Search results for the GEO ID: GSE47811  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1159936 | GPL1261 |
|
Mouse Saliva healthy 1
|
Healthy mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: healthy mice
|
153925
|
| Sample_geo_accession | GSM1159936
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159936/suppl/GSM1159936_153925-153913.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159937 | GPL1261 |
|
Mouse Saliva healthy 2
|
Healthy mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: healthy mice
|
153926
|
| Sample_geo_accession | GSM1159937
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159937/suppl/GSM1159937_153926-153914.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159938 | GPL1261 |
|
Mouse Saliva healthy 3
|
Healthy mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: healthy mice
|
153927
|
| Sample_geo_accession | GSM1159938
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159938/suppl/GSM1159938_153927-153915.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159939 | GPL1261 |
|
Mouse Saliva healthy 4
|
Healthy mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: healthy mice
|
153928
|
| Sample_geo_accession | GSM1159939
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159939/suppl/GSM1159939_153928-153916.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159940 | GPL1261 |
|
Mouse Saliva healthy 5
|
Healthy mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: healthy mice
|
153929
|
| Sample_geo_accession | GSM1159940
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159940/suppl/GSM1159940_153929-153917.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159941 | GPL1261 |
|
Mouse Saliva healthy 6
|
Healthy mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: healthy mice
|
153930
|
| Sample_geo_accession | GSM1159941
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159941/suppl/GSM1159941_153930-153918.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159942 | GPL1261 |
|
Mouse Saliva tumor 1
|
Tumor mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: mice with pancreatic tumor
|
153931
|
| Sample_geo_accession | GSM1159942
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159942/suppl/GSM1159942_153931-153919.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159943 | GPL1261 |
|
Mouse Saliva tumor 2
|
Tumor mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: mice with pancreatic tumor
|
153932
|
| Sample_geo_accession | GSM1159943
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159943/suppl/GSM1159943_153932-153920.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159944 | GPL1261 |
|
Mouse Saliva tumor 3
|
Tumor mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: mice with pancreatic tumor
|
153933
|
| Sample_geo_accession | GSM1159944
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159944/suppl/GSM1159944_153933-153921.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159945 | GPL1261 |
|
Mouse Saliva tumor 4
|
Tumor mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: mice with pancreatic tumor
|
153934
|
| Sample_geo_accession | GSM1159945
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159945/suppl/GSM1159945_153934-153922.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159946 | GPL1261 |
|
Mouse Saliva tumor 5
|
Tumor mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: mice with pancreatic tumor
|
153935
|
| Sample_geo_accession | GSM1159946
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159946/suppl/GSM1159946_153935-153923.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
| | |
|
GSM1159947 | GPL1261 |
|
Mouse Saliva tumor 6
|
Tumor mouse
|
strain background: C56BL/6
tissue: saliva supernatant
sample group: mice with pancreatic tumor
|
153936
|
| Sample_geo_accession | GSM1159947
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Jun 10 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
| | Sample_hyb_protocol | The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
| | Sample_scan_protocol | Array scanning was performed according to the manufacturer's instruction (Affymetrix)
| | Sample_data_processing | Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tristan,,Grogan
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 911 Broxton Ave, 3rd floor
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90024
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1159nnn/GSM1159947/suppl/GSM1159947_153936-153924.CEL.gz
| | Sample_series_id | GSE47811
| | Sample_data_row_count | 45101
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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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