 7.22238
AFFX-BkGr-GC04_st 7.52004
AFFX-BkGr-GC05_st 7.15137
AFFX-BkGr-GC06_st 6.38145
AFFX-BkGr-GC07_st 5.31907
AFFX-BkGr-GC08_st 4.27029
AFFX-BkGr-GC09_st 3.66879
AFFX-BkGr-GC10_st 3.15121
AFFX-BkGr-GC11_st 2.82627
AFFX-BkGr-GC12_st 2.58499
AFFX-BkGr-GC13_st 2.24232
AFFX-BkGr-GC14_st 2.11303
AFFX-BkGr-GC15_st 1.92271
AFFX-BkGr-GC16_st 2.03708
AFFX-BkGr-GC17_st 2.08188
AFFX-BkGr-GC18_st 2.43508
AFFX-BkGr-GC19_st 5.96352
AFFX-BkGr-GC20_st 6.23049
AFFX-BkGr-GC21_st 6.27881
AFFX-BkGr-GC22_st 6.47059

Total number of rows: 28846

Table truncated, full table size 749 Kbytes.




Supplementary file Size Download File type/resource
GSM5392346_HMB_MAC_LPS_HMB_3.CEL.gz 1.0 Mb (ftp)(http) CEL
GSM5392346_HMB_MAC_LPS_HMB_3.sst-rma-gene-full.chp.gz 207.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap