Search results for the GEO ID: GSE8611  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM212569 | GPL96 |
|
TUBULAR PROGENITOR CELL 1
|
progenitor cells isolated from renal tubular fraction
|
macroscopically normal cortical tissue from clear cell renal carcinoma affected kidney
donor ID: 1
donor gender: male
donor age: 76
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM212569
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 23 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_label_protocol_ch1 |
| | Sample_label_protocol_ch1 |
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM212nnn/GSM212569/suppl/GSM212569.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM212571 | GPL96 |
|
GLOMERULAR PROGENITOR CELL 1
|
progenitor cells isolated from renal glomerular fraction
|
macroscopically normal cortical tissue from clear cell renal carcinoma affected kidney
donor id: 1
donor gender: male
donor age: 76
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM212571
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 23 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_label_protocol_ch1 |
| | Sample_label_protocol_ch1 |
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM212nnn/GSM212571/suppl/GSM212571.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213459 | GPL96 |
|
TUBULAR PROGENITOR CELL 2
|
progenitor cells isolated from renal tubular fraction
|
macroscopically normal cortical tissue from clear cell renal carcinoma affected kidney
donor ID: 2
donor gender: female
donor age: 80
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213459
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213459/suppl/GSM213459.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213460 | GPL96 |
|
GLOMERULAR PROGENITOR CELL 2
|
progenitor cells isolated from renal glomerular fraction
|
macroscopically normal cortical tissue from clear cell renal carcinoma affected kidney
donor ID: 2
donor gender: female
donor age: 80
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213460
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213460/suppl/GSM213460.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213462 | GPL96 |
|
GLOMERULAR PROGENITOR 3
|
progenitor cells isolated from renal glomerular fraction
|
macroscopically normal cortical tissue from clear cell renal carcinoma affected kidney
donor ID: 3
donor gender: male
donor age: 72
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213462
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213462/suppl/GSM213462.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213463 | GPL96 |
|
TUBULAR PROGENITOR CELL 3
|
progenitor cells isolated from renal tubular fraction
|
macroscopically normal cortical tissue from clear cell renal carcinoma affected kidney
donor ID: 3
donor gender: male
donor age: 72
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213463
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213463/suppl/GSM213463.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213513 | GPL96 |
|
MESENCHYMAL STEM CELL 1
|
Human bone marrow derived stem cells.
|
Mesenchymal Stem Cells were purchased from Lonza (Valais, Switzerland)
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213513
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213513/suppl/GSM213513.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213514 | GPL96 |
|
MESENCHYMAL STEM CELL 2
|
Human bone marrow derived stem cells
|
Mesenchymal Stem Cells were purchased from Lonza (Valais, Switzerland)
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213514
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213514/suppl/GSM213514.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213515 | GPL96 |
|
MESENCHYMAL STEM CELL 3
|
Human bone marrow derived stem cells
|
Mesenchymal Stem Cells were purchased from Lonza (Valais, Switzerland)
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213515
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213515/suppl/GSM213515.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213519 | GPL96 |
|
renal proximal tubule epithelial cells 2
|
Primary epithelial cells from normal human renal proximal tubule
|
Primary human renal proximal tubule cells were purchased from Lonza (Valais, Switzerland)
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213519
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213519/suppl/GSM213519.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213523 | GPL96 |
|
renal proximal tubule epithelial cells 1
|
Primary epithelial cells from normal human renal proximal tubule
|
Primary human renal proximal tubule cells were purchased from Lonza (Valais, Switzerland)
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213523
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213523/suppl/GSM213523.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
GSM213525 | GPL96 |
|
renal proximal tubule epithelial cells 3
|
Primary epithelial cells from normal human renal proximal tubule
|
Primary human renal proximal tubule cells were purchased from Lonza (Valais, Switzerland)
|
We used the default settings of GCOS software to scan the chips
|
| Sample_geo_accession | GSM213525
| | Sample_status | Public on Nov 03 2009
| | Sample_submission_date | Jul 27 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from a minimum of 10^6 cultured cells for each line by using the SV Total RNA isolation kit (Promega, Madison, WI) according the manufacturer’s instructions. Total RNA was quantified by NanoDrop® ND-1000 Spectrophotometer and its quality was assessed by electrophoresis on agarose gel (1%).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays
| | Sample_hyb_protocol | Human Genome U133 A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions.
| | Sample_scan_protocol | We used the default settings of GCOS software to scan the chips.
| | Sample_data_processing | We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Fabio,,Sallustio
| | Sample_contact_email | fabsal74@gmail.com
| | Sample_contact_phone | 0805593234
| | Sample_contact_laboratory | Nephrology
| | Sample_contact_department | DETO
| | Sample_contact_institute | University of Bari
| | Sample_contact_address | P.zza G.Cesare
| | Sample_contact_city | BARI
| | Sample_contact_zip/postal_code | 70124
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM213nnn/GSM213525/suppl/GSM213525.CEL.gz
| | Sample_series_id | GSE8611
| | Sample_data_row_count | 22283
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
