Search results for the GEO ID: GSE42952  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
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
| | |
|
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
| | |
|
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
| | |
|
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
| | |
|
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
| | |
|
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
| | |
|
GSM1053825 | GPL570 |
|
16-TM1
|
PaCa, bad prognosis
|
gender: male
age: 67 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: M+
prognosis: bad
|
bad
|
| Sample_geo_accession | GSM1053825
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053825/suppl/GSM1053825_hyb7989.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053826 | GPL570 |
|
D-10167-BT
|
PaCa, good prognosis
|
gender: male
age: 78 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N0M0
tumor grade: 1
Stage: 2a
prognosis: good
|
good
|
| Sample_geo_accession | GSM1053826
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053826/suppl/GSM1053826_hyb7990.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053827 | GPL570 |
|
2-45
|
PaCa, liver metastasis
|
gender: male
age: 69 years
tissue: liver metastasis from pancreatic cancer
tumor stage: M+
|
LM
|
| Sample_geo_accession | GSM1053827
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053827/suppl/GSM1053827_hyb7991.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053828 | GPL570 |
|
3-149
|
PaCa, peritoneal metastasis
|
gender: male
age: 76 years
tissue: peritoneal metastasis from pancreatic cancer
tumor stage: M+
|
PM
|
| Sample_geo_accession | GSM1053828
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053828/suppl/GSM1053828_hyb7992.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053829 | GPL570 |
|
D-10578/1-BT
|
PaCa, bad prognosis
|
gender: female
age: 75 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N0M0
tumor grade: 3
Stage: 2a
prognosis: bad
|
bad
|
| Sample_geo_accession | GSM1053829
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053829/suppl/GSM1053829_hyb7993.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053830 | GPL570 |
|
D-10342-BT
|
PaCa, good prognosis
|
gender: male
age: 53 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N1M0
tumor grade: 3
Stage: 2b
prognosis: good
|
good
|
| Sample_geo_accession | GSM1053830
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053830/suppl/GSM1053830_hyb7994.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053831 | GPL570 |
|
4-M1
|
PaCa, liver metastasis
|
gender: male
age: 69 years
tissue: liver metastasis from pancreatic cancer
tumor stage: M+
|
LM
|
| Sample_geo_accession | GSM1053831
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053831/suppl/GSM1053831_hyb7995.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053832 | GPL570 |
|
7-M2
|
PaCa, peritoneal metastasis
|
gender: female
age: 65 years
tissue: peritoneal metastasis from pancreatic cancer
tumor stage: M+
|
PM
|
| Sample_geo_accession | GSM1053832
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053832/suppl/GSM1053832_hyb7996.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053833 | GPL570 |
|
D-11993-BT
|
PaCa, bad prognosis
|
gender: male
age: 72 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N1M0
tumor grade: 2
Stage: 2b
prognosis: bad
|
bad
|
| Sample_geo_accession | GSM1053833
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053833/suppl/GSM1053833_hyb7997.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053834 | GPL570 |
|
D-10865-BT
|
PaCa, good prognosis
|
gender: female
age: 61 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N0M0
tumor grade: 3
Stage: 2a
prognosis: good
|
good
|
| Sample_geo_accession | GSM1053834
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053834/suppl/GSM1053834_hyb7998.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053835 | GPL570 |
|
6-M2
|
PaCa, liver metastasis
|
gender: female
age: 65 years
tissue: liver metastasis from pancreatic cancer
tumor stage: M+
|
LM
|
| Sample_geo_accession | GSM1053835
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053835/suppl/GSM1053835_hyb7999.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053836 | GPL570 |
|
8-M3
|
PaCa, peritoneal metastasis
|
gender: female
age: 49 years
tissue: peritoneal metastasis from pancreatic cancer
tumor stage: M+
|
PM
|
| Sample_geo_accession | GSM1053836
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053836/suppl/GSM1053836_hyb8000.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053837 | GPL570 |
|
D-12341/2-BT
|
PaCa, bad prognosis
|
gender: male
age: 52 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N0M0
tumor grade: 3
Stage: 2a
prognosis: bad
|
bad
|
| Sample_geo_accession | GSM1053837
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053837/suppl/GSM1053837_hyb8001.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053838 | GPL570 |
|
D-11719*-BT
|
PaCa, good prognosis
|
gender: female
age: 62 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N1M0
tumor grade: 3
Stage: 2b
prognosis: good
|
good
|
| Sample_geo_accession | GSM1053838
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053838/suppl/GSM1053838_hyb8002.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053839 | GPL570 |
|
9-167
|
PaCa, liver metastasis
|
gender: female
age: 62 years
tissue: liver metastasis from pancreatic cancer
tumor stage: M+
|
LM
|
| Sample_geo_accession | GSM1053839
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053839/suppl/GSM1053839_hyb8003.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053840 | GPL570 |
|
14-210
|
PaCa, peritoneal metastasis
|
gender: male
age: 79 years
tissue: peritoneal metastasis from pancreatic cancer
tumor stage: M+
|
PM
|
| Sample_geo_accession | GSM1053840
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053840/suppl/GSM1053840_hyb8004.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053841 | GPL570 |
|
D-12411/1-BT
|
PaCa, bad prognosis
|
gender: female
age: 78 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N1M0
tumor grade: 2
Stage: 2b
prognosis: bad
|
bad
|
| Sample_geo_accession | GSM1053841
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053841/suppl/GSM1053841_hyb8005.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053842 | GPL570 |
|
11-179
|
PaCa, liver metastasis
|
gender: male
age: 69 years
tissue: liver metastasis from pancreatic cancer
tumor stage: M+
|
LM
|
| Sample_geo_accession | GSM1053842
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053842/suppl/GSM1053842_hyb8006.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053843 | GPL570 |
|
D-5115-BT
|
PaCa, good prognosis
|
gender: female
age: 55 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T2N0M0
tumor grade: 2
Stage: 1b
prognosis: good
|
good
|
| Sample_geo_accession | GSM1053843
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053843/suppl/GSM1053843_hyb8007.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053844 | GPL570 |
|
12-180
|
PaCa, liver metastasis
|
gender: male
age: 47 years
tissue: liver metastasis from pancreatic cancer
tumor stage: M+
|
LM
|
| Sample_geo_accession | GSM1053844
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053844/suppl/GSM1053844_hyb8008.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053845 | GPL570 |
|
D-12928/2-BT
|
PaCa, bad prognosis
|
gender: male
age: 59 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N1M0
tumor grade: 3
Stage: 2b
prognosis: bad
|
bad
|
| Sample_geo_accession | GSM1053845
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053845/suppl/GSM1053845_hyb8009.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053846 | GPL570 |
|
D-7730/A1-BT
|
PaCa, good prognosis
|
gender: male
age: 32 years
tissue: pancreatic ductal adenocarcinoma (PDAC)
tumor stage: T3N1M0
tumor grade: 3
Stage: 2b
prognosis: good
|
good
|
| Sample_geo_accession | GSM1053846
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053846/suppl/GSM1053846_hyb8010.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
GSM1053847 | GPL570 |
|
17-TM2
|
PaCa, liver metastasis
|
gender: male
age: 67 years
tissue: liver metastasis from pancreatic cancer
tumor stage: M+
|
LM
|
| Sample_geo_accession | GSM1053847
| | Sample_status | Public on Jan 09 2013
| | Sample_submission_date | Dec 17 2012
| | Sample_last_update_date | Jan 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | University hospital, Leuven
| | Sample_growth_protocol_ch1 | Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
| | 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/GSM1053nnn/GSM1053847/suppl/GSM1053847_hyb8011.CEL.gz
| | Sample_series_id | GSE42952
| | Sample_data_row_count | 54675
| | |
|
| |
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