|
| Status |
Public on Apr 12, 2024 |
| Title |
THP-1 conditioned with LrS for 24hrs Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
THP-1 with LrS for 24hrs Rep1
|
| 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 24hr Control Rep1
|
| 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 1 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 |
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