Search results for the GEO ID: GSE25330  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM623365 | GPL570 |
|
C2M control, biological rep 1
|
C2-M cell control
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: control
|
Gene expression data from C2M control cells
|
| Sample_geo_accession | GSM623365
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623365/suppl/GSM623365_C2Ma.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623365/suppl/GSM623365_C2Ma.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623366 | GPL570 |
|
C2M control, biological rep 2
|
C2-M cell control
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: control
|
Gene expression data from C2M control cells
|
| Sample_geo_accession | GSM623366
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623366/suppl/GSM623366_C2Mb.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623366/suppl/GSM623366_C2Mb.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623367 | GPL570 |
|
C2M control, biological rep 3
|
C2-M cell control
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: control
|
Gene expression data from C2M control cells
|
| Sample_geo_accession | GSM623367
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623367/suppl/GSM623367_C2Mc.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623367/suppl/GSM623367_C2Mc.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623368 | GPL570 |
|
C2M plus Lactobacillus salivarius, biological rep 1
|
C2-M plus Lactobacillus salivarius 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Lactobacillus salviarius
|
Gene expression data from C2M plus Lactobacillus salviarius
|
| Sample_geo_accession | GSM623368
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623368/suppl/GSM623368_C2M_Lab_a.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623368/suppl/GSM623368_C2M_Lab_a.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623369 | GPL570 |
|
C2M plus Lactobacillus salivarius, biological rep 2
|
C2-M plus Lactobacillus salivarius 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Lactobacillus salviarius
|
Gene expression data from C2M plus Lactobacillus salviarius
|
| Sample_geo_accession | GSM623369
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623369/suppl/GSM623369_C2M_Lab_b.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623369/suppl/GSM623369_C2M_Lab_b.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623370 | GPL570 |
|
C2M plus Lactobacillus salivarius, biological rep 3
|
C2-M plus Lactobacillus salivarius 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Lactobacillus salviarius
|
Gene expression data from C2M plus Lactobacillus salviarius
|
| Sample_geo_accession | GSM623370
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623370/suppl/GSM623370_C2M_Lab_c.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623370/suppl/GSM623370_C2M_Lab_c.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623371 | GPL570 |
|
C2M plus Escherichia coli, biological rep 1
|
C2-M plus Escherichia coli 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Escherichia coli
|
Gene expression data from C2M plus Escherichia coli
|
| Sample_geo_accession | GSM623371
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623371/suppl/GSM623371_C2M_Ecoli_a.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623371/suppl/GSM623371_C2M_Ecoli_a.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623372 | GPL570 |
|
C2M plus Escherichia coli, biological rep 2
|
C2-M plus Escherichia coli 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Escherichia coli
|
Gene expression data from C2M plus Escherichia coli
|
| Sample_geo_accession | GSM623372
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623372/suppl/GSM623372_C2M_Ecoli_b.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623372/suppl/GSM623372_C2M_Ecoli_b.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623373 | GPL570 |
|
C2M plus Escherichia coli, biological rep 3
|
C2-M plus Escherichia coli 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Escherichia coli
|
Gene expression data from C2M plus Escherichia coli
|
| Sample_geo_accession | GSM623373
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623373/suppl/GSM623373_C2M_Ecoli_c.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623373/suppl/GSM623373_C2M_Ecoli_c.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623374 | GPL570 |
|
C2M plus Bacteroides fragilis, biological rep 1
|
C2-M plus Bacteroides fragilis 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Bacteroides fragilis
|
Gene expression data from C2M plus Bacteroides fragilis
|
| Sample_geo_accession | GSM623374
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623374/suppl/GSM623374_C2M_Bfrag_a.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623374/suppl/GSM623374_C2M_Bfrag_a.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623375 | GPL570 |
|
C2M plus Bacteroides fragilis, biological rep 2
|
C2-M plus Bacteroides fragilis 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Bacteroides fragilis
|
Gene expression data from C2M plus Bacteroides fragilis
|
| Sample_geo_accession | GSM623375
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623375/suppl/GSM623375_C2M_Bfrag_b.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623375/suppl/GSM623375_C2M_Bfrag_b.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623376 | GPL570 |
|
C2M plus Bacteroides fragilis, biological rep 3
|
C2-M plus Bacteroides fragilis 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: Bacteroides fragilis
|
Gene expression data from C2M plus Bacteroides fragilis
|
| Sample_geo_accession | GSM623376
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623376/suppl/GSM623376_C2M_Bfrag_c.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623376/suppl/GSM623376_C2M_Bfrag_c.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623377 | GPL570 |
|
C2M plus polystyrene beads, biological rep 1
|
C2-M plus polystyrene beads 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: polystyrene beads
|
Gene expression data from C2M plus polystyrene beads
|
| Sample_geo_accession | GSM623377
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623377/suppl/GSM623377_C2M_Beads_a.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623377/suppl/GSM623377_C2M_Beads_a.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623378 | GPL570 |
|
C2M plus polystyrene beads, biological rep 2
|
C2-M plus polystyrene beads 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: polystyrene beads
|
Gene expression data from C2M plus polystyrene beads
|
| Sample_geo_accession | GSM623378
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623378/suppl/GSM623378_C2M_Beads_b.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623378/suppl/GSM623378_C2M_Beads_b.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
|
GSM623379 | GPL570 |
|
C2M plus polystyrene beads, biological rep 3
|
C2-M plus polystyrene beads 2 hours
|
cell type: C2-M cell
cell line source: C2BBe1
treatment: polystyrene beads
|
Gene expression data from C2M plus polystyrene beads
|
| Sample_geo_accession | GSM623379
| | Sample_status | Public on Jan 01 2011
| | Sample_submission_date | Nov 15 2010
| | Sample_last_update_date | Jan 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | C2M cells were co-incubated with bacteria or beads for 2 hours
| | Sample_growth_protocol_ch1 | C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)
| | Sample_hyb_protocol | Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_data_processing | The data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,Andrew,Mac Sharry
| | Sample_contact_email | j.macsharry@ucc.ie
| | Sample_contact_laboratory | Room 5.27/4.39
| | Sample_contact_department | APC, Biosciences Instiute
| | Sample_contact_institute | UCC
| | Sample_contact_address | College Road
| | Sample_contact_city | Cork
| | Sample_contact_state | Cork
| | Sample_contact_zip/postal_code | Cork1
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623379/suppl/GSM623379_C2M_Beads_c.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM623nnn/GSM623379/suppl/GSM623379_C2M_Beads_c.mas5.CHP.gz
| | Sample_series_id | GSE25330
| | Sample_data_row_count | 54675
| | |
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