Search results for the GEO ID: GSE21785  |
(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 |
GSM542661 | GPL96 |
|
Tubulus_LD5
|
Transplant Living Donor, microdissected Tubulus from kidney biopsy
|
gender: female
age: 35 years
|
NA
|
| Sample_geo_accession | GSM542661
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542661/suppl/GSM542661.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542662 | GPL96 |
|
Tubulus_LD6
|
Transplant Living Donor, microdissected Tubulus from kidney biopsy
|
gender: male
age: 39 years
|
NA
|
| Sample_geo_accession | GSM542662
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542662/suppl/GSM542662.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542663 | GPL96 |
|
Tubulus_LD7
|
Transplant Living Donor, microdissected Tubulus from kidney biopsy
|
gender: female
age: 56 years
|
NA
|
| Sample_geo_accession | GSM542663
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542663/suppl/GSM542663.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542664 | GPL96 |
|
Tubulus_LD8
|
Transplant Living Donor, microdissected Tubulus from kidney biopsy
|
gender: male
age: 41 years
|
NA
|
| Sample_geo_accession | GSM542664
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542664/suppl/GSM542664.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542665 | GPL96 |
|
Tubulus_LD9
|
Transplant Living Donor, microdissected Tubulus from kidney biopsy
|
gender: male
age: 62 years
|
NA
|
| Sample_geo_accession | GSM542665
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542665/suppl/GSM542665.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542666 | GPL96 |
|
Tubulus_LD10
|
Transplant Living Donor, microdissected Tubulus from kidney biopsy
|
gender: female
age: 58 years
|
NA
|
| Sample_geo_accession | GSM542666
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542666/suppl/GSM542666.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542667 | GPL96 |
|
Glomerulus_LD5
|
Transplant Living Donor, microdissected Glomerulus from kidney biopsy
|
gender: female
age: 35 years
|
NA
|
| Sample_geo_accession | GSM542667
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542667/suppl/GSM542667.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542668 | GPL96 |
|
Glomerulus_LD6
|
Transplant Living Donor, microdissected Glomerulus from kidney biopsy
|
gender: male
age: 39 years
|
NA
|
| Sample_geo_accession | GSM542668
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542668/suppl/GSM542668.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542669 | GPL96 |
|
Glomerulus_LD7
|
Transplant Living Donor, microdissected Glomerulus from kidney biopsy
|
gender: female
age: 56 years
|
NA
|
| Sample_geo_accession | GSM542669
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542669/suppl/GSM542669.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542670 | GPL96 |
|
Glomerulus_LD8
|
Transplant Living Donor, microdissected Glomerulus from kidney biopsy
|
gender: male
age: 41 years
|
NA
|
| Sample_geo_accession | GSM542670
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542670/suppl/GSM542670.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542671 | GPL96 |
|
Glomerulus_LD9
|
Transplant Living Donor, microdissected Glomerulus from kidney biopsy
|
gender: male
age: 62 years
|
NA
|
| Sample_geo_accession | GSM542671
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542671/suppl/GSM542671.CEL.gz
| | Sample_series_id | GSE21785
| | Sample_data_row_count | 22283
| | |
|
GSM542672 | GPL96 |
|
Glomerulus_LD10
|
Transplant Living Donor, microdissected Glomerulus from kidney biopsy
|
gender: female
age: 58 years
|
NA
|
| Sample_geo_accession | GSM542672
| | Sample_status | Public on Jul 19 2010
| | Sample_submission_date | May 11 2010
| | Sample_last_update_date | Jul 19 2010
| | 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 | RNA was isolated as described in:
| | Sample_extract_protocol_ch1 | Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
| | Sample_extract_protocol_ch1 | Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
| | Sample_extract_protocol_ch1 | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_extract_protocol_ch1 | and glomeruli:
| | Sample_extract_protocol_ch1 | Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For probe labeling, a modification of the Eberwine protocol was used:
| | Sample_label_protocol_ch1 | Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10 : 283 –288,1996
| | Sample_hyb_protocol | The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_scan_protocol | The imaging was performed according the Affymetrix Expression Analysis Technical Manual
| | Sample_data_processing | Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:
| | Sample_data_processing |
| | Sample_data_processing | Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
| | Sample_data_processing |
| | Sample_data_processing | A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Felix,,Eichinger
| | Sample_contact_laboratory | Kretzler
| | Sample_contact_department | Internal Medicine/Nephrology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 1150 W Med Center Drive
| | 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/GSM542nnn/GSM542672/suppl/GSM542672.CEL.gz
| | Sample_series_id | GSE21785
| | 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: |
|
|
|
