Search results for the GEO ID: GSE14538  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM363782 | GPL570 |
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Caco2, untreated
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Caco2 cells, untreated
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Colon cancer cell line
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Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133 Plus 2 GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 3µg of total RNA.
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| Sample_geo_accession | GSM363782
| | Sample_status | Public on Jan 23 2010
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Jan 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Untreated cells.
| | Sample_growth_protocol_ch1 | The Caco2 cell line was obtained from ATCC (Rockville, MD) and cultured in DMEM medium (Euroclone, Devon, UK), supplemented with 10% heat inactivated fetal bovine serum (Lonza, Walkersvillle, MD) and 1mM L-Glutamine (Euroclone).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from 5-10x105 cells of each sample using RNeasy Mini Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (3 µg) of Caco2 cells untreated and treated for 96 hours with 20 mM 5-ASA were converted in biotinylated cRNA according to the one-cycle target labeling protocol advised by Affymetrix (Affymetrix, Santa Clara,CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133 Plus 2 GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard FS450_0001 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=150. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alexis,,Grande
| | Sample_contact_email | alexis.grande@unimore.it
| | Sample_contact_phone | +390592055409
| | Sample_contact_fax | +390592055410
| | Sample_contact_laboratory | Biological Chemistry Section
| | Sample_contact_department | Department of Biomedical Sciences
| | Sample_contact_institute | University of Modena and Reggio Emilia
| | Sample_contact_address | via Campi n 287
| | Sample_contact_city | MODENA
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM363nnn/GSM363782/suppl/GSM363782.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM363nnn/GSM363782/suppl/GSM363782.CHP.gz
| | Sample_series_id | GSE14538
| | Sample_data_row_count | 54675
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GSM363784 | GPL570 |
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Caco2, 20 mM 5-ASA 96h
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Caco2 cells, treated with mesalazine
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Colon cancer cell line
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133 Plus 2 GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 3µg of total RNA.
|
| Sample_geo_accession | GSM363784
| | Sample_status | Public on Jan 23 2010
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Jan 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 5-ASA (SofarFarm S.p.A., Milano, Italy) was dissolved in cell culture medium at concentrations 20 mM. Caco2 cell line was treated with 5-ASA 20mM for 96h.
| | Sample_growth_protocol_ch1 | The Caco2 cell line was obtained from ATCC (Rockville, MD) and cultured in DMEM medium (Euroclone, Devon, UK), supplemented with 10% heat inactivated fetal bovine serum (Lonza, Walkersvillle, MD) and 1mM L-Glutamine (Euroclone).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from 5-10x105 cells of each sample using RNeasy Mini Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (3 µg) of Caco2 cells untreated and treated for 96 hours with 20 mM 5-ASA were converted in biotinylated cRNA according to the one-cycle target labeling protocol advised by Affymetrix (Affymetrix, Santa Clara,CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133 Plus 2 GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard FS450_0001 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=150. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alexis,,Grande
| | Sample_contact_email | alexis.grande@unimore.it
| | Sample_contact_phone | +390592055409
| | Sample_contact_fax | +390592055410
| | Sample_contact_laboratory | Biological Chemistry Section
| | Sample_contact_department | Department of Biomedical Sciences
| | Sample_contact_institute | University of Modena and Reggio Emilia
| | Sample_contact_address | via Campi n 287
| | Sample_contact_city | MODENA
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM363nnn/GSM363784/suppl/GSM363784.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM363nnn/GSM363784/suppl/GSM363784.CHP.gz
| | Sample_series_id | GSE14538
| | Sample_data_row_count | 54675
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