Search results for the GEO ID: GSE11839  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM299095 | GPL570 |
|
human cultured bladder HB DM, subject 8
|
human
|
Female, age 47
Disease status: HB (control (stress incontinence, no bladder pain))
Culture medium: DM (differentiating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299095
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | The initial growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). To induce differentiation, medium was changed two days before extraction to a high-calcium, serum-containing medium (DM) described by Keay: DMEM-F12 (Media Tech, Herndon, VA) with 10% fetal bovine serum , 1% antibiotic/antimycotic solution, 1% L-glutamine, 1.0 U/ml insulin (all from Sigma), and 5 ?g/ml hEGF (R & D Systems, Minneapolis, MN). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299095/suppl/GSM299095.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299096 | GPL570 |
|
human cultured bladder HB DM, subject 12
|
human
|
Female, age 57
Disease status: HB (control (stress incontinence, no bladder pain))
Culture medium: DM (differentiating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299096
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | The initial growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). To induce differentiation, medium was changed two days before extraction to a high-calcium, serum-containing medium (DM) described by Keay: DMEM-F12 (Media Tech, Herndon, VA) with 10% fetal bovine serum , 1% antibiotic/antimycotic solution, 1% L-glutamine, 1.0 U/ml insulin (all from Sigma), and 5 ?g/ml hEGF (R & D Systems, Minneapolis, MN). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299096/suppl/GSM299096.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299097 | GPL570 |
|
human cultured bladder HB DM, subject 13
|
human
|
Female, age 56
Disease status: HB (control (stress incontinence, no bladder pain))
Culture medium: DM (differentiating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299097
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | The initial growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). To induce differentiation, medium was changed two days before extraction to a high-calcium, serum-containing medium (DM) described by Keay: DMEM-F12 (Media Tech, Herndon, VA) with 10% fetal bovine serum , 1% antibiotic/antimycotic solution, 1% L-glutamine, 1.0 U/ml insulin (all from Sigma), and 5 ?g/ml hEGF (R & D Systems, Minneapolis, MN). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299097/suppl/GSM299097.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299098 | GPL570 |
|
human cultured bladder HB KM, subject 8
|
human
|
Female, age 47
Disease status: HB (control (stress incontinence, no bladder pain))
Culture medium: KM (proliferating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299098
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | Growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299098/suppl/GSM299098.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299099 | GPL570 |
|
human cultured bladder HB KM, subject 12
|
human
|
Female, age 57
Disease status: HB (control (stress incontinence, no bladder pain))
Culture medium: KM (proliferating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299099
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | Growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299099/suppl/GSM299099.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299100 | GPL570 |
|
human cultured bladder HB KM, subject 13
|
human
|
Female, age 56
Disease status: HB (control (stress incontinence, no bladder pain))
Culture medium: KM (proliferating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299100
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | Growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299100/suppl/GSM299100.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299101 | GPL570 |
|
human cultured bladder IC DM, subject 1
|
human
|
Female, age 29
Disease status: IC (interstitial cystitis)
Culture medium: DM (differentiating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299101
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | The initial growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). To induce differentiation, medium was changed two days before extraction to a high-calcium, serum-containing medium (DM) described by Keay: DMEM-F12 (Media Tech, Herndon, VA) with 10% fetal bovine serum , 1% antibiotic/antimycotic solution, 1% L-glutamine, 1.0 U/ml insulin (all from Sigma), and 5 ?g/ml hEGF (R & D Systems, Minneapolis, MN). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299101/suppl/GSM299101.CEL.gz
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299102 | GPL570 |
|
human cultured bladder IC DM, subject 3
|
human
|
Female, age 37
Disease status: IC (interstitial cystitis)
Culture medium: DM (differentiating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299102
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | The initial growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). To induce differentiation, medium was changed two days before extraction to a high-calcium, serum-containing medium (DM) described by Keay: DMEM-F12 (Media Tech, Herndon, VA) with 10% fetal bovine serum , 1% antibiotic/antimycotic solution, 1% L-glutamine, 1.0 U/ml insulin (all from Sigma), and 5 ?g/ml hEGF (R & D Systems, Minneapolis, MN). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299102/suppl/GSM299102.CEL.gz
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299103 | GPL570 |
|
human cultured bladder IC DM, subject 10
|
human
|
Female, age 39
Disease status: IC (interstitial cystitis)
Culture medium: DM (differentiating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299103
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | The initial growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). To induce differentiation, medium was changed two days before extraction to a high-calcium, serum-containing medium (DM) described by Keay: DMEM-F12 (Media Tech, Herndon, VA) with 10% fetal bovine serum , 1% antibiotic/antimycotic solution, 1% L-glutamine, 1.0 U/ml insulin (all from Sigma), and 5 ?g/ml hEGF (R & D Systems, Minneapolis, MN). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299103/suppl/GSM299103.CEL.gz
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299104 | GPL570 |
|
human cultured bladder IC KM, subject 1
|
human
|
Female, age 29
Disease status: IC (interstitial cystitis)
Culture medium: KM (proliferating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299104
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | Growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299104/suppl/GSM299104.CEL.gz
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299105 | GPL570 |
|
human cultured bladder IC KM, subject 3
|
human
|
Female, age 37
Disease status: IC (interstitial cystitis)
Culture medium: KM (proliferating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299105
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | Growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299105/suppl/GSM299105.CEL.gz
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
GSM299106 | GPL570 |
|
human cultured bladder IC KM, subject 10
|
human
|
Female, age 39
Disease status: IC (interstitial cystitis)
Culture medium: KM (proliferating medium)
|
Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
|
| Sample_geo_accession | GSM299106
| | Sample_status | Public on Sep 05 2008
| | Sample_submission_date | Jun 19 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
| | Sample_growth_protocol_ch1 | Growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). Total RNA was extracted from cells at passages 3 to 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Standard Affymetrix
| | Sample_label_ch1 | Standard Affymetrix
| | Sample_label_protocol_ch1 | Standard Affymetrix
| | Sample_hyb_protocol | Standard Affimetrix
| | Sample_scan_protocol | Affy
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Deborah,,Erickson
| | Sample_contact_email | dreric2@email.uky.edu
| | Sample_contact_phone | 859-323-3831
| | Sample_contact_laboratory | Urology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | University of Kentucky
| | Sample_contact_address | 800 Rose Street, MS275
| | Sample_contact_city | Lexington
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40536-0298
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299106/suppl/GSM299106.CEL.gz
| | Sample_series_id | GSE11839
| | Sample_data_row_count | 54675
| | |
|
| |
| |
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