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Sample GSM7043133 Query DataSets for GSM7043133
Status Public on Apr 12, 2024
Title THP-1 conditioned with LrS for 48hrs Replicate 2
Sample type RNA
 
Channel 1
Source name THP-1 with LrS for 48hrs Rep2
Organism Homo sapiens
Characteristics cell line: THP-1 (ATCC #TIB-202)
tissue: Peripheral Blood Monocyte
Treatment protocol THP-1 cells were incubated for 24-, 48-, or 72-hrs with either the Lacticaseibacillus rhamnosus R0011 secretome (LrS) (20% v/v) or a matched L-lactic acid control (LA). For some experiments, THP-1 cells were challenged with LPS (125ng/mL) alone for 6 hours or after 72-hrs of conditioning with the LrS.
Growth protocol The THP-1 human peripheral blood monocyte cell line (ATCC #TIB-202) was maintained in an undifferentiated state using RPMI-1640 medium supplemented with 0.05 mM β-mercaptoethanol, 10% calf serum and 0.05 mg/mL gentamicin and cultured in a humidified incubator at 37oC and 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by using TRIzol Reagent (ThermoFisher Scientific, MA, USA) following manufacturer's protocol with PhaseLock tubes (5 Prime, MD). Total extracted RNA was then purified using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). The purity and quality of RNA was determined using both the ND100 NanoDrop and an Agilent 2000 Bioanalyzer, respectively. Only samples with an RNA Integrity Number (RIN) greater than 9.0 were used for microarray analysis.
Label Cy5
Label protocol Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript IV (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).
 
Channel 2
Source name THP-1 48hr Control Rep2
Organism Homo sapiens
Characteristics cell line: THP-1 (ATCC #TIB-202)
tissue: Peripheral Blood Monocyte
Treatment protocol THP-1 cells were incubated for 24-, 48-, or 72-hrs with either the Lacticaseibacillus rhamnosus R0011 secretome (LrS) (20% v/v) or a matched L-lactic acid control (LA). For some experiments, THP-1 cells were challenged with LPS (125ng/mL) alone for 6 hours or after 72-hrs of conditioning with the LrS.
Growth protocol The THP-1 human peripheral blood monocyte cell line (ATCC #TIB-202) was maintained in an undifferentiated state using RPMI-1640 medium supplemented with 0.05 mM β-mercaptoethanol, 10% calf serum and 0.05 mg/mL gentamicin and cultured in a humidified incubator at 37oC and 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by using TRIzol Reagent (ThermoFisher Scientific, MA, USA) following manufacturer's protocol with PhaseLock tubes (5 Prime, MD). Total extracted RNA was then purified using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). The purity and quality of RNA was determined using both the ND100 NanoDrop and an Agilent 2000 Bioanalyzer, respectively. Only samples with an RNA Integrity Number (RIN) greater than 9.0 were used for microarray analysis.
Label Cy3
Label protocol Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript IV (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).
 
 
Hybridization protocol Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50C for 18h on the Agilent whole human gene expression microarray (GE 4x44K; GPL10332).
Scan protocol Each array was scanned with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with ImaGene® microarray analysis software.
Description Biological Replicate 2 of 4
Data processing Global LOWESS normalization was conducted with ImaGene® microarray analysis software.
 
Submission date Feb 14, 2023
Last update date Apr 12, 2024
Contact name Michael P Jeffrey
E-mail(s) michael.jeffrey@uoit.ca
Organization name Ontario Tech University
Department Faculty of Science
Street address 2000 Simcoe St N
City Oshawa
State/province Ontario
ZIP/Postal code L1G 0C5
Country Canada
 
Platform ID GPL10332
Series (1)
GSE225273 Transcriptional profiling of THP-1 monocytes conditioned with Lacticaseibacilli rhamnosus R0011 secretome

Data table header descriptions
ID_REF
VALUE LOWESS normalized log2 ratio (treatment/reference)

Data table
ID_REF VALUE
45220 null
45050 null
44880 0.6222
44710 0.2588
44540 -0.6649
44370 0.552
44200 -0.4571
44030 null
43860 -1.2534
43690 null
43520 null
43350 null
43180 null
43010 -0.6769
42840 null
42670 -0.1491
42500 -0.0299
42330 null
42160 null
41990 null

Total number of rows: 45220

Table truncated, full table size 548 Kbytes.




Supplementary file Size Download File type/resource
GSM7043133_LrS_48hr-Rep2.txt.gz 11.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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