Search results for the GEO ID: GSE26511  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM651831 | GPL570 |
|
Cervical cancer-lymph node negative-01-01
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 56.4
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651831
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651831/suppl/GSM651831.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651832 | GPL570 |
|
Cervical cancer-lymph node negative-02-02
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 45.8
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651832
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651832/suppl/GSM651832.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651833 | GPL570 |
|
Cervical cancer-lymph node negative-03-11
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 49.5
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651833
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651833/suppl/GSM651833.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651834 | GPL570 |
|
Cervical cancer-lymph node negative-04-13
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 34.7
figo stage: 2a
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651834
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651834/suppl/GSM651834.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651835 | GPL570 |
|
Cervical cancer-lymph node negative-05-18
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 55.5
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651835
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651835/suppl/GSM651835.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651836 | GPL570 |
|
Cervical cancer-lymph node negative-06-20
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 38.5
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651836
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651836/suppl/GSM651836.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651837 | GPL570 |
|
Cervical cancer-lymph node negative-07-27
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 34.9
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651837
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651837/suppl/GSM651837.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651838 | GPL570 |
|
Cervical cancer-lymph node negative-08-32
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 47.4
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651838
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651838/suppl/GSM651838.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651839 | GPL570 |
|
Cervical cancer-lymph node negative-09-33
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 42.3
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651839
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651839/suppl/GSM651839.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651840 | GPL570 |
|
Cervical cancer-lymph node negative-10-34
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 35.8
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651840
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651840/suppl/GSM651840.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651841 | GPL570 |
|
Cervical cancer-lymph node negative-11-35
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 51.6
figo stage: 2a
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651841
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651841/suppl/GSM651841.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651842 | GPL570 |
|
Cervical cancer-lymph node negative-12-36
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 72.0
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651842
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651842/suppl/GSM651842.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651843 | GPL570 |
|
Cervical cancer-lymph node negative-13-43
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 71.0
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651843
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651843/suppl/GSM651843.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651844 | GPL570 |
|
Cervical cancer-lymph node negative-14-44
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 35.9
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651844
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651844/suppl/GSM651844.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651845 | GPL570 |
|
Cervical cancer-lymph node negative-15-48
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 68.9
figo stage: 2a
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651845
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651845/suppl/GSM651845.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651846 | GPL570 |
|
Cervical cancer-lymph node negative-16-51
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 47.4
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651846
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651846/suppl/GSM651846.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651847 | GPL570 |
|
Cervical cancer-lymph node negative-17-52
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 31.5
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651847
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651847/suppl/GSM651847.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651848 | GPL570 |
|
Cervical cancer-lymph node negative-18-53
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 72.7
figo stage: 2a
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651848
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651848/suppl/GSM651848.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651849 | GPL570 |
|
Cervical cancer-lymph node negative-19-54
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 39.9
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651849
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651849/suppl/GSM651849.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651850 | GPL570 |
|
Cervical cancer-lymph node negative-20-62
|
Early stage cervical cancer
|
pelvic lymph nodes: Negative
age at diagnosis: 50.7
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651850
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651850/suppl/GSM651850.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651851 | GPL570 |
|
Cervical cancer-lymph node positive-21-04
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 56.2
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651851
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651851/suppl/GSM651851.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651852 | GPL570 |
|
Cervical cancer-lymph node positive-22-05
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 29.1
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651852
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651852/suppl/GSM651852.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651853 | GPL570 |
|
Cervical cancer-lymph node positive-23-07
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 32.2
figo stage: 2a
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651853
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651853/suppl/GSM651853.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651854 | GPL570 |
|
Cervical cancer-lymph node positive-24-09
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 60.6
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651854
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651854/suppl/GSM651854.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651855 | GPL570 |
|
Cervical cancer-lymph node positive-25-10
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 49.9
figo stage: 2a
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651855
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651855/suppl/GSM651855.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651856 | GPL570 |
|
Cervical cancer-lymph node positive-26-15
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 34.9
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651856
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651856/suppl/GSM651856.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651857 | GPL570 |
|
Cervical cancer-lymph node positive-27-21
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 32.7
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651857
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651857/suppl/GSM651857.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651858 | GPL570 |
|
Cervical cancer-lymph node positive-28-23
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 40.4
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651858
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651858/suppl/GSM651858.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651859 | GPL570 |
|
Cervical cancer-lymph node positive-29-25
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 48.5
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651859
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651859/suppl/GSM651859.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651860 | GPL570 |
|
Cervical cancer-lymph node positive-30-26
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 37.4
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651860
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651860/suppl/GSM651860.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651861 | GPL570 |
|
Cervical cancer-lymph node positive-31-28
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 37.0
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651861
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651861/suppl/GSM651861.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651862 | GPL570 |
|
Cervical cancer-lymph node positive-32-37
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 32.0
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651862
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651862/suppl/GSM651862.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651863 | GPL570 |
|
Cervical cancer-lymph node positive-33-38
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 37.4
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651863
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651863/suppl/GSM651863.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651864 | GPL570 |
|
Cervical cancer-lymph node positive-34-45
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 45.5
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651864
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651864/suppl/GSM651864.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651865 | GPL570 |
|
Cervical cancer-lymph node positive-35-46
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 72.5
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651865
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651865/suppl/GSM651865.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651866 | GPL570 |
|
Cervical cancer-lymph node positive-36-50
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 42.3
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651866
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651866/suppl/GSM651866.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651867 | GPL570 |
|
Cervical cancer-lymph node positive-37-56
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 46.3
figo stage: 1b1
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651867
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651867/suppl/GSM651867.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651868 | GPL570 |
|
Cervical cancer-lymph node positive-38-57
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 34.2
figo stage: 1b2
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651868
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651868/suppl/GSM651868.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
|
GSM651869 | GPL570 |
|
Cervical cancer-lymph node positive-39-59
|
Early stage cervical cancer
|
pelvic lymph nodes: Positive
age at diagnosis: 50.5
figo stage: 2a
|
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Sample_geo_accession | GSM651869
| | Sample_status | Public on Feb 15 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Feb 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
| | Sample_scan_protocol | After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
| | Sample_data_processing | Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maartje,,Noordhuis
| | Sample_contact_email | m.noordhuis@og.umcg.nl
| | Sample_contact_department | Gynecologic Oncology
| | Sample_contact_institute | University Medical Center Groningen
| | Sample_contact_address | PObox 30.001
| | Sample_contact_city | Groningen
| | Sample_contact_zip/postal_code | 9700RB
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM651nnn/GSM651869/suppl/GSM651869.CEL.gz
| | Sample_series_id | GSE26511
| | Sample_data_row_count | 54675
| | |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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