Search results for the GEO ID: GSE15636  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM391349 | GPL570 |
|
Medium-only control__8 h_rep1
|
Caco-2 cell line, medium-only control, 8 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 8 hrs
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391349
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391349/suppl/GSM391349.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391350 | GPL570 |
|
Medium-only control__8 h_rep2
|
Caco-2 cell line, medium-only control, 8 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 8 hrs
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391350
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391350/suppl/GSM391350.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391351 | GPL570 |
|
L. acidophilus NCFM™_coculture_8 h_rep1
|
Caco-2 cell line, cocultured with L. acidophilus NCFM™, 8 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 8 hrs
probiotic: Lactobacillus acidophilus NCFM™
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391351
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391351/suppl/GSM391351.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391352 | GPL570 |
|
L. acidophilus NCFM™_coculture_8 h_rep2
|
Caco-2 cell line, cocultured with L. acidophilus NCFM™, 8 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 8 hrs
probiotic: Lactobacillus acidophilus NCFM™
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391352
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391352/suppl/GSM391352.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391353 | GPL570 |
|
L. acidophilus NCFM™_cell-free supernatant_24 h_rep1
|
Caco-2 cell line, treated with L. acidophilus NCFM™ cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
probiotic: Lactobacillus acidophilus NCFM™
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391353
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391353/suppl/GSM391353.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391354 | GPL570 |
|
L. acidophilus NCFM™_cell-free supernatant_24 h_rep2
|
Caco-2 cell line, treated with L. acidophilus NCFM™ cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
probiotic: Lactobacillus acidophilus NCFM™
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391354
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391354/suppl/GSM391354.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391355 | GPL570 |
|
B. lactis 420_coculture_8 h_rep1
|
Caco-2 cell line, cocultured with B. lactis 420, 8 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 8 hrs
probiotic: Bifidobacterium lactis 420
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391355
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391355/suppl/GSM391355.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391356 | GPL570 |
|
B. lactis 420_coculture_8 h_rep2
|
Caco-2 cell line, cocultured with B. lactis 420, 8 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 8 hrs
probiotic: Bifidobacterium lactis 420
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391356
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391356/suppl/GSM391356.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391357 | GPL570 |
|
B. lactis 420_cell-free supernatant_24 h_rep1
|
Caco-2 cell line, treated with B. lactis 420 cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
probiotic: Bifidobacterium lactis 420
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391357
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391357/suppl/GSM391357.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391358 | GPL570 |
|
B. lactis 420_cell-free supernatant_24 h_rep2
|
Caco-2 cell line, treated with B. lactis 420 cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
probiotic: Bifidobacterium lactis 420
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391358
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391358/suppl/GSM391358.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391359 | GPL570 |
|
L. salivarius Ls-33_coculture_8 h_rep1
|
Caco-2 cell line, cocultured with L. salivarius Ls-33, 8 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 8 hrs
probiotic: Lactobacillus salivarius Ls-33
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391359
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391359/suppl/GSM391359.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391360 | GPL570 |
|
L. salivarius Ls-33_coculture_8 h_rep2
|
Caco-2 cell line, cocultured with L. salivarius Ls-33, 8 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 8 hrs
probiotic: Lactobacillus salivarius Ls-33
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391360
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391360/suppl/GSM391360.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391361 | GPL570 |
|
L. salivarius Ls-33_cell-free supernatant_24 h_rep1
|
Caco-2 cell line, treated with L. salivarius Ls-33 cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
probiotic: Lactobacillus salivarius Ls-33
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391361
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391361/suppl/GSM391361.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391362 | GPL570 |
|
L. salivarius Ls-33_cell-free supernatant_24 h_rep2
|
Caco-2 cell line, treated with L. salivarius Ls-33 cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
probiotic: Lactobacillus salivarius Ls-33
|
5 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391362
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391362/suppl/GSM391362.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391363 | GPL570 |
|
Medium-only control__24 h_rep1
|
Caco-2 cell line, medium-only control, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
|
1 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391363
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391363/suppl/GSM391363.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391364 | GPL570 |
|
Medium-only control__24 h_rep2
|
Caco-2 cell line, medium-only control, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
|
1 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391364
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391364/suppl/GSM391364.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391365 | GPL570 |
|
Medium-only control__24 h_rep3
|
Caco-2 cell line, medium-only control, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
|
1 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391365
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391365/suppl/GSM391365.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391366 | GPL570 |
|
E. coli O157:H7_cell-free supernatant_24 h_samle 1
|
Caco-2 cell line, treated with E. coli O157:H7 cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
pathogen: E. coli O157:H7
|
1 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391366
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391366/suppl/GSM391366.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391367 | GPL570 |
|
E. coli O157:H7_cell-free supernatant_24 h_sample 2
|
Caco-2 cell line, treated with E. coli O157:H7 cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
pathogen: E. coli O157:H7
|
1 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391367
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391367/suppl/GSM391367.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
|
GSM391368 | GPL570 |
|
E. coli O157:H7_cell-free supernatant_24 h_sample 3
|
Caco-2 cell line, treated with E. coli O157:H7 cell-free supernatant, 24 h
|
intestinal epithelial cells: differentiated Caco-2
treatment time: 24 hrs
pathogen: E. coli O157:H7
|
1 µg total RNA was used as starting material for sample preparation
|
| Sample_geo_accession | GSM391368
| | Sample_status | Public on Apr 11 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.
| | Sample_growth_protocol_ch1 = Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 | 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanning protocol
| | Sample_data_processing | Raw data was processed with R/Bioconductor and normalised with CG-RMA
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ilana,,Saarikko
| | Sample_contact_institute | Genolyze Ltd
| | Sample_contact_address | Linnankatu 55
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | 20100
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391368/suppl/GSM391368.CEL.gz
| | Sample_series_id | GSE15636
| | Sample_data_row_count | 54675
| | |
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