Search results for the GEO ID: GSE23630  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM579381 | GPL570 |
|
Control explants without any treatment, biological rep1
|
human colonic intestinal explants cultured without any treament
|
tissue: colonic intestinal mucosa
|
Gene expression data from colonic intestinal explants cultured without any stimulation
|
| Sample_geo_accession | GSM579381
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579381/suppl/GSM579381.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579382 | GPL570 |
|
Control explants without any treatment, biological rep2
|
human colonic intestinal explants cultured without any treament
|
tissue: colonic intestinal mucosa
|
Gene expression data from colonic intestinal explants cultured without any stimulation
|
| Sample_geo_accession | GSM579382
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579382/suppl/GSM579382.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579383 | GPL570 |
|
Control explants without any treatment, biological rep3
|
human colonic intestinal explants cultured without any treament
|
tissue: colonic intestinal mucosa
|
Gene expression data from colonic intestinal explants cultured without any stimulation
|
| Sample_geo_accession | GSM579383
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579383/suppl/GSM579383.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579384 | GPL570 |
|
Directly frozen tissue, biological rep1
|
human colonic intestinal tissue, immediately frozen after extirpation
|
tissue: colonic intestinal mucosa
|
Gene expression data from directly frozen colonic intestinal tissue after extirpation
|
| Sample_geo_accession | GSM579384
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579384/suppl/GSM579384.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579385 | GPL570 |
|
Directly frozen tissue, biological rep2
|
human colonic intestinal tissue, immediately frozen after extirpation
|
tissue: colonic intestinal mucosa
|
Gene expression data from directly frozen colonic intestinal tissue after extirpation
|
| Sample_geo_accession | GSM579385
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579385/suppl/GSM579385.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579386 | GPL570 |
|
Directly frozen tissue, biological rep3
|
human colonic intestinal tissue, immediately frozen after extirpation
|
tissue: colonic intestinal mucosa
|
Gene expression data from directly frozen colonic intestinal tissue after extirpation
|
| Sample_geo_accession | GSM579386
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579386/suppl/GSM579386.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579387 | GPL570 |
|
explants treated sucessively with PMA/IO and BL23, biological rep1
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with BL23 for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent BL23 incubation
|
| Sample_geo_accession | GSM579387
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579387/suppl/GSM579387.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579388 | GPL570 |
|
explants treated sucessively with PMA/IO and BL23, biological rep2
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with BL23 for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent BL23 incubation
|
| Sample_geo_accession | GSM579388
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579388/suppl/GSM579388.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579389 | GPL570 |
|
explants treated sucessively with PMA/IO and BL23, biological rep3
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with BL23 for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent BL23 incubation
|
| Sample_geo_accession | GSM579389
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579389/suppl/GSM579389.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579390 | GPL570 |
|
explants treated sucessively with PMA/IO and LP299v, biological rep1
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with LP299v for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent LP299v incubation
|
| Sample_geo_accession | GSM579390
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579390/suppl/GSM579390.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579391 | GPL570 |
|
explants treated sucessively with PMA/IO and LP299v, biological rep2
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with LP299v for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent LP299v incubation
|
| Sample_geo_accession | GSM579391
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579391/suppl/GSM579391.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579392 | GPL570 |
|
explants treated sucessively with PMA/IO and LP299v, biological rep3
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with LP299v for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent LP299v incubation
|
| Sample_geo_accession | GSM579392
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579392/suppl/GSM579392.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579393 | GPL570 |
|
explants treated sucessively with PMA/IO and LP299v (A-), biological rep1
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with LP299v (A-) for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent LP299v (A-)incubation
|
| Sample_geo_accession | GSM579393
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579393/suppl/GSM579393.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579394 | GPL570 |
|
explants treated sucessively with PMA/IO and LP299v (A-), biological rep2
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with LP299v (A-) for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent LP299v (A-)incubation
|
| Sample_geo_accession | GSM579394
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579394/suppl/GSM579394.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579395 | GPL570 |
|
explants treated sucessively with PMA/IO and LP299v (A-), biological rep3
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with LP299v (A-) for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent LP299v (A-)incubation
|
| Sample_geo_accession | GSM579395
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579395/suppl/GSM579395.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579396 | GPL570 |
|
explants treated with PMA/IO biolocial rep1
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with culture medium for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent control medium incubation
|
| Sample_geo_accession | GSM579396
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579396/suppl/GSM579396.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
| | |
|
GSM579397 | GPL570 |
|
explants treated with PMA/IO biolocial rep2
|
human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with culture medium for 4 hours
|
tissue: colonic intestinal mucosa
|
Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent control medium incubation
|
| Sample_geo_accession | GSM579397
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579397/suppl/GSM579397.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
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GSM579398 | GPL570 |
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explants treated with PMA/IO biolocial rep3
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human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with culture medium for 4 hours
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tissue: colonic intestinal mucosa
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Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent control medium incubation
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| Sample_geo_accession | GSM579398
| | Sample_status | Public on Jun 20 2012
| | Sample_submission_date | Aug 13 2010
| | Sample_last_update_date | Jun 20 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.
| | Sample_growth_protocol_ch1 | human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.
| | Sample_hyb_protocol | Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.
| | Sample_data_processing | Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gaspar,,Perez Martinez
| | Sample_contact_email | gaspar.perez@iata.csic.es
| | Sample_contact_laboratory | Laboratory of Lactic Acid Bacteria and Probiotics
| | Sample_contact_department | Food Biotechnology
| | Sample_contact_institute | Institute of Agrochemistry and Food Technology (CSIC)
| | Sample_contact_address | P.O. Box 73
| | Sample_contact_city | Burjassot (Valencia)
| | Sample_contact_state | Valencia
| | Sample_contact_zip/postal_code | 46100
| | Sample_contact_country | Spain
| | Sample_contact_web_link | www.iata.csic.es
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM579nnn/GSM579398/suppl/GSM579398.CEL.gz
| | Sample_series_id | GSE23630
| | Sample_data_row_count | 54613
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