Search results for the GEO ID: GSE18670 |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM463723 | GPL570 |
|
T117
|
PDAC_T_117
|
patient code: 117
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 0
ajcc classif. (2002): 2a
|
Gene expression data of original tumor tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463723
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463723/suppl/GSM463723.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463724 | GPL570 |
|
P117
|
PDAC_P_117
|
patient code: 117
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 0
ajcc classif. (2002): 2a
|
Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463724
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463724/suppl/GSM463724.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463725 | GPL570 |
|
G117
|
PDAC_G_117
|
patient code: 117
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 0
ajcc classif. (2002): 2a
|
Gene expression data of haematological cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463725
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463725/suppl/GSM463725.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463726 | GPL570 |
|
CTC117
|
PDAC_CTC_117
|
patient code: 117
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 0
ajcc classif. (2002): 2a
|
Gene expression data of circulating tumor cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463726
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463726/suppl/GSM463726.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463727 | GPL570 |
|
T104
|
PDAC_T_104
|
patient code: 104
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of original tumor tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463727
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463727/suppl/GSM463727.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463728 | GPL570 |
|
P104
|
PDAC_P_104
|
patient code: 104
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463728
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463728/suppl/GSM463728.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463729 | GPL570 |
|
G104
|
PDAC_G_104
|
patient code: 104
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of haematological cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463729
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463729/suppl/GSM463729.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463730 | GPL570 |
|
CTC104
|
PDAC_CTC_104
|
patient code: 104
gender: Female
age: 72
tumor grade: 3
t-stage: 3
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of circulating tumor cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463730
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463730/suppl/GSM463730.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463731 | GPL570 |
|
T105
|
PDAC_T_105
|
patient code: 105
gender: Male
age: 68
tumor grade: 3
t-stage: 2
n-stage: 0
ajcc classif. (2002): 1b
|
Gene expression data of original tumor tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463731
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463731/suppl/GSM463731.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463732 | GPL570 |
|
P105
|
PDAC_P_105
|
patient code: 105
gender: Male
age: 68
tumor grade: 3
t-stage: 2
n-stage: 0
ajcc classif. (2002): 1b
|
Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463732
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463732/suppl/GSM463732.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463733 | GPL570 |
|
G105
|
PDAC_G_105
|
patient code: 105
gender: Male
age: 68
tumor grade: 3
t-stage: 2
n-stage: 0
ajcc classif. (2002): 1b
|
Gene expression data of haematological cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463733
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463733/suppl/GSM463733.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463734 | GPL570 |
|
CTC105
|
PDAC_CTC_105
|
patient code: 105
gender: Male
age: 68
tumor grade: 3
t-stage: 2
n-stage: 0
ajcc classif. (2002): 1b
|
Gene expression data of circulating tumor cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463734
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463734/suppl/GSM463734.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463735 | GPL570 |
|
T91
|
PDAC_T_91
|
patient code: 91
gender: Female
age: 51
tumor grade: 3
t-stage: 3
n-stage: 0
ajcc classif. (2002): 2a
|
Gene expression data of original tumor tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463735
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463735/suppl/GSM463735.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463736 | GPL570 |
|
P91
|
PDAC_P_91
|
patient code: 91
gender: Female
age: 51
tumor grade: 3
t-stage: 3
n-stage: 0
ajcc classif. (2002): 2a
|
Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463736
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463736/suppl/GSM463736.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463737 | GPL570 |
|
G91
|
PDAC_G_91
|
patient code: 91
gender: Female
age: 51
tumor grade: 3
t-stage: 3
n-stage: 0
ajcc classif. (2002): 2a
|
Gene expression data of haematological cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463737
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463737/suppl/GSM463737.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463738 | GPL570 |
|
CTC91
|
PDAC_CTC_91
|
patient code: 91
gender: Female
age: 51
tumor grade: 3
t-stage: 3
n-stage: 0
ajcc classif. (2002): 2a
|
Gene expression data of circulating tumor cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463738
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463738/suppl/GSM463738.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463739 | GPL570 |
|
T138
|
PDAC_T_138
|
patient code: 138
gender: Male
age: 50
tumor grade: 2
t-stage: 2
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of original tumor tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463739
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463739/suppl/GSM463739.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463740 | GPL570 |
|
P138
|
PDAC_P_138
|
patient code: 138
gender: Male
age: 50
tumor grade: 2
t-stage: 2
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463740
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463740/suppl/GSM463740.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463741 | GPL570 |
|
G138
|
PDAC_G_138
|
patient code: 138
gender: Male
age: 50
tumor grade: 2
t-stage: 2
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of haematological cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463741
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463741/suppl/GSM463741.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463742 | GPL570 |
|
CTC138
|
PDAC_CTC_138
|
patient code: 138
gender: Male
age: 50
tumor grade: 2
t-stage: 2
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of circulating tumor cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463742
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463742/suppl/GSM463742.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463743 | GPL570 |
|
T123
|
PDAC_T_123
|
patient code: 123
gender: Male
age: 74
tumor grade: 3
t-stage: 1
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of original tumor tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463743
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463743/suppl/GSM463743.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463744 | GPL570 |
|
P123
|
PDAC_P_123
|
patient code: 123
gender: Male
age: 74
tumor grade: 3
t-stage: 1
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463744
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463744/suppl/GSM463744.CEL.gz
| Sample_series_id | GSE18670
| Sample_series_id | GSE42952
| Sample_data_row_count | 8152
| |
|
GSM463745 | GPL570 |
|
G123
|
PDAC_G_123
|
patient code: 123
gender: Male
age: 74
tumor grade: 3
t-stage: 1
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of haematological cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463745
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463745/suppl/GSM463745.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
|
GSM463746 | GPL570 |
|
CTC123
|
PDAC_CTC_123
|
patient code: 123
gender: Male
age: 74
tumor grade: 3
t-stage: 1
n-stage: 1
ajcc classif. (2002): 2b
|
Gene expression data of circulating tumor cells of pancreatic ductal adenocarcinoma patient
|
Sample_geo_accession | GSM463746
| Sample_status | Public on Dec 18 2012
| Sample_submission_date | Oct 21 2009
| Sample_last_update_date | Dec 19 2012
| 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 | RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).
| Sample_hyb_protocol | Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).
| Sample_data_processing | To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).
| Sample_platform_id | GPL570
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463746/suppl/GSM463746.CEL.gz
| Sample_series_id | GSE18670
| Sample_data_row_count | 8152
| |
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