Search results for the GEO ID: GSE19855  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM463608 | GPL339 |
|
Control soft tissue 1
|
Control tissue, no infection 1
|
tissue: soft tissue overlying calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control tissue.
|
| Sample_geo_accession | GSM463608
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463608/suppl/GSM463608.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM463609 | GPL339 |
|
Control soft tissue 2
|
Control tissue, no infection 2
|
tissue: soft tissue overlying calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control tissue.
|
| Sample_geo_accession | GSM463609
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463609/suppl/GSM463609.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM463610 | GPL339 |
|
Control soft tissue 3
|
Control tissue, no infection 3
|
tissue: soft tissue overlying calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control tissue.
|
| Sample_geo_accession | GSM463610
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463610/suppl/GSM463610.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM463611 | GPL339 |
|
Control soft tissue 4
|
Control tissue, no infection 4
|
tissue: soft tissue overlying calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control tissue.
|
| Sample_geo_accession | GSM463611
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463611/suppl/GSM463611.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM463612 | GPL339 |
|
Control soft tissue 5
|
Control tissue, no infection 5
|
tissue: soft tissue overlying calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control tissue.
|
| Sample_geo_accession | GSM463612
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463612/suppl/GSM463612.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM463618 | GPL339 |
|
Control bone 1
|
Control bone, no infection 1
|
tissue: calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control bone.
|
| Sample_geo_accession | GSM463618
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463618/suppl/GSM463618.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM463619 | GPL339 |
|
Control bone 2
|
Control bone, no infection 2
|
tissue: calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control bone.
|
| Sample_geo_accession | GSM463619
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463619/suppl/GSM463619.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM463620 | GPL339 |
|
Control bone 3
|
Control bone, no infection 3
|
tissue: calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control bone.
|
| Sample_geo_accession | GSM463620
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463620/suppl/GSM463620.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM463621 | GPL339 |
|
Control bone 4
|
Control bone, no infection 4
|
tissue: calvarial bone
infection: uninfected (control)
age: 9 weeks
|
Gene expression data from control bone.
|
| Sample_geo_accession | GSM463621
| | Sample_status | Public on Feb 07 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Feb 07 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463621/suppl/GSM463621.CEL.gz
| | Sample_series_id | GSE17110
| | Sample_series_id | GSE19855
| | Sample_series_id | GSE20389
| | Sample_data_row_count | 22690
| | |
|
GSM495867 | GPL339 |
|
T. denticola tissue 1
|
T. denticola infected tissue 1
|
tissue: soft tissue overlying calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Tissue_1T
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495867
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495867/suppl/GSM495867.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495868 | GPL339 |
|
T. denticola tissue 2
|
T. denticola infected tissue 2
|
tissue: soft tissue overlying calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Tissue_2T
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495868
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495868/suppl/GSM495868.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495869 | GPL339 |
|
T. denticola tissue 3
|
T. denticola infected tissue 3
|
tissue: soft tissue overlying calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Tissue_3T
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495869
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495869/suppl/GSM495869.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495870 | GPL339 |
|
T. denticola tissue 4
|
T. denticola infected tissue 4
|
tissue: soft tissue overlying calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Tissue_4T
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495870
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495870/suppl/GSM495870.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495871 | GPL339 |
|
T. denticola tissue 5
|
T. denticola infected tissue 5
|
tissue: soft tissue overlying calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Tissue_5T
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495871
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495871/suppl/GSM495871.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495872 | GPL339 |
|
T. denticola bone 1
|
T. denticola infected bone 1
|
tissue: calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Bone_1B
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495872
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495872/suppl/GSM495872.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495873 | GPL339 |
|
T. denticola bone 2
|
T. denticola infected bone 2
|
tissue: calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Bone_2B
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495873
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495873/suppl/GSM495873.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495874 | GPL339 |
|
T. denticola bone 3
|
T. denticola infected bone 3
|
tissue: calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Bone_3B
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495874
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495874/suppl/GSM495874.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495875 | GPL339 |
|
T. denticola bone 4
|
T. denticola infected bone 4
|
tissue: calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Bone_4B
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495875
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495875/suppl/GSM495875.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
GSM495876 | GPL339 |
|
T. denticola bone 5
|
T. denticola infected bone 5
|
tissue: calvarial bone
infection: T. denticola
age: 9 weeks
|
T. denticola_Bone_5B
Gene expression data from T. denticola infected tissue.
|
| Sample_geo_accession | GSM495876
| | Sample_status | Public on Nov 16 2010
| | Sample_submission_date | Jan 12 2010
| | Sample_last_update_date | Jan 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N | 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection. The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.
| | Sample_growth_protocol_ch1 | T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
| | Sample_hyb_protocol | Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.
| | Sample_data_processing | The data was normalized using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kesavalu,Naidu,Lakshmyya
| | Sample_contact_laboratory | Oral Microbiology
| | Sample_contact_department | Periodontology
| | Sample_contact_institute | University of Florida, College of Dentistry
| | Sample_contact_address | 1600 SW Archer road, D11-24
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32608
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM495nnn/GSM495876/suppl/GSM495876.CEL.gz
| | Sample_series_id | GSE19855
| | Sample_data_row_count | 22690
| | |
|
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