Search results for the GEO ID: GSE24089  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM593029 | GPL570 |
|
SCC4 HPV(-), expression
|
RNA from HNSCC cell line, HPV(-)
|
cell line: SCC4
cell type: head and neck squamous cell carcinoma (HNSCC)
tissue derivation: tongue
hpv status: negative
age: 47
gender: female
|
Gene expression data from HNSCC HPV(-) cell line.
|
| Sample_geo_accession | GSM593029
| | Sample_status | Public on Dec 01 2010
| | Sample_submission_date | Sep 12 2010
| | Sample_last_update_date | Sep 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | UM SPORE Tissue Core
| | Sample_growth_protocol_ch1 | HPV(+) and HPV(-) SCC cell lines were cultured to near confluence in ventilated 75cm2 cell culture flasks in DMEM (Gibco) supplemented with 20% fetal bovine serum (FBS) and prophylactic antibiotics. At 90-95% confluence, the cells were photographed through a 20x objective lens, and then harvested with Trypsin/EDTA. Total cell counts for each flask were obtained using a Coulter Particle Counter (Beckman Coulter). Trypsin was neutralized with culture media containing 2% FBS, and cell pellets were washed with sterile phosphate-buffered saline (PBS), pH 7.4, prior to digestion for nucleic acid isolation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested at near confluence with trypsin/EDTA, counted, and washed. Nucleic acids were isolated using the RNEasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).
| | Sample_hyb_protocol | Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 at the University of Michigan Affymetrix Core facility using the standard Affymetrix protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader at the University of Michigan Affymetrix Core facility.
| | Sample_data_processing | Raw data was preprocessed and normalized using RMA. Differential expression and significance was assessed using Intensity-Based Moderated T-statistic (IBMT). Analysis was performed using R and Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jung,,Kim
| | Sample_contact_email | junghk@umich.edu
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1420 Washington Heights
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593029/suppl/GSM593029.CEL.gz
| | Sample_series_id | GSE24089
| | Sample_series_id | GSE24091
| | Sample_data_row_count | 54675
| | |
|
GSM593030 | GPL570 |
|
SCC74A HPV(-), expression
|
RNA from HNSCC cell line, HPV(-)
|
cell line: SCC74A
cell type: head and neck squamous cell carcinoma (HNSCC)
tissue derivation: tongue
hpv status: negative
age: 59
gender: male
|
Gene expression data from HNSCC HPV(-) cell line.
|
| Sample_geo_accession | GSM593030
| | Sample_status | Public on Dec 01 2010
| | Sample_submission_date | Sep 12 2010
| | Sample_last_update_date | Sep 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | UM SPORE Tissue Core
| | Sample_growth_protocol_ch1 | HPV(+) and HPV(-) SCC cell lines were cultured to near confluence in ventilated 75cm2 cell culture flasks in DMEM (Gibco) supplemented with 20% fetal bovine serum (FBS) and prophylactic antibiotics. At 90-95% confluence, the cells were photographed through a 20x objective lens, and then harvested with Trypsin/EDTA. Total cell counts for each flask were obtained using a Coulter Particle Counter (Beckman Coulter). Trypsin was neutralized with culture media containing 2% FBS, and cell pellets were washed with sterile phosphate-buffered saline (PBS), pH 7.4, prior to digestion for nucleic acid isolation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested at near confluence with trypsin/EDTA, counted, and washed. Nucleic acids were isolated using the RNEasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).
| | Sample_hyb_protocol | Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 at the University of Michigan Affymetrix Core facility using the standard Affymetrix protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader at the University of Michigan Affymetrix Core facility.
| | Sample_data_processing | Raw data was preprocessed and normalized using RMA. Differential expression and significance was assessed using Intensity-Based Moderated T-statistic (IBMT). Analysis was performed using R and Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jung,,Kim
| | Sample_contact_email | junghk@umich.edu
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1420 Washington Heights
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593030/suppl/GSM593030.CEL.gz
| | Sample_series_id | GSE24089
| | Sample_series_id | GSE24091
| | Sample_data_row_count | 54675
| | |
|
GSM593031 | GPL570 |
|
SCC47 HPV(+), expression
|
RNA from HNSCC cell line, HPV(+)
|
cell line: SCC47
cell type: head and neck squamous cell carcinoma (HNSCC)
tissue derivation: tongue
hpv status: positive
age: 53
gender: male
|
Gene expression data from HNSCC HPV(+) cell line.
|
| Sample_geo_accession | GSM593031
| | Sample_status | Public on Dec 01 2010
| | Sample_submission_date | Sep 12 2010
| | Sample_last_update_date | Sep 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | UM SPORE Tissue Core
| | Sample_growth_protocol_ch1 | HPV(+) and HPV(-) SCC cell lines were cultured to near confluence in ventilated 75cm2 cell culture flasks in DMEM (Gibco) supplemented with 20% fetal bovine serum (FBS) and prophylactic antibiotics. At 90-95% confluence, the cells were photographed through a 20x objective lens, and then harvested with Trypsin/EDTA. Total cell counts for each flask were obtained using a Coulter Particle Counter (Beckman Coulter). Trypsin was neutralized with culture media containing 2% FBS, and cell pellets were washed with sterile phosphate-buffered saline (PBS), pH 7.4, prior to digestion for nucleic acid isolation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested at near confluence with trypsin/EDTA, counted, and washed. Nucleic acids were isolated using the RNEasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).
| | Sample_hyb_protocol | Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 at the University of Michigan Affymetrix Core facility using the standard Affymetrix protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader at the University of Michigan Affymetrix Core facility.
| | Sample_data_processing | Raw data was preprocessed and normalized using RMA. Differential expression and significance was assessed using Intensity-Based Moderated T-statistic (IBMT). Analysis was performed using R and Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jung,,Kim
| | Sample_contact_email | junghk@umich.edu
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1420 Washington Heights
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593031/suppl/GSM593031.CEL.gz
| | Sample_series_id | GSE24089
| | Sample_series_id | GSE24091
| | Sample_data_row_count | 54675
| | |
|
GSM593032 | GPL570 |
|
CaSki HPV(+), expression
|
RNA from SCC cell line, HPV(+)
|
cell line: CaSki
cell type: female genital squamous cell carcinoma
tissue derivation: cervix
hpv status: positive
age: 43
gender: female
|
Gene expression data from SCC HPV(+) cell line.
|
| Sample_geo_accession | GSM593032
| | Sample_status | Public on Dec 01 2010
| | Sample_submission_date | Sep 12 2010
| | Sample_last_update_date | Sep 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | UM SPORE Tissue Core
| | Sample_growth_protocol_ch1 | HPV(+) and HPV(-) SCC cell lines were cultured to near confluence in ventilated 75cm2 cell culture flasks in DMEM (Gibco) supplemented with 20% fetal bovine serum (FBS) and prophylactic antibiotics. At 90-95% confluence, the cells were photographed through a 20x objective lens, and then harvested with Trypsin/EDTA. Total cell counts for each flask were obtained using a Coulter Particle Counter (Beckman Coulter). Trypsin was neutralized with culture media containing 2% FBS, and cell pellets were washed with sterile phosphate-buffered saline (PBS), pH 7.4, prior to digestion for nucleic acid isolation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested at near confluence with trypsin/EDTA, counted, and washed. Nucleic acids were isolated using the RNEasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).
| | Sample_hyb_protocol | Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 at the University of Michigan Affymetrix Core facility using the standard Affymetrix protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader at the University of Michigan Affymetrix Core facility.
| | Sample_data_processing | Raw data was preprocessed and normalized using RMA. Differential expression and significance was assessed using Intensity-Based Moderated T-statistic (IBMT). Analysis was performed using R and Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jung,,Kim
| | Sample_contact_email | junghk@umich.edu
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1420 Washington Heights
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593032/suppl/GSM593032.CEL.gz
| | Sample_series_id | GSE24089
| | Sample_series_id | GSE24091
| | Sample_data_row_count | 54675
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