Search results for the GEO ID: GSE32175  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM797551 | GPL570 |
|
Healthy control saliva-lc1
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797551
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797551/suppl/GSM797551.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797551/suppl/GSM797551.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797552 | GPL570 |
|
Healthy control saliva-lc2
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797552
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797552/suppl/GSM797552.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797552/suppl/GSM797552.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797553 | GPL570 |
|
Healthy control saliva-lc3
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797553
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797553/suppl/GSM797553.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797553/suppl/GSM797553.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797554 | GPL570 |
|
Healthy control saliva-lc4
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797554
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797554/suppl/GSM797554.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797554/suppl/GSM797554.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797555 | GPL570 |
|
Healthy control saliva-lc5
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797555
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797555/suppl/GSM797555.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797555/suppl/GSM797555.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797556 | GPL570 |
|
Healthy control saliva-lc6
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797556
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797556/suppl/GSM797556.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797556/suppl/GSM797556.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797557 | GPL570 |
|
Healthy control saliva-lc7
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797557
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797557/suppl/GSM797557.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797557/suppl/GSM797557.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797558 | GPL570 |
|
Healthy control saliva-lc8
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797558
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797558/suppl/GSM797558.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797558/suppl/GSM797558.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797559 | GPL570 |
|
Healthy control saliva-lc9
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797559
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797559/suppl/GSM797559.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797559/suppl/GSM797559.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797560 | GPL570 |
|
Healthy control saliva-lc10
|
saliva
|
disease status: Healthy Control
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797560
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797560/suppl/GSM797560.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797560/suppl/GSM797560.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797561 | GPL570 |
|
Lung cancer saliva-1
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797561
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797561/suppl/GSM797561.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797561/suppl/GSM797561.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797562 | GPL570 |
|
Lung cancer saliva-2
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797562
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797562/suppl/GSM797562.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797562/suppl/GSM797562.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797563 | GPL570 |
|
Lung cancer saliva-3
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797563
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797563/suppl/GSM797563.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797563/suppl/GSM797563.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797564 | GPL570 |
|
Lung cancer saliva-4
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797564
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797564/suppl/GSM797564.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797564/suppl/GSM797564.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797565 | GPL570 |
|
Lung cancer saliva-5
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797565
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797565/suppl/GSM797565.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797565/suppl/GSM797565.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797566 | GPL570 |
|
Lung cancer saliva-6
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797566
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797566/suppl/GSM797566.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797566/suppl/GSM797566.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797567 | GPL570 |
|
Lung cancer saliva-7
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797567
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797567/suppl/GSM797567.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797567/suppl/GSM797567.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797568 | GPL570 |
|
Lung cancer saliva-8
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797568
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797568/suppl/GSM797568.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797568/suppl/GSM797568.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
| | |
|
GSM797569 | GPL570 |
|
Lung cancer saliva-9
|
saliva
|
disease status: Lung Cancer
|
Gene expression data from human saliva
|
| Sample_geo_accession | GSM797569
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797569/suppl/GSM797569.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797569/suppl/GSM797569.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
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GSM797570 | GPL570 |
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Lung cancer saliva-10
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saliva
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disease status: Lung Cancer
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Gene expression data from human saliva
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| Sample_geo_accession | GSM797570
| | Sample_status | Public on Jan 11 2013
| | Sample_submission_date | Sep 15 2011
| | Sample_last_update_date | Jan 11 2013
| | 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 Lung 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 lung 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 | Hua,,Xiao
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 10833 Le Conte Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797570/suppl/GSM797570.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM797nnn/GSM797570/suppl/GSM797570.chp.gz
| | Sample_series_id | GSE32175
| | Sample_data_row_count | 54675
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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