Search results for the GEO ID: GSE38583  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM945775 | GPL570 |
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UM-SCC-81B at T0
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Head & Neck tumor UM-SCC-81B cells, without GD treatment
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cell line: UM-SCC-81B
cell type: oral squamous cell carcinoma cells
treatment: normal glucose
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UM-SCC-81B-NT
Gene expression data from UM-SCC-81B cells cultured under normal conditions (25 mM, glucose).
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| Sample_geo_accession | GSM945775
| | Sample_status | Public on Oct 25 2012
| | Sample_submission_date | Jun 07 2012
| | Sample_last_update_date | Oct 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DMEM complete medium (10% FBS) with glucose (25 mM) and DMEM complete medium (10% FBS) without glucose were used to prepare low-glucose (0.1 mM) medium. Tumor cells were split into 6-cm dishes the day before treatment. Before treatment, tumor cells were washed twice with PBS to remove residual medium and then treated with low glucose medium for 4 hours and 24 hours. Tumor cells cultured with DMEM complete medium were used as a non-treatment control.
| | Sample_growth_protocol_ch1 | UM-SCC-81B cells were maintained in Dulbecco's Modified Eagle Medium high glucose (DMEM, Invitrogen, Carlsbad, CA) with 10% (vol/vol) FBS, penicillin (100 U/mL), and streptomycin (100 μg/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from UM-SCC-81B cells using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg of total RNA was amplified and biotin-labeled according to the GeneChip Expression Analysis Technical Manual. Briefly, RNA was converted to double-stranded complementary DNA (cDNA) using SuperScript II RT (Invitrogen, Carlsbad, CA USA) with a T7-(dT)24 primer (Affymetrix, Inc., Santa Clara, CA, USA). Then, the cDNA was used in an in vitro transcription reaction in the presence of biotin-modified ribonucleotides (Enzo, Farmingdale, NY USA) to produce large amounts of single-stranded RNA.
| | Sample_hyb_protocol | The biotin-labeled RNA was fragmented and 10μg of it was hybridized to Human Genome U133 Plus 2.0 Arrays (Affymetrix) at 45°C for 16 hours. Labeled bacterial RNAs of known concentration were spiked in the hybridization to generate an internal standard and to allow normalization between chips. Chips were washed, and stained with streptavidin R-phycoerythrin (Molecular Probes, Eugene, OR USA).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000, which can acquire high-resolution scanning at 1.56 μm pixel resolution.
| | Sample_data_processing | After scanning the chips, the data ware analyzed by using Affymetrix GeneChip-related software such as GCOS, Data Mining Tool and Affymetrix web database 'NetAffx'.
| | Sample_platform_id | GPL570
| | Sample_contact_name | yugang,,wang
| | Sample_contact_email | yugawang@umich.edu
| | Sample_contact_laboratory | Peter Polverini's Lab
| | Sample_contact_department | BMS
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1011 N Universtiy Dr., room 5205
| | 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/GSM945nnn/GSM945775/suppl/GSM945775_001_0hr_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE38583
| | Sample_data_row_count | 54675
| | |
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GSM945776 | GPL570 |
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UM-SCC-81B at T4
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Head & Neck tumor UM-SCC-81B cells, 4 hr GD treatment
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cell line: UM-SCC-81B
cell type: oral squamous cell carcinoma cells
treatment: low glucose (0.1 mM)
treatment duration: 4 hrs
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UM-SCC-81B-GD-4
Gene expression data from UM-SCC-81B cells cultured under low glucose (0.1 mM) for 4 hours.
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| Sample_geo_accession | GSM945776
| | Sample_status | Public on Oct 25 2012
| | Sample_submission_date | Jun 07 2012
| | Sample_last_update_date | Oct 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DMEM complete medium (10% FBS) with glucose (25 mM) and DMEM complete medium (10% FBS) without glucose were used to prepare low-glucose (0.1 mM) medium. Tumor cells were split into 6-cm dishes the day before treatment. Before treatment, tumor cells were washed twice with PBS to remove residual medium and then treated with low glucose medium for 4 hours and 24 hours. Tumor cells cultured with DMEM complete medium were used as a non-treatment control.
| | Sample_growth_protocol_ch1 | UM-SCC-81B cells were maintained in Dulbecco's Modified Eagle Medium high glucose (DMEM, Invitrogen, Carlsbad, CA) with 10% (vol/vol) FBS, penicillin (100 U/mL), and streptomycin (100 μg/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from UM-SCC-81B cells using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg of total RNA was amplified and biotin-labeled according to the GeneChip Expression Analysis Technical Manual. Briefly, RNA was converted to double-stranded complementary DNA (cDNA) using SuperScript II RT (Invitrogen, Carlsbad, CA USA) with a T7-(dT)24 primer (Affymetrix, Inc., Santa Clara, CA, USA). Then, the cDNA was used in an in vitro transcription reaction in the presence of biotin-modified ribonucleotides (Enzo, Farmingdale, NY USA) to produce large amounts of single-stranded RNA.
| | Sample_hyb_protocol | The biotin-labeled RNA was fragmented and 10μg of it was hybridized to Human Genome U133 Plus 2.0 Arrays (Affymetrix) at 45°C for 16 hours. Labeled bacterial RNAs of known concentration were spiked in the hybridization to generate an internal standard and to allow normalization between chips. Chips were washed, and stained with streptavidin R-phycoerythrin (Molecular Probes, Eugene, OR USA).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000, which can acquire high-resolution scanning at 1.56 μm pixel resolution.
| | Sample_data_processing | After scanning the chips, the data ware analyzed by using Affymetrix GeneChip-related software such as GCOS, Data Mining Tool and Affymetrix web database 'NetAffx'.
| | Sample_platform_id | GPL570
| | Sample_contact_name | yugang,,wang
| | Sample_contact_email | yugawang@umich.edu
| | Sample_contact_laboratory | Peter Polverini's Lab
| | Sample_contact_department | BMS
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1011 N Universtiy Dr., room 5205
| | 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/GSM945nnn/GSM945776/suppl/GSM945776_002_4hr_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE38583
| | Sample_data_row_count | 54675
| | |
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GSM945777 | GPL570 |
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UM-SCC-81B at T24
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Head & Neck tumor UM-SCC-81B cells, 24 hr GD treatment
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cell line: UM-SCC-81B
cell type: oral squamous cell carcinoma cells
treatment: low glucose (0.1 mM)
treatment duration: 24 hrs
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UM-SCC-81B-GD24
Gene expression data from UM-SCC-81B cells cultured under low glucose (0.1 mM) for 24 hours.
|
| Sample_geo_accession | GSM945777
| | Sample_status | Public on Oct 25 2012
| | Sample_submission_date | Jun 07 2012
| | Sample_last_update_date | Oct 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DMEM complete medium (10% FBS) with glucose (25 mM) and DMEM complete medium (10% FBS) without glucose were used to prepare low-glucose (0.1 mM) medium. Tumor cells were split into 6-cm dishes the day before treatment. Before treatment, tumor cells were washed twice with PBS to remove residual medium and then treated with low glucose medium for 4 hours and 24 hours. Tumor cells cultured with DMEM complete medium were used as a non-treatment control.
| | Sample_growth_protocol_ch1 | UM-SCC-81B cells were maintained in Dulbecco's Modified Eagle Medium high glucose (DMEM, Invitrogen, Carlsbad, CA) with 10% (vol/vol) FBS, penicillin (100 U/mL), and streptomycin (100 μg/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from UM-SCC-81B cells using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg of total RNA was amplified and biotin-labeled according to the GeneChip Expression Analysis Technical Manual. Briefly, RNA was converted to double-stranded complementary DNA (cDNA) using SuperScript II RT (Invitrogen, Carlsbad, CA USA) with a T7-(dT)24 primer (Affymetrix, Inc., Santa Clara, CA, USA). Then, the cDNA was used in an in vitro transcription reaction in the presence of biotin-modified ribonucleotides (Enzo, Farmingdale, NY USA) to produce large amounts of single-stranded RNA.
| | Sample_hyb_protocol | The biotin-labeled RNA was fragmented and 10μg of it was hybridized to Human Genome U133 Plus 2.0 Arrays (Affymetrix) at 45°C for 16 hours. Labeled bacterial RNAs of known concentration were spiked in the hybridization to generate an internal standard and to allow normalization between chips. Chips were washed, and stained with streptavidin R-phycoerythrin (Molecular Probes, Eugene, OR USA).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000, which can acquire high-resolution scanning at 1.56 μm pixel resolution.
| | Sample_data_processing | After scanning the chips, the data ware analyzed by using Affymetrix GeneChip-related software such as GCOS, Data Mining Tool and Affymetrix web database 'NetAffx'.
| | Sample_platform_id | GPL570
| | Sample_contact_name | yugang,,wang
| | Sample_contact_email | yugawang@umich.edu
| | Sample_contact_laboratory | Peter Polverini's Lab
| | Sample_contact_department | BMS
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1011 N Universtiy Dr., room 5205
| | 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/GSM945nnn/GSM945777/suppl/GSM945777_003_24hr_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE38583
| | Sample_data_row_count | 54675
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