Search results for the GEO ID: GSE20266  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM507949 | GPL570 |
|
Breast cancer saliva-1
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122146-122124.CEL
|
| Sample_geo_accession | GSM507949
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507949/suppl/GSM507949.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507950 | GPL570 |
|
Breast cancer saliva-2
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122147-122125.CEL
|
| Sample_geo_accession | GSM507950
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507950/suppl/GSM507950.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507951 | GPL570 |
|
Breast cancer saliva-3
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122148-122126.CEL
|
| Sample_geo_accession | GSM507951
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507951/suppl/GSM507951.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507952 | GPL570 |
|
Breast cancer saliva-4
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122149-122127.CEL
|
| Sample_geo_accession | GSM507952
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507952/suppl/GSM507952.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507953 | GPL570 |
|
Breast cancer saliva-5
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122150-122128.CEL
|
| Sample_geo_accession | GSM507953
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507953/suppl/GSM507953.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507954 | GPL570 |
|
Breast cancer saliva-6
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122151-122129.CEL
|
| Sample_geo_accession | GSM507954
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507954/suppl/GSM507954.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507955 | GPL570 |
|
Breast cancer saliva-7
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122152-122130.CEL
|
| Sample_geo_accession | GSM507955
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507955/suppl/GSM507955.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507956 | GPL570 |
|
Breast cancer saliva-8
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122153-122131.CEL
|
| Sample_geo_accession | GSM507956
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507956/suppl/GSM507956.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507957 | GPL570 |
|
Breast cancer saliva-9
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122154-122132.CEL
|
| Sample_geo_accession | GSM507957
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507957/suppl/GSM507957.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507958 | GPL570 |
|
Breast cancer saliva-10
|
saliva
|
biomaterial source: saliva
disease status: Breast Cancer
|
122155-122133.CEL
|
| Sample_geo_accession | GSM507958
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507958/suppl/GSM507958.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507959 | GPL570 |
|
Healthy control saliva-bc1
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122158-122136.CEL
|
| Sample_geo_accession | GSM507959
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507959/suppl/GSM507959.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507960 | GPL570 |
|
Healthy control saliva-bc2
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122159-122137.CEL
|
| Sample_geo_accession | GSM507960
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507960/suppl/GSM507960.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507961 | GPL570 |
|
Healthy control saliva-bc3
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122160-122138.CEL
|
| Sample_geo_accession | GSM507961
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507961/suppl/GSM507961.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507962 | GPL570 |
|
Healthy control saliva-bc4
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122161-122139.CEL
|
| Sample_geo_accession | GSM507962
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507962/suppl/GSM507962.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507963 | GPL570 |
|
Healthy control saliva-bc5
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122162-122140.CEL
|
| Sample_geo_accession | GSM507963
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507963/suppl/GSM507963.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507964 | GPL570 |
|
Healthy control saliva-bc6
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122163-122141.CEL
|
| Sample_geo_accession | GSM507964
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507964/suppl/GSM507964.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507965 | GPL570 |
|
Healthy control saliva-bc7
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122164-122142.CEL
|
| Sample_geo_accession | GSM507965
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507965/suppl/GSM507965.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507966 | GPL570 |
|
Healthy control saliva-bc8
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122165-122143.CEL
|
| Sample_geo_accession | GSM507966
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507966/suppl/GSM507966.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
| | |
|
GSM507967 | GPL570 |
|
Healthy control saliva-bc9
|
saliva
|
biomaterial source: saliva
disease status: Healthy Control
|
122166-122144.CEL
|
| Sample_geo_accession | GSM507967
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507967/suppl/GSM507967.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
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GSM507968 | GPL570 |
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Healthy control saliva-bc10
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saliva
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biomaterial source: saliva
disease status: Healthy Control
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122167-122145.CEL
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| Sample_geo_accession | GSM507968
| | Sample_status | Public on Feb 11 2010
| | Sample_submission_date | Feb 10 2010
| | Sample_last_update_date | Feb 10 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Ten Breast cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/).
| | Sample_hyb_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_scan_protocol | Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
| | Sample_data_processing | The CEL files from all datasets (array data from 10 breast cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lei,,Zhang
| | Sample_contact_email | leizhang@ucla.edu
| | Sample_contact_institute | UCLA Dental Research Institute
| | Sample_contact_address | 10833 Le Conte Ave., CHS 73-029
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90066
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507968/suppl/GSM507968.CEL.gz
| | Sample_series_id | GSE20266
| | Sample_data_row_count | 54675
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